{row.getVisibleCells().map(cell => (
- |
+ |
{flexRender(
cell.column.columnDef.cell,
cell.getContext()
diff --git a/src/components/Content.js b/src/components/Content.js
index 87bcd29..1bffacb 100644
--- a/src/components/Content.js
+++ b/src/components/Content.js
@@ -3,6 +3,8 @@ import { Routes, Route } from "react-router-dom"
import Home from "./Home"
import About from "./About"
import Resources from "./Resources"
+import SeroBAnk from "./SeroBAnk"
+import GPSC from "./GPSC"
import Publications from "./Publications"
import CapacityBuilding from "./CapacityBuilding"
import Training from "./Training"
@@ -15,6 +17,8 @@ const Content = () => (
} />
} />
} />
+ } />
+ } />
} />
} />
} />
diff --git a/src/components/GPSC.js b/src/components/GPSC.js
new file mode 100644
index 0000000..7a2bce2
--- /dev/null
+++ b/src/components/GPSC.js
@@ -0,0 +1,15 @@
+import Lineages from "./Lineages"
+import GPSCSTLookupTable from "./GPSCSTLookupTable"
+import PMENClones from "./PMENClones"
+import GPSCTopTrumps from "./GPSCTopTrumps"
+
+const GPSC = () => (
+
+)
+
+export default GPSC
\ No newline at end of file
diff --git a/src/components/GPSCSTLookupTable.js b/src/components/GPSCSTLookupTable.js
index 72045d6..9c98ebc 100644
--- a/src/components/GPSCSTLookupTable.js
+++ b/src/components/GPSCSTLookupTable.js
@@ -39,7 +39,7 @@ const GPSCSTLookupTable = () => {
{content.sections.map( (props, index) =>
)}
-
+
)
}
diff --git a/src/components/GPSPipeline.js b/src/components/GPSPipeline.js
new file mode 100644
index 0000000..0645edc
--- /dev/null
+++ b/src/components/GPSPipeline.js
@@ -0,0 +1,16 @@
+import { TitleText, Section } from "./Common"
+
+import content from '../content/gpsPipelineContent'
+
+const GPSPipline = () => (
+
+
+
+
+ {content.sections.map( (props, index) =>
+
+ )}
+
+
+
+
+ {content.sections.map( (props, index) =>
+
+ )}
+
+
+
+
+ {content.sections.map( (props, index) =>
+
+ )}
+
+
diff --git a/src/components/OneToOneTraining.js b/src/components/OneToOneTraining.js
new file mode 100644
index 0000000..0814848
--- /dev/null
+++ b/src/components/OneToOneTraining.js
@@ -0,0 +1,16 @@
+import { TitleText, Section } from "./Common"
+
+import content from '../content/oneToOneTrainingContent'
+
+const OneToOneTraining = () => (
+
+
+
+
+ {content.sections.map( (props, index) =>
+
+ )}
+
+
+
+
+
+)
+
+export default SeroBAnk
\ No newline at end of file
diff --git a/src/components/Serotypes.js b/src/components/Serotypes.js
index e8ae2ed..10a39d3 100644
--- a/src/components/Serotypes.js
+++ b/src/components/Serotypes.js
@@ -19,6 +19,9 @@ const Serortype = () => {
header: "Serotype",
accessorKey: "serotype",
enableColumnFilter: true,
+ meta: {
+ className: "sticky left-0 glass z-10"
+ },
cell: props => {
const cellValue = props.getValue()
const commentvalue = props.row.original.comments
@@ -89,41 +92,143 @@ const Serortype = () => {
}
}
},
+ {
+ header: ,
+ accessorKey: "otherSerum",
+ meta: {
+ className: "!align-middle"
+ },
+ cell: props => {
+ const otherSerumValue = props.getValue()
+ const otherSerumValueRemark = props.row.original.otherSerumRemark
+ const poolSerumValue = props.row.original.poolSerum
+ const typeSerumValue = props.row.original.typeSerum
+ const groupSerumValue = props.row.original.groupSerum
+ const factorSerumValue = props.row.original.factorSerum
+ const antiserumNote = props.row.original.antiserumNote
+
+ if (otherSerumValue === '-' && poolSerumValue === '-' && typeSerumValue === '-' && groupSerumValue === '-' && factorSerumValue === '-' ){
+ return No Serological Profile
+ }
+
+ return (
+
+ {
+ antiserumNote === '-' ? null :
+ }
+ {
+ poolSerumValue === '-' ? null : poolSerumValue.split(",").map((val) => {val} )
+ }
+ {
+ typeSerumValue === '-' ? null : typeSerumValue.split(",").map((val) => {val} )
+ }
+ {
+ groupSerumValue === '-' ? null : groupSerumValue.split(",").map((val) => {val} )
+ }
+ {
+ factorSerumValue === '-' ? null : factorSerumValue.split(",").map((val) => {val} )
+ }
+ {
+ otherSerumValue === '-'
+ ?
+ null
+ :
+ otherSerumValue.indexOf(",") === -1
+ ?
+
+ :
+ otherSerumValue.split(',').map((element, index) =>
+
+ )
+ }
+ -
- } else if (remarkValue === '-') {
+ return {remarkValue === '-' ? "No Sequence Available" : remarkValue}
+ } else {
return (
-
+
+ {remarkValue === "-" ? null : {remarkValue} }
)
+ }
+ }
+ },
+ {
+ header: ,
+ accessorKey: "capsularStructureImage",
+ meta: {
+ className: "!align-middle"
+ },
+ cell: props => {
+ const cellValue = props.getValue()
+ const serotypeValue = props.row.original.serotype
+ const remarkValue = props.row.original.capsularStructureRemark
+
+ if (cellValue === '-'){
+ return {remarkValue === '-' ? "No Structure Available" : remarkValue}
} else {
return (
-
+
- {remarkValue}
+ {remarkValue === "-" ? null : {remarkValue} }
)
}
}
},
-
+ {
+ header: "Annotation (.gb)",
+ accessorKey: "genBankFile",
+ meta: {
+ className: "!align-middle"
+ },
+ cell: props => {
+ const cellValue = props.getValue()
+ if (cellValue === '-'){
+ return -
+ } else {
+ return (
+
+
+ )
+ }
+ }
+ },
], [])
return (
diff --git a/src/components/VaccineHistory.js b/src/components/VaccineHistory.js
new file mode 100644
index 0000000..c07c114
--- /dev/null
+++ b/src/components/VaccineHistory.js
@@ -0,0 +1,16 @@
+import { TitleText, Section } from "./Common"
+
+import content from '../content/vaccineHistoryContent'
+
+const VaccineHistory = () => (
+
+
+
+
+ {content.sections.map( (props, index) =>
+
+ )}
+
+)
+
+export default VaccineHistory
diff --git a/src/components/VaccineInformation.js b/src/components/VaccineInformation.js
new file mode 100644
index 0000000..4f012c1
--- /dev/null
+++ b/src/components/VaccineInformation.js
@@ -0,0 +1,16 @@
+import { TitleText, Section } from "./Common"
+
+import content from '../content/vaccineInformationContent'
+
+const VaccineInformation = () => (
+
+
+
+
+ {content.sections.map( (props, index) =>
+
+ )}
+
+)
+
+export default VaccineInformation
diff --git a/src/content/capacityBuildingContent.js b/src/content/capacityBuildingContent.js
index 3c5797e..90f00d8 100644
--- a/src/content/capacityBuildingContent.js
+++ b/src/content/capacityBuildingContent.js
@@ -9,153 +9,6 @@ const content = {
},
]
},
- {
- subtitle: {
- content: 'Sustainable Local Sequencing'
- },
- content: [
- {
- type: 'md',
- content: 'At the beginning of GPS2, the GPS team engaged with key partners to discuss the feasibility of local data generation and resources required, identifying 8 institutes in 6 LMIC countries with which the GPS project is now working to establish decentralised data generation and analysis:'
- },
- {
- type: 'md',
- content: '- Bangladesh ([CHRF](https://chrfbd.org/))'
- },
- {
- type: 'md',
- content: '- India ([CMC](https://www.cmch-vellore.edu/) and [KIMS](https://www.kimsbangalore.edu.in/))'
- },
- {
- type: 'md',
- content: '- Malawi ([MLW](https://www.mlw.mw/))'
- },
- {
- type: 'md',
- content: '- Pakistan ([AKU](https://www.aku.edu/) and [LUMS](https://lums.edu.pk/))'
- },
- {
- type: 'md',
- content: '- South Africa ([NICD](https://www.nicd.ac.za/))'
- },
- {
- type: 'md',
- content: '- The Gambia ([LSHTM MRC Unit The Gambia](https://www.mrc.gm/))'
- },
- ]
- },
- {
- subtitle: {
- content: 'Enhancing Local Capacity for Data Analysis'
- },
- content: [
- {
- type: 'md',
- content: 'A key aim of GPS2 is to support the development of skills of local researchers who become confident to independently analyse genomic data. Supporting the development of bioinformatics expertise is achieved through a multi-faceted approach, through a combination of online training, in person workshops and ongoing mentoring.'
- },
- {
- type: 'carousel',
- content: [
- {
- url: 'img/advanced_bioinformatics_workshop_colombia.jpg',
- alt: 'Advanced Bioinformatics Workshop in Colombia'
- },
- {
- url: 'img/advanced_bioinformatics_workshop_gambia.jpg',
- alt: 'Advanced Bioinformatics Workshop in the Gambia'
- },
- {
- url: 'img/advanced_bioinformatics_workshop_india.jpg',
- alt: 'Advanced Bioinformatics Workshop in India'
- },
- {
- url: 'img/advanced_bioinformatics_workshop_turkey.jpg',
- alt: 'Advanced Bioinformatics Workshop in Turkey'
- },
- ]
- },
- {
- type: 'md',
- content: '###### Participants and trainers in Advanced Bioinformatics Training Workshops in different locations'
- },
- {
- type: 'md',
- content: 'In 2019, collaborators from six LMIC countries joined the GPS team at the Wellcome Sanger institute for an intensive week focused on analysis and drafting of country analysis papers for publication, [many of which have since been published](https://www.microbiologyresearch.org/content/global-pneumococcal-sequencing-collection/). After a hiatus owing to the COVID-19 pandemic, in person bioinformatics workshop have since been resumed in 2023.'
- },
- {
- type: 'md',
- content: 'In addition, free [online training](https://training.bactgen.sanger.ac.uk/) resources have been developed by the GPS and JUNO training lead Jolynne Mokaya and we are working with colleagues from Wellcome Connecting Science (WCS) to develop and deploy face-to-face and virtual 5 day bioinformatics courses to supplement the existing online courses. [Other free courses](https://www.futurelearn.com/partners/wellcome-genome-campus) from WCS, in partnership with FutureLearn are currently available online for anyone to take in their own time. Some of these courses offer [continuing professional development](https://cpduk.co.uk/explained) (CPD) credits.'
- },
- {
- type: 'md',
- content: "Below is some feedback from two of our partners who attended the writers workshop. You can also find out more about [Samanta Almeida's](https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000635) and [Paula Gagetti's](https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000636) in-depth country level *S. pneumoniae* genomic analysis work through their publications in Microbial Genomics."
- },
- {
- type: 'quoteCard',
- content: {
- photo: 'img/samanta_almeida.jpg',
- name: 'Samanta Almeida, Center of Bacteriology, Adolfo Lutz Institute, São Paulo, Brazil',
- quotes: ["The participation in the GPS project was an experience analysing WGS data and meeting the challenge of handling a large volume of data. The GPS team made a great effort to help me with the analysis and to address difficulties. In my opinion, it is a project that goes far beyond data generation, as there is a real effort to build capacity by sharing knowledge and providing bioinformatics training. During my participation, I received many incentives to develop studies and opportunities to present these results. I presented abstracts in the most important pneumococcus international events, the International Symposium on Pneumococcal and Pneumococcal Diseases (ISPPD), Australia (2018), and Toronto (2020) editions."]
- }
- },
- {
- type: 'quoteCard',
- content: {
- photo: 'img/paula_gagetti.jpg',
- name: 'Paula Gagetti (National Reference Laboratory on AMR of the National Institute of Infectious Diseases, Buenos Aires, Argentina)',
- quotes: ["The most exciting thing was that prestigious professionals in the pneumococcal area dedicated a week of their time to sit down with us, discuss our results and draw conclusions about the impact of vaccines in different regions of the world. That was really amazing. Added to the human warmth of each of them that also allowed us to share beautiful moments drinking a beer in the pubs of Hinxton and Cambridge.", "From there, a very important link was generated. I worked a lot with Steph, whom I thank for the recognition and respect for our work and for answering all my questions immediately. Working with such a prestigious group of experts with the highest level of responsibility gives us the confidence to do other works in the future."]
- }
- },
- ]
- },
- {
- subtitle: {
- content: 'One-to-One Training'
- },
- content: [
- {
- type: 'md',
- content: "Nida Javaid is a PhD student from a partner group in the Department of Biology, Lahore University of Management Sciences, Pakistan. Nida obtained an 8 months research fellowship funded by Higher Education Commission in Pakistan and joined the Bentley group the Wellcome Sanger Institute for hands-on training in genomic analyses of *S. pneumoniae*. Unfortunately, Nida's arrival coincided with the UK national lockdown and the switch to working from home. Despite these challenges, Nida quickly integrated with the team, and learnt how to apply key tools used for characterising the genomic epidemiology of pneumococci to datasets from South Africa and Pakistan. Dr. Stephanie Lo is Nida's main mentor and together they made a great mentor-mentee team. As the lockdown restrictions started easing, Nida started having weekly in-person meetings with Stephanie, and joined occasional get-togethers with other team members."
- },
- {
- type: 'imageHalfWidth',
- content: {
- url: 'img/steph_and_nida.jpg',
- alt: 'Nida Javaid and Stephanie Lo at the Wellcome Genome Campus'
- }
- },
- {
- type: 'md',
- content: '###### Nida Javaid and Stephanie Lo at the Wellcome Genome Campus'
- },
- {
- type: 'md',
- content: "Find out more about Nida's work with the Bentley team:"
- },
- {
- type: 'quoteCard',
- content: {
- name: 'Nida Javid (Department of Biology, Lahore University of Management Sciences, Pakistan)',
- quotes: ["The original plan was that I will be working on the population genomics analysis of pneumococcal isolates from Pakistan. However, due to the lockdown, sequencing of isolates from Pakistan was delayed and I started working on the country analysis of pneumococcal carriage isolates from South Africa. I started with running quality control analysis of the sequenced data, followed by *in silico* serotyping, genotyping, prediction of antimicrobial resistance and phylogenetic analysis from pneumococcal genomes using a wide range of command-line tools such as SeroBA and PopPUNK. I then visualized the output using Microreact, a tool that allows me to interactively explore the phylogeny with temporal and geographical data. Now almost a year and a half later, this manuscript is ready for submission. I would like to thank Dr. Shabbir Madhi for allowing me to work on his dataset.", "After a few months, pneumococcal isolates from Pakistan were sequenced. I then analysed these data using the approach and tools that I had learnt during my first few months at Sanger, and am working towards publication of my Pakistan country analysis. We also presented our preliminary results at the ABPHM online conference. Although I am back in Pakistan now, I am still actively working with Stephanie and attend the team meetings regularly. I would like to thank Stephen, Stephanie, and the team for their support and kindness. I would also like to thank my PhD advisor, Dr. Shaper Mirza, for her support and guidance through my PhD."]
- }
- },
- ]
- },
- {
- subtitle: {
- content: 'GPS Pipeline: A Portable Pipeline to Reduce the Bioinformatics Burden'
- },
- content: [
- {
- type: 'md',
- content: "Ensuring quality control of sequence data and generating succinct, reliable data characterising genomes can be time consuming and require substantial bioinformatic training. During GPS2, a portable pipeline named GPS Pipeline is being developed which will enable collaborators to easily input whole genome sequencing data and generate the *in silico* typing data required for downstream analysis. Although the pipeline is still under active development, its latest version is available on GitHub for testing: [https://github.com/sanger-bentley-group/gps-pipeline/](https://github.com/sanger-bentley-group/gps-pipeline/)"
- },
- {
- type: 'md',
- content: ''
- },
- ]
- },
]
}
diff --git a/src/content/commandLineContent.js b/src/content/commandLineContent.js
index 12486a6..3624e05 100644
--- a/src/content/commandLineContent.js
+++ b/src/content/commandLineContent.js
@@ -184,7 +184,7 @@ const content = {
},
{
type: 'md',
- content: '- GPSC235;9 is an exception. This lineage is a mixture of GPSC9 and GPSC235, but do not indicate the merging of GPSC9 and GPSC235 lineages.',
+ content: '- GPSC235;9 is an exception. This lineage is a mixture of GPSC9 and GPSC235, but do not indicate the merging of GPSC9 and GPSC235 lineages based on current evidence.',
},
]
}
diff --git a/src/content/gpsPipelineContent.js b/src/content/gpsPipelineContent.js
new file mode 100644
index 0000000..641707c
--- /dev/null
+++ b/src/content/gpsPipelineContent.js
@@ -0,0 +1,22 @@
+const content = {
+ title: "GPS Pipeline",
+ sections: [
+ {
+ subtitle: {
+ content: 'A Portable Pipeline to Reduce the Bioinformatics Burden'
+ },
+ content: [
+ {
+ type: 'md',
+ content: "Ensuring quality control of sequence data and generating succinct, reliable data characterising genomes can be time consuming and require substantial bioinformatic training. During GPS2, a portable pipeline named GPS Pipeline is being developed which will enable collaborators to easily input whole genome sequencing data and generate the *in silico* typing data required for downstream analysis. The pipeline is still under active development, its latest version is available on GitHub: [https://github.com/GlobalPneumoSeq/gps-pipeline](https://github.com/GlobalPneumoSeq/gps-pipeline)"
+ },
+ {
+ type: 'md',
+ content: ''
+ },
+ ]
+ },
+ ]
+}
+
+export default content
diff --git a/src/content/localDataAnalysisContent.js b/src/content/localDataAnalysisContent.js
new file mode 100644
index 0000000..75c1bd1
--- /dev/null
+++ b/src/content/localDataAnalysisContent.js
@@ -0,0 +1,68 @@
+const content = {
+ title: 'Enhancing Local Capacity for Data Analysis',
+ sections: [
+ {
+ content: [
+ {
+ type: 'md',
+ content: 'A key aim of GPS2 is to support the development of skills of local researchers who become confident to independently analyse genomic data. Supporting the development of bioinformatics expertise is achieved through a multi-faceted approach, through a combination of online training, in person workshops and ongoing mentoring.'
+ },
+ {
+ type: 'carousel',
+ content: [
+ {
+ url: 'img/advanced_bioinformatics_workshop_colombia.jpg',
+ alt: 'Advanced Bioinformatics Workshop in Colombia'
+ },
+ {
+ url: 'img/advanced_bioinformatics_workshop_gambia.jpg',
+ alt: 'Advanced Bioinformatics Workshop in the Gambia'
+ },
+ {
+ url: 'img/advanced_bioinformatics_workshop_india.jpg',
+ alt: 'Advanced Bioinformatics Workshop in India'
+ },
+ {
+ url: 'img/advanced_bioinformatics_workshop_turkey.jpg',
+ alt: 'Advanced Bioinformatics Workshop in Turkey'
+ },
+ ]
+ },
+ {
+ type: 'md',
+ content: '###### Participants and trainers in Advanced Bioinformatics Training Workshops in different locations'
+ },
+ {
+ type: 'md',
+ content: 'In 2019, collaborators from six LMIC countries joined the GPS team at the Wellcome Sanger institute for an intensive week focused on analysis and drafting of country analysis papers for publication, [many of which have since been published](https://www.microbiologyresearch.org/content/global-pneumococcal-sequencing-collection/). After a hiatus owing to the COVID-19 pandemic, in person bioinformatics workshop have since been resumed in 2023.'
+ },
+ {
+ type: 'md',
+ content: 'In addition, free [online training](https://training.bactgen.sanger.ac.uk/) resources have been developed by the GPS and JUNO training lead Jolynne Mokaya and we are working with colleagues from Wellcome Connecting Science (WCS) to develop and deploy face-to-face and virtual 5 day bioinformatics courses to supplement the existing online courses. [Other free courses](https://www.futurelearn.com/partners/wellcome-genome-campus) from WCS, in partnership with FutureLearn are currently available online for anyone to take in their own time. Some of these courses offer [continuing professional development](https://cpduk.co.uk/explained) (CPD) credits.'
+ },
+ {
+ type: 'md',
+ content: "Below is some feedback from two of our partners who attended the writers workshop. You can also find out more about [Samanta Almeida's](https://doi.org/10.1099/mgen.0.000635) and [Paula Gagetti's](https://doi.org/10.1099/mgen.0.000636) in-depth country level *S. pneumoniae* genomic analysis work through their publications in Microbial Genomics."
+ },
+ {
+ type: 'quoteCard',
+ content: {
+ photo: 'img/samanta_almeida.jpg',
+ name: 'Samanta Almeida, Center of Bacteriology, Adolfo Lutz Institute, São Paulo, Brazil',
+ quotes: ["The participation in the GPS project was an experience analysing WGS data and meeting the challenge of handling a large volume of data. The GPS team made a great effort to help me with the analysis and to address difficulties. In my opinion, it is a project that goes far beyond data generation, as there is a real effort to build capacity by sharing knowledge and providing bioinformatics training. During my participation, I received many incentives to develop studies and opportunities to present these results. I presented abstracts in the most important pneumococcus international events, the International Symposium on Pneumococcal and Pneumococcal Diseases (ISPPD), Australia (2018), and Toronto (2020) editions."]
+ }
+ },
+ {
+ type: 'quoteCard',
+ content: {
+ photo: 'img/paula_gagetti.jpg',
+ name: 'Paula Gagetti (National Reference Laboratory on AMR of the National Institute of Infectious Diseases, Buenos Aires, Argentina)',
+ quotes: ["The most exciting thing was that prestigious professionals in the pneumococcal area dedicated a week of their time to sit down with us, discuss our results and draw conclusions about the impact of vaccines in different regions of the world. That was really amazing. Added to the human warmth of each of them that also allowed us to share beautiful moments drinking a beer in the pubs of Hinxton and Cambridge.", "From there, a very important link was generated. I worked a lot with Steph, whom I thank for the recognition and respect for our work and for answering all my questions immediately. Working with such a prestigious group of experts with the highest level of responsibility gives us the confidence to do other works in the future."]
+ }
+ },
+ ]
+ }
+ ]
+}
+
+export default content
diff --git a/src/content/localSequencingContent.js b/src/content/localSequencingContent.js
new file mode 100644
index 0000000..c237502
--- /dev/null
+++ b/src/content/localSequencingContent.js
@@ -0,0 +1,39 @@
+const content = {
+ title: 'Sustainable Local Sequencing',
+ sections: [
+ {
+ content: [
+ {
+ type: 'md',
+ content: 'At the beginning of GPS2, the GPS team engaged with key partners to discuss the feasibility of local data generation and resources required, identifying 8 institutes in 6 LMIC countries with which the GPS project is now working to establish decentralised data generation and analysis:'
+ },
+ {
+ type: 'md',
+ content: '- Bangladesh ([CHRF](https://chrfbd.org/))'
+ },
+ {
+ type: 'md',
+ content: '- India ([CMC](https://www.cmch-vellore.edu/) and [KIMS](https://www.kimsbangalore.edu.in/))'
+ },
+ {
+ type: 'md',
+ content: '- Malawi ([MLW](https://www.mlw.mw/))'
+ },
+ {
+ type: 'md',
+ content: '- Pakistan ([AKU](https://www.aku.edu/) and [LUMS](https://lums.edu.pk/))'
+ },
+ {
+ type: 'md',
+ content: '- South Africa ([NICD](https://www.nicd.ac.za/))'
+ },
+ {
+ type: 'md',
+ content: '- The Gambia ([LSHTM MRC Unit The Gambia](https://www.mrc.gm/))'
+ },
+ ]
+ }
+ ]
+}
+
+export default content
diff --git a/src/content/navbarContent.js b/src/content/navbarContent.js
index 8b8c621..a3d3374 100644
--- a/src/content/navbarContent.js
+++ b/src/content/navbarContent.js
@@ -34,28 +34,57 @@ const content = [
url: '/resources#countries',
},
{
- title: 'Lineages',
- url: '/resources#lineages',
+ title: 'GPS Pipeline',
+ url: '/resources#gps-pipeline',
},
{
- title: 'GPSC-ST Lookup Table',
- url: '/resources#gpsc-st-lookup-table',
+ title: 'Isolate Bank Request',
+ url: '/resources#isolate-bank-request',
},
+ {
+ title: 'GPS Visualiser',
+ url: './gps-visualiser/',
+ external: true
+ },
+ ]
+ },
+ {
+ title: 'SeroBAnk',
+ url: '/serobank',
+ submenu: [
{
title: 'Serotypes',
- url: '/resources#serotypes',
+ url: '/serobank#serotypes',
},
{
- title: 'PMEN Clones',
- url: '/resources#pmen-clones',
+ title: 'Vaccine Information',
+ url: '/serobank#vaccine-information',
},
{
- title: 'Isolate Bank Request',
- url: '/resources#isolate-bank-request',
+ title: 'Vaccine History',
+ url: '/serobank#vaccine-history',
+ }
+ ]
+ },
+ {
+ title: 'GPSC',
+ url: '/gpsc',
+ submenu: [
+ {
+ title: 'Lineages',
+ url: '/gpsc#lineages',
+ },
+ {
+ title: 'GPSC-ST Lookup Table',
+ url: '/gpsc#gpsc-st-lookup-table',
+ },
+ {
+ title: 'PMEN Clones',
+ url: '/gpsc#pmen-clones',
},
{
title: 'GPSC Top Trumps',
- url: '/resources#gpsc-top-trumps',
+ url: '/gpsc#gpsc-top-trumps',
},
]
},
@@ -65,7 +94,21 @@ const content = [
},
{
title: 'Capacity Building',
- url: '/capacity-building'
+ url: '/capacity-building',
+ submenu: [
+ {
+ title: 'Local Sequencing',
+ url: '/capacity-building#local-sequencing',
+ },
+ {
+ title: 'Local Data Analysis',
+ url: '/capacity-building#local-data-analysis',
+ },
+ {
+ title: 'One-to-One Training',
+ url: '/capacity-building#one-to-one-training',
+ },
+ ]
},
{
title: 'Training',
@@ -94,11 +137,6 @@ const content = [
url: './gps-database-overview/',
external: true
},
- {
- title: 'GPS Visualiser',
- url: './gps-visualiser/',
- external: true
- },
]
export default content
\ No newline at end of file
diff --git a/src/content/oneToOneTrainingContent.js b/src/content/oneToOneTrainingContent.js
new file mode 100644
index 0000000..19acaea
--- /dev/null
+++ b/src/content/oneToOneTrainingContent.js
@@ -0,0 +1,37 @@
+const content = {
+ title: 'One-to-One Training',
+ sections: [
+ {
+ content: [
+ {
+ type: 'md',
+ content: "Nida Javaid is a PhD student from a partner group in the Department of Biology, Lahore University of Management Sciences, Pakistan. Nida obtained an 8 months research fellowship funded by Higher Education Commission in Pakistan and joined the Bentley group the Wellcome Sanger Institute for hands-on training in genomic analyses of *S. pneumoniae*. Unfortunately, Nida's arrival coincided with the UK national lockdown and the switch to working from home. Despite these challenges, Nida quickly integrated with the team, and learnt how to apply key tools used for characterising the genomic epidemiology of pneumococci to datasets from South Africa and Pakistan. Dr. Stephanie Lo is Nida's main mentor and together they made a great mentor-mentee team. As the lockdown restrictions started easing, Nida started having weekly in-person meetings with Stephanie, and joined occasional get-togethers with other team members."
+ },
+ {
+ type: 'imageHalfWidth',
+ content: {
+ url: 'img/steph_and_nida.jpg',
+ alt: 'Nida Javaid and Stephanie Lo at the Wellcome Genome Campus'
+ }
+ },
+ {
+ type: 'md',
+ content: '###### Nida Javaid and Stephanie Lo at the Wellcome Genome Campus'
+ },
+ {
+ type: 'md',
+ content: "Find out more about Nida's work with the Bentley team:"
+ },
+ {
+ type: 'quoteCard',
+ content: {
+ name: 'Nida Javid (Department of Biology, Lahore University of Management Sciences, Pakistan)',
+ quotes: ["The original plan was that I will be working on the population genomics analysis of pneumococcal isolates from Pakistan. However, due to the lockdown, sequencing of isolates from Pakistan was delayed and I started working on the country analysis of pneumococcal carriage isolates from South Africa. I started with running quality control analysis of the sequenced data, followed by *in silico* serotyping, genotyping, prediction of antimicrobial resistance and phylogenetic analysis from pneumococcal genomes using a wide range of command-line tools such as SeroBA and PopPUNK. I then visualized the output using Microreact, a tool that allows me to interactively explore the phylogeny with temporal and geographical data. Now almost a year and a half later, this manuscript is ready for submission. I would like to thank Dr. Shabbir Madhi for allowing me to work on his dataset.", "After a few months, pneumococcal isolates from Pakistan were sequenced. I then analysed these data using the approach and tools that I had learnt during my first few months at Sanger, and am working towards publication of my Pakistan country analysis. We also presented our preliminary results at the ABPHM online conference. Although I am back in Pakistan now, I am still actively working with Stephanie and attend the team meetings regularly. I would like to thank Stephen, Stephanie, and the team for their support and kindness. I would also like to thank my PhD advisor, Dr. Shaper Mirza, for her support and guidance through my PhD."]
+ }
+ },
+ ]
+ }
+ ]
+}
+
+export default content
diff --git a/src/content/outlineContent.js b/src/content/outlineContent.js
index 5525c13..9da6eb9 100644
--- a/src/content/outlineContent.js
+++ b/src/content/outlineContent.js
@@ -23,7 +23,7 @@ const content = {
},
{
type: 'md',
- content: 'Pneumococcal conjugate vaccines (PCVs) target the protective capsule surrounding pneumococcal cells and have proven to be very effective in reducing pneumococcal disease since their first introduction in 2000. However, there are at least [100 different forms of capsule](../resources#serotypes), each giving rise to a distinct "serotype" determined based on interactions between antibodies and antigens on the capsule. Current PCVs only target some serotypes, and the overall pneumococcus population can evolve through a process known as "serotype switching" to evade the vaccines. This creates an arms race between the vaccines and the pneumococcus.'
+ content: 'Pneumococcal conjugate vaccines (PCVs) target the protective capsule surrounding pneumococcal cells and have proven to be very effective in reducing pneumococcal disease since their first introduction in 2000. However, there are at least [100 different forms of capsule](../serobank), each giving rise to a distinct "serotype" determined based on interactions between antibodies and antigens on the capsule. Current PCVs only target some serotypes, and the overall pneumococcus population can evolve through a process known as "serotype switching" to evade the vaccines. This creates an arms race between the vaccines and the pneumococcus.'
},
{
type: 'md',
@@ -62,7 +62,7 @@ const content = {
},
{
type: 'md',
- content: 'GPS sequence data confirmed that after the introduction of vaccines, pneumococci with vaccine serotypes were replaced by those with non-vaccine serotypes. Importantly, with such large-scale genome data, we were able to classify all the strains circulating globally, for the first time. Pneumococcal strains could be defined at high-resolution by taking genome-wide DNA variations into account ([Gladstone and Lo *et al* 2019](https://doi.org/10.1016/j.ebiom.2019.04.021)). This robust typing method is coupled with a coherent and dynamic naming system known as [global pneumococcal sequence clusters (GPSCs)](../resources#lineages), which enable collaborations in the tracking of pneumococcal lineages across geographical regions and over time, especially before and after the roll-out of PCVs.'
+ content: 'GPS sequence data confirmed that after the introduction of vaccines, pneumococci with vaccine serotypes were replaced by those with non-vaccine serotypes. Importantly, with such large-scale genome data, we were able to classify all the strains circulating globally, for the first time. Pneumococcal strains could be defined at high-resolution by taking genome-wide DNA variations into account ([Gladstone and Lo *et al* 2019](https://doi.org/10.1016/j.ebiom.2019.04.021)). This robust typing method is coupled with a coherent and dynamic naming system known as [global pneumococcal sequence clusters (GPSCs)](../gpsc#lineages), which enable collaborations in the tracking of pneumococcal lineages across geographical regions and over time, especially before and after the roll-out of PCVs.'
},
{
type: 'md',
@@ -81,7 +81,7 @@ const content = {
content: [
{
type: 'md',
- content: 'The GPS project generates a rich source of genome and epidemiological data for tracking pneumococcal transmission and evolution on both national and international levels. The genome data are deposited in [ENA](https://www.ebi.ac.uk/ena/data/view/PRJEB3084). High-level analyses are interactively presented by [countries](../resources#countries) and by [strains](../resources#lineages) using [Microreact](https://microreact.org/) and [Phandango](https://jameshadfield.github.io/phandango/#/GPS). Illustrations of how to use these resources are summarised in a publication ([Gladstone *et al* 2020](https://doi.org/10.1099/mgen.0.000357)) and videos on the [Resources pages](../resources#overview). '
+ content: 'The GPS project generates a rich source of genome and epidemiological data for tracking pneumococcal transmission and evolution on both national and international levels. The genome data are deposited in [ENA](https://www.ebi.ac.uk/ena/data/view/PRJEB3084). High-level analyses are interactively presented by [countries](../resources#countries) and by [strains](../gpsc#lineages) using [Microreact](https://microreact.org/) and [Phandango](https://jameshadfield.github.io/phandango/#/GPS). Illustrations of how to use these resources are summarised in a publication ([Gladstone *et al* 2020](https://doi.org/10.1099/mgen.0.000357)) and videos on the [Resources pages](../resources#overview). '
},
]
},
diff --git a/src/content/serotypeTableContent.tsv b/src/content/serotypeTableContent.tsv
index bb3ec75..19805e4 100644
--- a/src/content/serotypeTableContent.tsv
+++ b/src/content/serotypeTableContent.tsv
@@ -1,119 +1,123 @@
-count serotype accessionNumber comments reference referenceUrl cpsImage cpsRemark
-1 1 CR931632 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_1_cps.svg -
-2 2 CR931633 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_2_cps.svg -
-3 3 CR931634 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_3_cps.svg -
-4 4 CR931635 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_4_cps.svg -
-5 5 CR931637 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_5_cps.svg -
-6 6A CR931638 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_6A_cps.svg -
-- 6E(6A) - Genetic variant of 6A Park et al 2017 Genome Announc https://doi.org/10.1128/genomeA.01728-16 - -
-7 6B CR931639 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_6B_cps.svg -
-- 6E(6B) KU168827 Genetic variant of 6B Burton et al 2016 J Clin Microbiol https://doi.org/10.1128/JCM.03194-15 - -
-8 6C "EF538714,EF538715,EF538716,EF538717,EF538718" - "Park et al 2007 J Clin Microbiol,Park et al 2007 Infect Immun" "https://doi.org/10.1128/JCM.02199-06,https://doi.org/10.1128/iai.00510-07" img/serotype_cps/serotype_6C_cps.svg -
-9 6D HM448897 - Nahm et al 2011 J Med Microbiol https://doi.org/10.1099%2Fjmm.0.023853-0 img/serotype_cps/serotype_6D_cps.svg -
-10 6H KF597302 - Park et al 2015 Clin Vaccine Immunol https://doi.org/10.1128/CVI.00647-14 img/serotype_cps/serotype_6H_cps.svg Partial sequence only
-11 7A CR931640 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_7A_cps.svg -
-12 7B CR931641 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_7B_cps.svg -
-13 7C CR931642 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_7C_cps.svg -
-14 7D - - Kjeldsen et al 2018 Carbohydr Res https://doi.org/10.1016/j.carres.2018.04.011 - -
-15 7F CR931643 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_7F_cps.svg -
-16 8 CR931644 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_8_cps.svg -
-17 9A CR931645 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_9A_cps.svg -
-18 9L CR931646 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_9L_cps.svg -
-19 9N CR931647 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_9N_cps.svg -
-20 9V CR931648 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_9V_cps.svg -
-21 10A CR931649 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_10A_cps.svg -
-22 10B CR931650 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_10B_cps.svg -
-23 10C CR931651 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_10C_cps.svg -
-24 10D ERR051587 - Ganaie et al 2020 mBio https://doi.org/10.1128/mBio.00937-20 img/serotype_cps/serotype_10D_cps.svg -
-25 10F CR931652 - "Bentley et al 2006 PloS Genet,Yang et al 2011 J Biol Chem" "https://doi.org/10.1371/journal.pgen.0020031,https://doi.org/10.1074/jbc.M111.255422" img/serotype_cps/serotype_10F_cps.svg -
-26 11A CR931653 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_11A_cps.svg -
-27 11B CR931654 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_11B_cps.svg -
-28 11C CR931655 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_11C_cps.svg -
-29 11D CR931656 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_11D_cps.svg -
-30 11E - - Calix et al 2010 J Infect Dis https://doi.org/10.1086/653123 img/serotype_cps/serotype_11E_cps.svg -
-- 11Av - A serovariant which is an intermediate variant of 11A and 11E Camilli et al 2014 PloS ONE https://doi.org/10.1371/journal.pone.0100722 - -
-31 11F CR931657 - Calix et al 2011 J Bacteriology https://doi.org/10.1128/JB.05034-11 img/serotype_cps/serotype_11F_cps.svg -
-32 11F_like MF140334 - Manna et al 2018 Clin Microbiol Infect https://doi.org/10.1016%2Fj.cmi.2017.06.031 img/serotype_cps/serotype_11F_like_cps.svg -
-33 12A CR931658 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_12A_cps.svg -
-34 12B CR931659 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_12B_cps.svg -
-35 12F CR931660 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_12F_cps.svg -
-36 13 CR931661 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_13_cps.svg -
-37 14 CR931662 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_14_cps.svg -
-38 15A CR931663 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_15A_cps.svg -
-39 15B CR931664 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_15B_cps.svg -
-40 15C CR931665 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_15C_cps.svg -
-41 15D SAMN14150919 - Pimenta et al 2021 J Clin Microbiol https://doi.org/10.1128/jcm.00329-21 img/serotype_cps/serotype_15D_cps.svg -
-42 15F CR931666 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_15F_cps.svg -
-43 16A CR931667 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_16A_cps.svg -
-44 16F CR931668 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_16F_cps.svg -
-45 17A CR931669 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_17A_cps.svg -
-46 17F CR931670 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_17F_cps.svg -
-47 18A CR931671 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_18A_cps.svg -
-48 18B CR931672 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_18B_cps.svg -
-49 18C CR931673 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_18C_cps.svg -
-50 18F CR931674 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_18F_cps.svg -
-51 19A CR931675 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_19A_cps.svg -
-52 19B CR931676 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_19B_cps.svg -
-53 19C CR931677 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_19C_cps.svg -
-54 19F CR931678 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_19F_cps.svg -
-55 20A JQ653094 - Calix et al 2012 J Biol Chem https://doi.org/10.1074/jbc.M112.380451 img/serotype_cps/serotype_20A_cps.svg -
-56 20B JQ653093 - Calix et al 2012 J Biol Chem https://doi.org/10.1074/jbc.M112.380451 img/serotype_cps/serotype_20B_cps.svg -
-57 21 CR931680 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_21_cps.svg -
-58 22A CR931681 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_22A_cps.svg -
-59 22F CR931682 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_22F_cps.svg -
-60 23A CR931683 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_23A_cps.svg -
-61 23B CR931684 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_23B_cps.svg -
-62 23F CR931685 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_23F_cps.svg -
-63 24A CR931686 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_24A_cps.svg -
-64 24B CR931687 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_24B_cps.svg -
-65 24C MW683298 - Ganaie et al 2021 J Clin Microbiol https://doi.org/10.1128/JCM.00540-21 img/serotype_cps/serotype_24C_cps.svg -
-66 24F CR931688 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_24F_cps.svg -
-67 25A CR931689 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_25A_cps.svg -
-68 25F CR931690 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_25F_cps.svg -
-69 27 CR931691 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_27_cps.svg -
-70 28A CR931692 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_28A_cps.svg -
-71 28F CR931693 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_28F_cps.svg -
-72 29 CR931694 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_29_cps.svg -
-73 31 CR931695 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_31_cps.svg -
-74 32A CR931696 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_32A_cps.svg -
-75 32F CR931697 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_32F_cps.svg -
-76 33A CR931698 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_33A_cps.svg -
-77 33B CR931699 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_33B_cps.svg -
-78 33C CR931700 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_33C_cps.svg -
-79 33D CR931701 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_33D_cps.svg -
-80 33E SAMEA2203953 - Ganaie et al 2023 J Biol Chem https://doi.org/10.1016/j.jbc.2023.105085 img/serotype_cps/serotype_33E_cps.svg -
-81 33F CR931702 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_33F_cps.svg -
-82 33G OR509570 - Manna et al 2023 Microbiol Spectr https://doi.org/10.1128%2Fspectrum.03579-23 img/serotype_cps/serotype_33G_cps.svg -
-83 34 CR931703 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_34_cps.svg -
-84 35A CR931704 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_35A_cps.svg -
-85 35B CR931705 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_35B_cps.svg -
-86 35C CR931706 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_35C_cps.svg -
-87 35D KY084476 various disruptive mutations in wciG "Geno et al 2017 J Clin Microbiol,Lo et al 2018 J Clin Microbiol" "https://doi.org/10.1128/JCM.00054-17,https://doi.org/10.1128/jcm.00228-18" img/serotype_cps/serotype_35D_cps.svg -
-88 35F CR931707 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_35F_cps.svg -
-89 36A CR931708 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_36A_cps.svg -
-90 36B MK606436 - Ganaie et al 2023 J Clin Microbiol https://doi.org/10.1128/jcm.00024-23 img/serotype_cps/serotype_36B_cps.svg -
-91 37 CR931709 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_37_cps.svg -
-92 38 CR931710 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_38_cps.svg -
-93 39 CR931711 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_39_cps.svg -
-94 40 CR931712 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_40_cps.svg -
-95 41A CR931713 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_41A_cps.svg -
-96 41F CR931714 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_41F_cps.svg -
-97 42 CR931715 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_42_cps.svg -
-98 43 CR931716 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_43_cps.svg -
-99 44 CR931717 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_44_cps.svg -
-100 45 CR931718 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_45_cps.svg -
-101 46 CR931719 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_46_cps.svg -
-102 47A CR931720 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_47A_cps.svg -
-103 47F CR931721 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_47F_cps.svg -
-104 48 CR931722 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_48_cps.svg -
-- 9X MK606437 putative novel serotype based on nucleotide sequence encoding pneumococcal capsule van Tonder et al 2019 Mgen https://doi.org/10.1099/mgen.0.000274 img/serotype_cps/serotype_9X_cps.svg -
-- 11X MK606429 putative novel serotype based on nucleotide sequence encoding pneumococcal capsule van Tonder et al 2019 Mgen https://doi.org/10.1099/mgen.0.000274 img/serotype_cps/serotype_11X_cps.svg -
-- 16X MK606430 putative novel serotype based on nucleotide sequence encoding pneumococcal capsule van Tonder et al 2019 Mgen https://doi.org/10.1099/mgen.0.000274 img/serotype_cps/serotype_16X_cps.svg -
-- 18X1 MK606431 putative novel serotype based on nucleotide sequence encoding pneumococcal capsule van Tonder et al 2019 Mgen https://doi.org/10.1099/mgen.0.000274 img/serotype_cps/serotype_18X1_cps.svg -
-- 18X2 MK606432 putative novel serotype based on nucleotide sequence encoding pneumococcal capsule van Tonder et al 2019 Mgen https://doi.org/10.1099/mgen.0.000274 img/serotype_cps/serotype_18X2_cps.svg -
-- 18X3 MK606433 putative novel serotype based on nucleotide sequence encoding pneumococcal capsule van Tonder et al 2019 Mgen https://doi.org/10.1099/mgen.0.000274 img/serotype_cps/serotype_18X3_cps.svg -
-- 29X MK606434 putative novel serotype based on nucleotide sequence encoding pneumococcal capsule van Tonder et al 2019 Mgen https://doi.org/10.1099/mgen.0.000274 img/serotype_cps/serotype_29X_cps.svg -
-- 33X MK606435 putative novel serotype based on nucleotide sequence encoding pneumococcal capsule van Tonder et al 2019 Mgen https://doi.org/10.1099/mgen.0.000274 img/serotype_cps/serotype_33X_cps.svg -
-- 36X MK606436 putative novel serotype based on nucleotide sequence encoding pneumococcal capsule van Tonder et al 2019 Mgen https://doi.org/10.1099/mgen.0.000274 img/serotype_cps/serotype_36X_cps.svg -
-- Group I nonencapsulated - do not produce capsule due to mutations or deletion of genes encoding capsule Hathaway et al 2014 J Bacteriology https://doi.org/10.1128/JB.186.12.3721-3729.2004 - -
-- Group II nonencapsulated - do not produce capsule due to novel genes in place of genes encoding capsule "Park et al 2012 mBio,Salter et al 2012 Microbiology" "https://doi.org/10.1128/mBio.00035-12,https://doi.org/10.1099%2Fmic.0.056580-0" - -
\ No newline at end of file
+count serotype accessionNumber comments reference referenceUrl cpsImage cpsRemark genBankFile poolSerum typeSerum groupSerum factorSerum otherSerum otherSerumRemark antiserumNote capsularStructureImage capsularStructureRemark
+1 1 CR931632 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_1_cps.svg - res/serotype_genbank/serotype_1.gb "A,P" 1 - - - - - img/serotype_capsular_structure/serotype_1_capsular_structure.svg -
+2 2 CR931633 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_2_cps.svg - res/serotype_genbank/serotype_2.gb "A,T" 2 - - - - - img/serotype_capsular_structure/serotype_2_capsular_structure.svg -
+3 3 CR931634 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_3_cps.svg - res/serotype_genbank/serotype_3.gb "B,R" 3 - - - - - img/serotype_capsular_structure/serotype_3_capsular_structure.svg -
+4 4 CR931635 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_4_cps.svg - res/serotype_genbank/serotype_4.gb "A,R" 4 - - - - - img/serotype_capsular_structure/serotype_4_capsular_structure.svg -
+5 5 CR931637 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_5_cps.svg - res/serotype_genbank/serotype_5.gb "A,S" 5 - - - - - img/serotype_capsular_structure/serotype_5_capsular_structure.svg -
+6 6A CR931638 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_6A_cps.svg - res/serotype_genbank/serotype_6A.gb "B,Q" - 6 6b - - - img/serotype_capsular_structure/serotype_6A_capsular_structure.svg -
+- 6E(6A) - Genetic variant of 6A Park et al 2017 Genome Announc https://doi.org/10.1128/genomeA.01728-16 - - - "B,Q" - 6 6b - - - - -
+7 6B CR931639 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_6B_cps.svg - res/serotype_genbank/serotype_6B.gb "B,Q" - 6 6c - - - img/serotype_capsular_structure/serotype_6B_capsular_structure.svg -
+- 6E(6B) LT594599 Genetic variant of 6B Kapatai et al 2016 PeerJ https://doi.org/10.7717%2Fpeerj.2477 - - res/serotype_genbank/serotype_6E_6B.gb "B,Q" - 6 6c - - - - -
+8 6C "EF538714,EF538715,EF538716,EF538717,EF538718" - "Park et al 2007 J Clin Microbiol,Park et al 2007 Infect Immun" "https://doi.org/10.1128/JCM.02199-06,https://doi.org/10.1128/iai.00510-07" img/serotype_cps/serotype_6C_cps.svg - res/serotype_genbank/serotype_6C.gb "B,Q" - 6 6d - - - img/serotype_capsular_structure/serotype_6C_capsular_structure.svg -
+9 6D HM448897 - Nahm et al 2011 J Med Microbiol https://doi.org/10.1099%2Fjmm.0.023853-0 img/serotype_cps/serotype_6D_cps.svg - res/serotype_genbank/serotype_6D.gb "B,Q" - 6 "6c,6d" - - - img/serotype_capsular_structure/serotype_6D_capsular_structure.svg -
+10 6F KC832410 - Oliver et al 2013 J Biol Chem https://doi.org/10.1074%2Fjbc.M113.480152 img/serotype_cps/serotype_6F_cps.svg - res/serotype_genbank/serotype_6F.gb - - - - - - - - 6A + 6C
+11 6G KC832411 - Oliver et al 2013 J Biol Chem https://doi.org/10.1074%2Fjbc.M113.480152 img/serotype_cps/serotype_6G_cps.svg - res/serotype_genbank/serotype_6G.gb - - - - - - - - 6B + 6D
+12 6H KF597302 - Park et al 2015 Clin Vaccine Immunol https://doi.org/10.1128/CVI.00647-14 img/serotype_cps/serotype_6H_cps.svg Partial sequence only res/serotype_genbank/serotype_6H.gb - - - - - - - - 6A + 6B
+13 7A CR931640 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_7A_cps.svg - res/serotype_genbank/serotype_7A.gb "C,P" - 7 "7b,7c" - - - img/serotype_capsular_structure/serotype_7A_capsular_structure.svg -
+14 7B CR931641 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_7B_cps.svg - res/serotype_genbank/serotype_7B.gb "C,P" - 7 7e - - - img/serotype_capsular_structure/serotype_7B_capsular_structure.svg -
+15 7C CR931642 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_7C_cps.svg - res/serotype_genbank/serotype_7C.gb "C,P" - 7 7f - - - img/serotype_capsular_structure/serotype_7C_capsular_structure.svg -
+16 7D - - Kjeldsen et al 2018 Carbohydr Res https://doi.org/10.1016/j.carres.2018.04.011 - - - - - - - - - - - 7B (1X) + 7C (5X)
+17 7F CR931643 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_7F_cps.svg - res/serotype_genbank/serotype_7F.gb "C,P" - 7 7b - - - img/serotype_capsular_structure/serotype_7F_capsular_structure.svg -
+18 8 CR931644 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_8_cps.svg - res/serotype_genbank/serotype_8.gb "B,S" 8 - - - - - img/serotype_capsular_structure/serotype_8_capsular_structure.svg -
+19 9A CR931645 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_9A_cps.svg - res/serotype_genbank/serotype_9A.gb "D,R" - 9 9d - - - img/serotype_capsular_structure/serotype_9A_capsular_structure.svg -
+20 9L CR931646 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_9L_cps.svg - res/serotype_genbank/serotype_9L.gb "D,R" - 9 9b - - - img/serotype_capsular_structure/serotype_9L_capsular_structure.svg -
+21 9N CR931647 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_9N_cps.svg - res/serotype_genbank/serotype_9N.gb "D,R" - 9 "9b,9e" - - - img/serotype_capsular_structure/serotype_9N_capsular_structure.svg -
+22 9V CR931648 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_9V_cps.svg - res/serotype_genbank/serotype_9V.gb "D,R" - 9 "9d,9g" - - - img/serotype_capsular_structure/serotype_9V_capsular_structure.svg -
+23 10A CR931649 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_10A_cps.svg - res/serotype_genbank/serotype_10A.gb "E,S" - 10 10d - - - img/serotype_capsular_structure/serotype_10A_capsular_structure.svg -
+24 10B CR931650 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_10B_cps.svg - res/serotype_genbank/serotype_10B.gb "E,S" - 10 "10b,10d" - - - img/serotype_capsular_structure/serotype_10B_capsular_structure.svg -
+25 10C CR931651 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_10C_cps.svg - res/serotype_genbank/serotype_10C.gb "E,S" - 10 "10b,10f" - - - img/serotype_capsular_structure/serotype_10C_capsular_structure.svg -
+26 10D ERR051587 - Ganaie et al 2020 mBio https://doi.org/10.1128/mBio.00937-20 img/serotype_cps/serotype_10D_cps.svg - res/serotype_genbank/serotype_10D.gb - - - - - - - img/serotype_capsular_structure/serotype_10D_capsular_structure.svg -
+27 10F CR931652 - "Bentley et al 2006 PloS Genet,Yang et al 2011 J Biol Chem" "https://doi.org/10.1371/journal.pgen.0020031,https://doi.org/10.1074/jbc.M111.255422" img/serotype_cps/serotype_10F_cps.svg - res/serotype_genbank/serotype_10F.gb "E,S" - 10 10b - - - img/serotype_capsular_structure/serotype_10F_capsular_structure.svg -
+28 11A CR931653 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_11A_cps.svg - res/serotype_genbank/serotype_11A.gb "D,T" - 11 11c - - - img/serotype_capsular_structure/serotype_11A_capsular_structure.svg -
+29 11B CR931654 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_11B_cps.svg - res/serotype_genbank/serotype_11B.gb "D,T" - 11 "11b,11f,11g" - - - img/serotype_capsular_structure/serotype_11B_capsular_structure.svg -
+30 11C CR931655 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_11C_cps.svg - res/serotype_genbank/serotype_11C.gb "D,T" - 11 "11b,11c,11f" - - - img/serotype_capsular_structure/serotype_11C_capsular_structure.svg -
+31 11D CR931656 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_11D_cps.svg - res/serotype_genbank/serotype_11D.gb "D,T" - 11 "11b,11c" - - - img/serotype_capsular_structure/serotype_11D_capsular_structure.svg -
+32 11E - - Calix et al 2010 J Infect Dis https://doi.org/10.1086/653123 img/serotype_cps/serotype_11E_cps.svg - res/serotype_genbank/serotype_11E.gb - - - - - - - img/serotype_capsular_structure/serotype_11E_capsular_structure.svg -
+- 11Av - A serovariant which is an intermediate variant of 11A and 11E Camilli et al 2014 PloS ONE https://doi.org/10.1371/journal.pone.0100722 - - - - - - - - - - - -
+33 11F CR931657 - Calix et al 2011 J Bacteriology https://doi.org/10.1128/JB.05034-11 img/serotype_cps/serotype_11F_cps.svg - res/serotype_genbank/serotype_11F.gb "D,T" - 11 "11b,11g" - - - img/serotype_capsular_structure/serotype_11F_capsular_structure.svg -
+_ 11F-like MF140334 Genetic variant of 11A Manna et al 2018 Clin Microbiol Infect https://doi.org/10.1016%2Fj.cmi.2017.06.031 img/serotype_cps/serotype_11F-like_cps.svg - res/serotype_genbank/serotype_11F-like.gb - - - - - - - - -
+34 12A CR931658 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_12A_cps.svg - res/serotype_genbank/serotype_12A.gb "E,R" - 12 12c - - - img/serotype_capsular_structure/serotype_12A_capsular_structure.svg -
+35 12B CR931659 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_12B_cps.svg - res/serotype_genbank/serotype_12B.gb "E,R" - 12 "12b,12c,12e" - - - - -
+36 12F CR931660 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_12F_cps.svg - res/serotype_genbank/serotype_12F.gb "E,R" - 12 12b - - - img/serotype_capsular_structure/serotype_12F_capsular_structure.svg -
+37 13 CR931661 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_13_cps.svg - res/serotype_genbank/serotype_13.gb H 13 - - - - - img/serotype_capsular_structure/serotype_13_capsular_structure.svg -
+38 14 CR931662 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_14_cps.svg - res/serotype_genbank/serotype_14.gb "H,P" 14 - - - - - img/serotype_capsular_structure/serotype_14_capsular_structure.svg -
+39 15A CR931663 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_15A_cps.svg - res/serotype_genbank/serotype_15A.gb "H,S" - 15 15c - - - img/serotype_capsular_structure/serotype_15A_capsular_structure.svg -
+40 15B CR931664 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_15B_cps.svg - res/serotype_genbank/serotype_15B.gb "H,S" - 15 "15b,15e,15h" - - - img/serotype_capsular_structure/serotype_15B_capsular_structure.svg -
+41 15C CR931665 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_15C_cps.svg - res/serotype_genbank/serotype_15C.gb "H,S" - 15 15e - - - img/serotype_capsular_structure/serotype_15C_capsular_structure.svg -
+42 15D SAMN14150919 - Pimenta et al 2021 J Clin Microbiol https://doi.org/10.1128/jcm.00329-21 img/serotype_cps/serotype_15D_cps.svg - res/serotype_genbank/serotype_15D.gb "H,S" - 15 "15b,15c" "15bf,15g" "Antiserum available at CDC,Antiserum available at CDC" Cannot be identified only by SSI Antiseria img/serotype_capsular_structure/serotype_15F_capsular_structure.svg Predicted
+43 15F CR931666 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_15F_cps.svg - res/serotype_genbank/serotype_15F.gb "H,S" - 15 "15b,15c" - - - img/serotype_capsular_structure/serotype_15F_capsular_structure.svg -
+44 16A CR931667 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_16A_cps.svg - res/serotype_genbank/serotype_16A.gb D - 16 16c - - - img/serotype_capsular_structure/serotype_16A_capsular_structure.svg -
+45 16F CR931668 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_16F_cps.svg - res/serotype_genbank/serotype_16F.gb D - 16 16b - - - img/serotype_capsular_structure/serotype_16F_capsular_structure.svg -
+46 17A CR931669 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_17A_cps.svg - res/serotype_genbank/serotype_17A.gb "F,S" - 17 17c - - - img/serotype_capsular_structure/serotype_17A_capsular_structure.svg -
+47 17F CR931670 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_17F_cps.svg - res/serotype_genbank/serotype_17F.gb "F,S" - 17 17b - - - img/serotype_capsular_structure/serotype_17F_capsular_structure.svg -
+48 18A CR931671 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_18A_cps.svg - res/serotype_genbank/serotype_18A.gb "A,Q" - 18 18d - - - img/serotype_capsular_structure/serotype_18A_capsular_structure.svg -
+49 18B CR931672 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_18B_cps.svg - res/serotype_genbank/serotype_18B.gb "A,Q" - 18 18e - - - img/serotype_capsular_structure/serotype_18B_capsular_structure.svg -
+50 18C CR931673 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_18C_cps.svg - res/serotype_genbank/serotype_18C.gb "A,Q" - 18 "18c,18e" - - - img/serotype_capsular_structure/serotype_18C_capsular_structure.svg -
+51 18F CR931674 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_18F_cps.svg - res/serotype_genbank/serotype_18F.gb "A,Q" - 18 "18c,18e,18f" - - - img/serotype_capsular_structure/serotype_18F_capsular_structure.svg -
+52 19A CR931675 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_19A_cps.svg - res/serotype_genbank/serotype_19A.gb "B,P" - 19 19c - - - img/serotype_capsular_structure/serotype_19A_capsular_structure.svg -
+53 19B CR931676 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_19B_cps.svg - res/serotype_genbank/serotype_19B.gb "B,P" - 19 7h - - - img/serotype_capsular_structure/serotype_19B_capsular_structure.svg -
+54 19C CR931677 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_19C_cps.svg - res/serotype_genbank/serotype_19C.gb "B,P" - 19 "19f,7h" - - - img/serotype_capsular_structure/serotype_19C_capsular_structure.svg -
+55 19F CR931678 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_19F_cps.svg - res/serotype_genbank/serotype_19F.gb "B,P" - 19 19b - - - img/serotype_capsular_structure/serotype_19F_capsular_structure.svg -
+56 20A JQ653094 - Calix et al 2012 J Biol Chem https://doi.org/10.1074/jbc.M112.380451 img/serotype_cps/serotype_20A_cps.svg - res/serotype_genbank/serotype_20A.gb - - - - - - - img/serotype_capsular_structure/serotype_20A_capsular_structure.svg -
+57 20B JQ653093 - Calix et al 2012 J Biol Chem https://doi.org/10.1074/jbc.M112.380451 img/serotype_cps/serotype_20B_cps.svg - res/serotype_genbank/serotype_20B.gb - - - - - - - img/serotype_capsular_structure/serotype_20B_capsular_structure.svg -
+58 20C ERR980181 - Yu et al 2024 Microbiol Spectr https://doi.org/10.1128/spectrum.02443-24 img/serotype_cps/serotype_20C_cps.svg - res/serotype_genbank/serotype_20C.gb - - - - - - - img/serotype_capsular_structure/serotype_20C_capsular_structure.svg -
+59 21 CR931680 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_21_cps.svg - res/serotype_genbank/serotype_21.gb E 21 - - - - - - -
+60 22A CR931681 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_22A_cps.svg - res/serotype_genbank/serotype_22A.gb "F,T" - 22 22c - - - img/serotype_capsular_structure/serotype_22A_capsular_structure.svg -
+61 22F CR931682 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_22F_cps.svg - res/serotype_genbank/serotype_22F.gb "F,T" - 22 22b - - - img/serotype_capsular_structure/serotype_22F_capsular_structure.svg -
+62 23A CR931683 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_23A_cps.svg - res/serotype_genbank/serotype_23A.gb "H,Q" - 23 23c - - - img/serotype_capsular_structure/serotype_23A_capsular_structure.svg -
+63 23B CR931684 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_23B_cps.svg - res/serotype_genbank/serotype_23B.gb "H,Q" - 23 23d - - - img/serotype_capsular_structure/serotype_23B_capsular_structure.svg -
+64 23F CR931685 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_23F_cps.svg - res/serotype_genbank/serotype_23F.gb "H,Q" - 23 23b - - - img/serotype_capsular_structure/serotype_23F_capsular_structure.svg -
+65 24A CR931686 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_24A_cps.svg - res/serotype_genbank/serotype_24A.gb C - 24 "24c,24d" - - - img/serotype_capsular_structure/serotype_24A_capsular_structure.svg -
+66 24B CR931687 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_24B_cps.svg - res/serotype_genbank/serotype_24B.gb C - 24 24e - - - img/serotype_capsular_structure/serotype_24B_capsular_structure.svg -
+67 24C MW683298 - Ganaie et al 2021 J Clin Microbiol https://doi.org/10.1128/JCM.00540-21 img/serotype_cps/serotype_24C_cps.svg - res/serotype_genbank/serotype_24C.gb - - - - - - - - 24B + 24F
+68 24F CR931688 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_24F_cps.svg - res/serotype_genbank/serotype_24F.gb C - 24 24d - - - img/serotype_capsular_structure/serotype_24F_capsular_structure.svg -
+69 25A CR931689 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_25A_cps.svg - res/serotype_genbank/serotype_25A.gb I - 25 25c - - - - -
+70 25F CR931690 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_25F_cps.svg - res/serotype_genbank/serotype_25F.gb I - 25 25b - - - - -
+71 27 CR931691 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_27_cps.svg - res/serotype_genbank/serotype_27.gb F 27 - - - - - img/serotype_capsular_structure/serotype_27_capsular_structure.svg -
+72 28A CR931692 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_28A_cps.svg - res/serotype_genbank/serotype_28A.gb H - 28 28c - - - img/serotype_capsular_structure/serotype_28A_capsular_structure.svg -
+73 28F CR931693 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_28F_cps.svg - res/serotype_genbank/serotype_28F.gb H - 28 28b - - - img/serotype_capsular_structure/serotype_28F_capsular_structure.svg -
+74 29 CR931694 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_29_cps.svg - res/serotype_genbank/serotype_29.gb G 29 - - - - - img/serotype_capsular_structure/serotype_29_capsular_structure.svg -
+75 31 CR931695 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_31_cps.svg - res/serotype_genbank/serotype_31.gb C 31 - - - - - img/serotype_capsular_structure/serotype_31_capsular_structure.svg -
+76 32A CR931696 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_32A_cps.svg - res/serotype_genbank/serotype_32A.gb F - 32 "32a,32b" - - - img/serotype_capsular_structure/serotype_32A_capsular_structure.svg -
+77 32F CR931697 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_32F_cps.svg - res/serotype_genbank/serotype_32F.gb F - 32 32a - - - img/serotype_capsular_structure/serotype_32F_capsular_structure.svg -
+78 33A CR931698 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_33A_cps.svg - res/serotype_genbank/serotype_33A.gb "E,T" - 33 "33b,20b" - - - img/serotype_capsular_structure/serotype_33A_capsular_structure.svg -
+79 33B CR931699 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_33B_cps.svg - res/serotype_genbank/serotype_33B.gb "E,T" - 33 33f - - - img/serotype_capsular_structure/serotype_33B_capsular_structure.svg -
+80 33C CR931700 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_33C_cps.svg - res/serotype_genbank/serotype_33C.gb "E,T" - 33 33e(33f) - - - img/serotype_capsular_structure/serotype_33C_capsular_structure.svg -
+81 33D CR931701 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_33D_cps.svg - res/serotype_genbank/serotype_33D.gb "E,T" - 33 "33f,6a" - - - img/serotype_capsular_structure/serotype_33D_capsular_structure.svg -
+82 33E SAMEA2203953 - Ganaie et al 2023 J Biol Chem https://doi.org/10.1016/j.jbc.2023.105085 img/serotype_cps/serotype_33E_cps.svg - res/serotype_genbank/serotype_33E.gb - - - - - - - img/serotype_capsular_structure/serotype_33E_capsular_structure.svg -
+83 33F CR931702 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_33F_cps.svg - res/serotype_genbank/serotype_33F.gb "E,T" - 33 33b - - - img/serotype_capsular_structure/serotype_33F_capsular_structure.svg -
+84 33G OR509570 - Manna et al 2023 Microbiol Spectr https://doi.org/10.1128%2Fspectrum.03579-23 img/serotype_cps/serotype_33G_cps.svg - res/serotype_genbank/serotype_33G.gb - - - - - - - img/serotype_capsular_structure/serotype_33G_capsular_structure.svg -
+85 34 CR931703 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_34_cps.svg - res/serotype_genbank/serotype_34.gb G 34 - - - - - img/serotype_capsular_structure/serotype_34_capsular_structure.svg -
+86 35A CR931704 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_35A_cps.svg - res/serotype_genbank/serotype_35A.gb G - 35 "35a,35c" - - - img/serotype_capsular_structure/serotype_35A_capsular_structure.svg -
+87 35B CR931705 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_35B_cps.svg - res/serotype_genbank/serotype_35B.gb G - 35 "35a,35c,29b" - - - img/serotype_capsular_structure/serotype_35B_capsular_structure.svg -
+88 35C CR931706 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_35C_cps.svg - res/serotype_genbank/serotype_35C.gb G - 35 "35a,35c,42a" - - - img/serotype_capsular_structure/serotype_35C_capsular_structure.svg -
+89 35D KY084476 various disruptive mutations in wciG "Geno et al 2017 J Clin Microbiol,Lo et al 2018 J Clin Microbiol" "https://doi.org/10.1128/JCM.00054-17,https://doi.org/10.1128/jcm.00228-18" img/serotype_cps/serotype_35D_cps.svg - res/serotype_genbank/serotype_35D.gb G - - - "fs29b,fs35c" "Antiserum available at Nahm Lab,Antiserum available at Nahm Lab" Can be differentiated from 35B by SSI antisera based on the absence of reaction with SSI Factor Serum 35a img/serotype_capsular_structure/serotype_35D_capsular_structure.svg -
+90 35F CR931707 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_35F_cps.svg - res/serotype_genbank/serotype_35F.gb G - 35 "35a,35b" - - - img/serotype_capsular_structure/serotype_35F_capsular_structure.svg -
+91 36A CR931708 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_36A_cps.svg - res/serotype_genbank/serotype_36A.gb D 36 - 9e - - - img/serotype_capsular_structure/serotype_36A_capsular_structure.svg -
+92 36B MK606436 - Ganaie et al 2023 J Clin Microbiol https://doi.org/10.1128/jcm.00024-23 img/serotype_cps/serotype_36B_cps.svg - res/serotype_genbank/serotype_36B.gb D 36 - - - - - img/serotype_capsular_structure/serotype_36B_capsular_structure.svg -
+93 37 CR931709 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_37_cps.svg - res/serotype_genbank/serotype_37.gb D 37 - - - - - img/serotype_capsular_structure/serotype_37_capsular_structure.svg -
+94 38 CR931710 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_38_cps.svg - res/serotype_genbank/serotype_38.gb I 38 - - - - - img/serotype_capsular_structure/serotype_38_capsular_structure.svg -
+95 39 CR931711 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_39_cps.svg - res/serotype_genbank/serotype_39.gb E 39 - - - - - img/serotype_capsular_structure/serotype_39_capsular_structure.svg -
+96 40 CR931712 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_40_cps.svg - res/serotype_genbank/serotype_40.gb C 40 - - - - - - -
+97 41A CR931713 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_41A_cps.svg - res/serotype_genbank/serotype_41A.gb F - 41 41a - - - img/serotype_capsular_structure/serotype_41A_capsular_structure.svg -
+98 41F CR931714 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_41F_cps.svg - res/serotype_genbank/serotype_41F.gb F - 41 "41a,41b" - - - img/serotype_capsular_structure/serotype_41F_capsular_structure.svg -
+99 42 CR931715 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_42_cps.svg - res/serotype_genbank/serotype_42.gb G 42 - - - - - img/serotype_capsular_structure/serotype_42_capsular_structure.svg -
+100 43 CR931716 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_43_cps.svg - res/serotype_genbank/serotype_43.gb I 43 - - - - - - -
+101 44 CR931717 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_44_cps.svg - res/serotype_genbank/serotype_44.gb I 44 - - - - - - -
+102 45 CR931718 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_45_cps.svg - res/serotype_genbank/serotype_45.gb I 45 - - - - - img/serotype_capsular_structure/serotype_45_capsular_structure.svg -
+103 46 CR931719 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_46_cps.svg - res/serotype_genbank/serotype_46.gb I 46 - - - - - - -
+104 47A CR931720 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_47A_cps.svg - res/serotype_genbank/serotype_47A.gb G - 47 "47a,43b" - - - img/serotype_capsular_structure/serotype_47A_capsular_structure.svg -
+105 47F CR931721 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_47F_cps.svg - res/serotype_genbank/serotype_47F.gb G - 47 47a - - - img/serotype_capsular_structure/serotype_47F_capsular_structure.svg -
+106 48 CR931722 - Bentley et al 2006 PloS Genet https://doi.org/10.1371/journal.pgen.0020031 img/serotype_cps/serotype_48_cps.svg - res/serotype_genbank/serotype_48.gb I 48 - - - - - - -
+- 9X MK606437 putative novel serotype based on nucleotide sequence encoding pneumococcal capsule van Tonder et al 2019 Mgen https://doi.org/10.1099/mgen.0.000274 img/serotype_cps/serotype_9X_cps.svg - res/serotype_genbank/serotype_9X.gb - - - - - - - - -
+- 11X MK606429 putative novel serotype based on nucleotide sequence encoding pneumococcal capsule van Tonder et al 2019 Mgen https://doi.org/10.1099/mgen.0.000274 img/serotype_cps/serotype_11X_cps.svg - res/serotype_genbank/serotype_11X.gb - - - - - - - - -
+- 16X MK606430 putative novel serotype based on nucleotide sequence encoding pneumococcal capsule van Tonder et al 2019 Mgen https://doi.org/10.1099/mgen.0.000274 img/serotype_cps/serotype_16X_cps.svg - res/serotype_genbank/serotype_16X.gb - - - - - - - - -
+- 18X1 MK606431 putative novel serotype based on nucleotide sequence encoding pneumococcal capsule van Tonder et al 2019 Mgen https://doi.org/10.1099/mgen.0.000274 img/serotype_cps/serotype_18X1_cps.svg - res/serotype_genbank/serotype_18X1.gb - - - - - - - - -
+- 18X2 MK606432 putative novel serotype based on nucleotide sequence encoding pneumococcal capsule van Tonder et al 2019 Mgen https://doi.org/10.1099/mgen.0.000274 img/serotype_cps/serotype_18X2_cps.svg - res/serotype_genbank/serotype_18X2.gb - - - - - - - - -
+- 18X3 MK606433 putative novel serotype based on nucleotide sequence encoding pneumococcal capsule van Tonder et al 2019 Mgen https://doi.org/10.1099/mgen.0.000274 img/serotype_cps/serotype_18X3_cps.svg - res/serotype_genbank/serotype_18X3.gb - - - - - - - - -
+- 29X MK606434 putative novel serotype based on nucleotide sequence encoding pneumococcal capsule van Tonder et al 2019 Mgen https://doi.org/10.1099/mgen.0.000274 img/serotype_cps/serotype_29X_cps.svg - res/serotype_genbank/serotype_29X.gb - - - - - - - - -
+- Group I nonencapsulated - do not produce capsule due to mutations or deletion of genes encoding capsule Hathaway et al 2014 J Bacteriology https://doi.org/10.1128/JB.186.12.3721-3729.2004 - - - - - - - - - - - N/A - Nonencapsulated
+- Group II nonencapsulated - NCC1 pspK JF489996 do not produce capsule due to novel genes in place of genes encoding capsule Park et al 2012 mBio https://doi.org/10.1128/mbio.00035-12 img/serotype_cps/group_II_nonencapsulated-NCC1_pspK.svg - - - - - - - - - - N/A - Nonencapsulated
+- Group II nonencapsulated - NCC2 aliC aliD HE651292 do not produce capsule due to novel genes in place of genes encoding capsule "Park et al 2012 mBio,Salter et al 2012 Microbiology (Reading)" "https://doi.org/10.1128/mbio.00035-12,https://doi.org/10.1099/mic.0.056580-0" img/serotype_cps/group_II_nonencapsulated-NCC2_aliC_aliD.svg - - - - - - - - - - N/A - Nonencapsulated
+- Group II nonencapsulated - NCC2 S. mitis aliC aliD HE651274 do not produce capsule due to novel genes in place of genes encoding capsule "Park et al 2012 mBio,Salter et al 2012 Microbiology (Reading)" "https://doi.org/10.1128/mbio.00035-12,https://doi.org/10.1099/mic.0.056580-0" img/serotype_cps/group_II_nonencapsulated-NCC2_S_mitis_aliC_aliD.svg - - - - - - - - - - N/A - Nonencapsulated
+- Group II nonencapsulated - NCC3 aliD JF490008 do not produce capsule due to novel genes in place of genes encoding capsule Park et al 2012 mBio https://doi.org/10.1128/mbio.00035-12 img/serotype_cps/group_II_nonencapsulated-NCC3_aliD.svg - - - - - - - - - - N/A - Nonencapsulated
\ No newline at end of file
diff --git a/src/content/substudiesContent.js b/src/content/substudiesContent.js
index 30c8222..f11b348 100644
--- a/src/content/substudiesContent.js
+++ b/src/content/substudiesContent.js
@@ -75,7 +75,7 @@ const content = {
title: 'Diversity of ribosomal mutations associated with MLS resistance',
authors: 'Paulina Hawkins',
affiliations: 'Centers for Disease Control and Prevention',
- details: 'Macrolide has increasingly been used as empirical treatment for respiratory tract infection. After PCV13, rising macrolide resistance was observed in pneumococci with non-vaccine serotype ([Lo *et al* 2019](https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(19)30297-X/fulltext)). This study will improve our understanding of the genetic diversity of ribosomal mutations related to macrolide resistance in *S. pneumoniae.*'
+ details: 'Macrolide has increasingly been used as empirical treatment for respiratory tract infection. After PCV13, rising macrolide resistance was observed in pneumococci with non-vaccine serotype ([Lo *et al* 2019](https://doi.org/10.1016/s1473-3099(19)30297-x)). This study will improve our understanding of the genetic diversity of ribosomal mutations related to macrolide resistance in *S. pneumoniae.*'
},
{
title: 'Genetic diversity and distribution of the pneumococcal ABC transporter proteins and implications on potential protein-based vaccines',
@@ -93,13 +93,13 @@ const content = {
title: 'Global distribution and evolution of major penicillin binding proteins that determine β-lactam resistance in *Streptococcus pneumoniae*',
authors: 'Yuan Li, Benjamin Metcalf, Lesley McGee, Bernard Beall, Stephen Bentley, Rebecca Gladstone',
affiliations: 'Centers for Disease Control and Prevention',
- details: '[CDC Strep Lab](https://www.cdc.gov/streplab/index.html) has a strong expertise in using genomic data to predict antibiotic resistance in *S. pneumoniae*. This project will appreciate the genetic diversity and evolution of the penicillin binding protein, that confer resistance to the first-line antibiotic, β-lactam, in treating pneumococcal disease.'
+ details: '[CDC Strep Lab](https://www.cdc.gov/strep-lab/) has a strong expertise in using genomic data to predict antibiotic resistance in *S. pneumoniae*. This project will appreciate the genetic diversity and evolution of the penicillin binding protein, that confer resistance to the first-line antibiotic, β-lactam, in treating pneumococcal disease.'
},
{
title: 'Global distribution and evolution of Streptococcus pneumoniae GPSC3 (PMEN33)',
authors: 'Stephanie Lo',
affiliations: 'Wellcome Sanger Institute',
- details: 'GPS headline paper on [Lancet Infectious Diseases](https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(19)30297-X/fulltext) has pointed out that GPSC3 is a major pneumococcal strain expressing non-vaccine serotype after PCV13. Using a global collection, we will investigate the evolutionary history of this important lineage and shed light on its secret of success.'
+ details: 'GPS headline paper on [Lancet Infectious Diseases](https://doi.org/10.1016/s1473-3099(19)30297-x) has pointed out that GPSC3 is a major pneumococcal strain expressing non-vaccine serotype after PCV13. Using a global collection, we will investigate the evolutionary history of this important lineage and shed light on its secret of success.'
},
{
title: 'Global distribution and genomic diversity of serotype 5 in context of PCVs',
@@ -111,7 +111,7 @@ const content = {
title: 'Global diversity of *Streptococcus pneumoniae* serotype 3 isolates; changes in the pre and post PCV eras in comparison with the changes observed in a local collection set in Hong Kong',
authors: 'Pak-Leung Ho, Pierra Law',
affiliations: 'University of Hong Kong',
- details: "[Ho *et al*](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6422485/pdf/khvi-15-02-1526555.pdf) has importantly reported that serotype 3 emerged after PCV13 in Hong Kong and its increase was due to a regional-specific lineage that replaced the common serotype 3 clone CC180. This study will elucidate the circulating serotype 3 strains in Hong Kong and understand this emerging strain's pathogenicity."
+ details: "[Ho *et al*](https://doi.org/10.1080/21645515.2018.1526555) has importantly reported that serotype 3 emerged after PCV13 in Hong Kong and its increase was due to a regional-specific lineage that replaced the common serotype 3 clone CC180. This study will elucidate the circulating serotype 3 strains in Hong Kong and understand this emerging strain's pathogenicity."
},
{
title: 'Global emergence and population dynamics of *Streptococcus pneumoniae* serotype 19A/F CC320 (GPSC1)',
@@ -153,7 +153,7 @@ const content = {
title: 'PneumoCaT2: an investigation into 19A-like cps from serotype 19F pneumococcal isolates',
authors: 'Carmen Sheppard, Stephanie Lo',
affiliations: 'Public Health of England and Wellcome Sanger Institute',
- details: 'PHE developed a WGS-based tool [PneumoCaT](https://pubmed.ncbi.nlm.nih.gov/27672516/) to infer serotype from genome data. This study will harness the global collection in the GPS project to understand a 19F divergent. The knowledge learned will ultimately be integrated into a new version of PneumoCaT.'
+ details: 'PHE developed a WGS-based tool [PneumoCaT](https://doi.org/10.7717/peerj.2477) to infer serotype from genome data. This study will harness the global collection in the GPS project to understand a 19F divergent. The knowledge learned will ultimately be integrated into a new version of PneumoCaT.'
},
{
title: 'Population genomics of mobile genetic elements',
@@ -183,7 +183,7 @@ const content = {
title: 'Validation and improvement of predicting β-Lactam minimum inhibitory concentration of *Streptococcus pneumoniae* using whole-genome sequencing and PBP typing',
authors: 'Yuan Li, Benjamin Metcalf, Lesley McGee, Bernard Beall, Mignon du Plessis, Anne von Gottberg',
affiliations: 'Centers for Disease Control and Prevention',
- details: 'The current machine learning model for prediction of β-Lactam MIC was built and validated using a pneumococcal dataset from the USA (Li *et al* [2016](https://mbio.asm.org/content/7/3/e00756-16) and [2017](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5558719/)). This study will validate and improve the prediction model using genome data from South Africa.'
+ details: 'The current machine learning model for prediction of β-Lactam MIC was built and validated using a pneumococcal dataset from the USA (Li *et al* [2016](https://doi.org/10.1128/mbio.00756-16) and [2017](https://doi.org/10.1186%2Fs12864-017-4017-7)). This study will validate and improve the prediction model using genome data from South Africa.'
},
]
}
diff --git a/src/content/vaccineHistoryContent.js b/src/content/vaccineHistoryContent.js
new file mode 100644
index 0000000..c827807
--- /dev/null
+++ b/src/content/vaccineHistoryContent.js
@@ -0,0 +1,105 @@
+const content = {
+ title: 'Vaccine History',
+ sections: [
+ {
+ content: [
+ {
+ type: 'timeline',
+ content: [
+ {
+ time: '1881',
+ content: "First independently discovered by Louis Pasteur (who called it *microbe septicemique de la salive*) in France from the saliva of a rabies patient, and by George M. Sternberg in the U.S. (who named it *Micrococcus pasteuri*)",
+ reference: "https://doi.org/10.1093/clinids/17.5.913"
+ },
+ {
+ time: '1886',
+ content: "Renamed 'pneumococcus' for its close association with pneumonia",
+ reference: "https://maidenlab.zoo.ox.ac.uk/history-and-biology-istreptococcus-pneumoniaei"
+ },
+ {
+ time: '1911',
+ content: "Start of efforts to develop an effective pneumococcal vaccine",
+ reference: "https://doi.org/10.1016/S0140-6736(01)56449-1"
+ },
+ {
+ time: '1920',
+ content: "Renamed as *Diplococcus pneumoniae* since it was typically observed in pairs",
+ reference: "https://doi.org/10.1128%2Fjb.5.3.191-229.1920"
+ },
+ {
+ time: '1928',
+ content: "The transformation of life was demonstrated by Frederick Griffith, where harmless pneumococci were turned into a lethal form through the co-inoculation of live harmless pneumococci with heat-killed virulent pneumococci in a mouse; This experiment played a vital role in identifying DNA as the genetic material",
+ reference: "https://doi.org/10.1017%2Fs0022172400031879"
+ },
+ {
+ time: '1929',
+ content: "The first 32 serotypes were described by Georgia Cooper",
+ reference: "https://doi.org/10.1084/jem.49.3.461"
+ },
+ {
+ time: '1939',
+ content: "Danish Prince Valdemar died of pneumonia and his failed treatment with serogroup 9 antisera revealed additional diversity in serogroup 9, allowing for the identification of serotype 9V",
+ reference: "https://doi.org/10.4049/jimmunol.37.4.359"
+ },
+ {
+ time: '1960s',
+ content: "Start of efforts to develop a polyvalent pneumococcal vaccine",
+ reference: "https://www.cdc.gov/pinkbook/hcp/table-of-contents/index.html"
+ },
+ {
+ time: '1974',
+ content: "Renamed *Streptococcus pneumoniae* for its similarities in chain formation similar to other *Streptococcus spp.*",
+ reference: "https://maidenlab.zoo.ox.ac.uk/history-and-biology-istreptococcus-pneumoniaei"
+ },
+ {
+ time: '1977',
+ content: "First pneumococcal polysaccharide vaccine licensed in U.S., contained which antigens from 14 serotypes of pneumococci",
+ reference: "https://www.cdc.gov/pinkbook/hcp/table-of-contents/index.html"
+ },
+ {
+ time: '1983',
+ content: "The 23-valent polysaccharide vaccine was licensed (PPSV23), replacing the 14-valent",
+ reference: "https://www.cdc.gov/pinkbook/hcp/table-of-contents/index.html"
+ },
+ {
+ time: '2000',
+ content: "First conjugate pneumococcal vaccine licensed in U.S., covering 7 serotypes (PCV7)",
+ reference: "https://www.cdc.gov/pinkbook/hcp/table-of-contents/index.html"
+ },
+ {
+ time: '2010',
+ content: "Introduction of 13-valent pneumococcal conjugate vaccine (PCV13), covering 6 more serotypes in addition to PCV7",
+ reference: "https://www.cdc.gov/pinkbook/hcp/table-of-contents/index.html"
+ },
+ {
+ time: '2020',
+ content: "The 100th serotype, 10D, is identified",
+ reference: "https://doi.org/10.1128/mBio.00937-20"
+ },
+ {
+ time: '2022',
+ content: "PCV15 is licensed for use in children in the US",
+ reference: "https://www.cdc.gov/acip/evidence-to-recommendations/pneumo-pcv15-child-etr.html"
+ },
+ {
+ time: '2023',
+ content: "PCV20 is licensed for us in children in the US",
+ reference: "https://www.cdc.gov/acip/evidence-to-recommendations/pcv20-child-etr.html"
+ },
+ {
+ time: '2024',
+ content: "PCV20 is licensed for use in children in Europe",
+ reference: "https://www.ema.europa.eu/en/medicines/human/EPAR/prevenar-20"
+ },
+ ]
+ },
+ {
+ type: 'md',
+ content: '###### The above timeline is based on the [curation](https://pneumococcalcapsules.github.io/serotypes/) of Chessley B. Blacklock, Daniel M. Weinberger, Stephanie Perniciaro, and Anne L. Wyllie at the Yale School of Public Health'
+ },
+ ]
+ }
+ ]
+}
+
+export default content
diff --git a/src/content/vaccineInformationContent.js b/src/content/vaccineInformationContent.js
new file mode 100644
index 0000000..172dee7
--- /dev/null
+++ b/src/content/vaccineInformationContent.js
@@ -0,0 +1,19 @@
+const content = {
+ title: 'Vaccine Information',
+ sections: [
+ {
+ content: [
+ {
+ type: 'md',
+ content: ''
+ },
+ {
+ type: 'md',
+ content: '###### The table above shows the serotypes covered by different pneumococcal vaccines. A blue block in the table indicates the serotype of its column is covered by that vaccine of its row. The shade of the colour represents how frequently that serotype is being covered across all vaccines. The darker the colour, the more frequently the serotype is being covered.'
+ },
+ ]
+ }
+ ]
+}
+
+export default content
|