The effect of interventions on the transmission and spread of HIV in South Africa: a phylodynamic analysis View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2019-12

AUTHORS

Eduan Wilkinson, Dennis Maletich Junqueira, Richard Lessells, Susan Engelbrecht, Gert van Zyl, Tulio de Oliveira, Marco Salemi

ABSTRACT

The epidemic in South Africa is characterized by high genetic diversity driven by multiple independent introductions. The bulk of these introductions occurred between 1985-2000 during which time HIV prevalence increased exponentially. Epidemic growth has stabilized in recent years with the implementation of several interventions. Here we identified distinct HIV clades from a large sequence dataset of southern African HIV sequences (n = 15,332). Each clade was characterized using phylodynamic and phylogeographic methods to infer their growth through time and space. The estimated date of origin for the 18 clades that were found, fell between 1979-1992 with strong growth during the 1990's. Phylogeographic reconstruction revealed wide dispersal of clades throughout the country with the city of Johannesburg as the focal point of viral dispersal. We found clear signs of decreasing growth rate in four of the clades since the advent of interventions, while other clades have continued to growth and expand. Our results demonstrate that interventions do not affect the HIV epidemic universally with major difference between different clades over time and space. Here we demonstrate the utility and flexibility of molecular epidemiological methods and demonstrate how they can potentially be a powerful tool in HIV epidemic monitoring in South Africa. More... »

PAGES

2640

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/s41598-018-37749-3

DOI

http://dx.doi.org/10.1038/s41598-018-37749-3

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1112362803

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/30804361


Indexing Status Check whether this publication has been indexed by Scopus and Web Of Science using the SN Indexing Status Tool
Incoming Citations Browse incoming citations for this publication using opencitations.net

JSON-LD is the canonical representation for SciGraph data.

TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT

[
  {
    "@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json", 
    "about": [
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0102", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Applied Mathematics", 
        "type": "DefinedTerm"
      }, 
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/01", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Mathematical Sciences", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "University of KwaZulu-Natal", 
          "id": "https://www.grid.ac/institutes/grid.16463.36", 
          "name": [
            "Emerging Pathogens Institute, University of Florida, 32608, Gainesville, Florida, United States of America", 
            "KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, 4001, Durban, South Africa", 
            "School of Laboratory Medicine and Medical Science, Department of Health Sciences, University of KwaZulu-Natal, 4001, Durban, South Africa"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Wilkinson", 
        "givenName": "Eduan", 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "University of KwaZulu-Natal", 
          "id": "https://www.grid.ac/institutes/grid.16463.36", 
          "name": [
            "KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, 4001, Durban, South Africa", 
            "School of Laboratory Medicine and Medical Science, Department of Health Sciences, University of KwaZulu-Natal, 4001, Durban, South Africa"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Junqueira", 
        "givenName": "Dennis Maletich", 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "University of KwaZulu-Natal", 
          "id": "https://www.grid.ac/institutes/grid.16463.36", 
          "name": [
            "School of Laboratory Medicine and Medical Science, Department of Health Sciences, University of KwaZulu-Natal, 4001, Durban, South Africa"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Lessells", 
        "givenName": "Richard", 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Stellenbosch University", 
          "id": "https://www.grid.ac/institutes/grid.11956.3a", 
          "name": [
            "Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa", 
            "National Health Laboratory Services (NHLS), Tygerberg Coastal, Cape Town, South Africa"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Engelbrecht", 
        "givenName": "Susan", 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Stellenbosch University", 
          "id": "https://www.grid.ac/institutes/grid.11956.3a", 
          "name": [
            "Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa", 
            "National Health Laboratory Services (NHLS), Tygerberg Coastal, Cape Town, South Africa"
          ], 
          "type": "Organization"
        }, 
        "familyName": "van Zyl", 
        "givenName": "Gert", 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "University of KwaZulu-Natal", 
          "id": "https://www.grid.ac/institutes/grid.16463.36", 
          "name": [
            "KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, 4001, Durban, South Africa", 
            "School of Laboratory Medicine and Medical Science, Department of Health Sciences, University of KwaZulu-Natal, 4001, Durban, South Africa"
          ], 
          "type": "Organization"
        }, 
        "familyName": "de Oliveira", 
        "givenName": "Tulio", 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "University of Florida", 
          "id": "https://www.grid.ac/institutes/grid.15276.37", 
          "name": [
            "Emerging Pathogens Institute, University of Florida, 32608, Gainesville, Florida, United States of America"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Salemi", 
        "givenName": "Marco", 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "sg:pub.10.1186/1471-2105-14-317", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1000087427", 
          "https://doi.org/10.1186/1471-2105-14-317"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1471-2105-14-317", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1000087427", 
          "https://doi.org/10.1186/1471-2105-14-317"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1471-2105-14-317", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1000087427", 
          "https://doi.org/10.1186/1471-2105-14-317"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/molbev/mss265", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1004959029"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/16.6.562", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1007650275"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/16.7.573", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1010590069"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/molbev/mss075", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1013930907"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.meegid.2013.04.032", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1014275875"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.241370698", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1016109150"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s2352-3018(16)30186-2", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1020680319"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.1207965110", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1022732702"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gkh340", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1025846396"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/molbev/msn090", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1025856837"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1128/jvi.01556-08", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1028912207"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gks414", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1029700001"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1534/genetics.106.068874", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1032068700"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1534/genetics.106.068874", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1032068700"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/ve/vev003", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1034021905"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/313277a0", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1034786339", 
          "https://doi.org/10.1038/313277a0"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/btt010", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1036385399"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1371/journal.pbio.0040088", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1037373684"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1371/journal.pbio.0040088", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1037373684"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.meegid.2016.07.008", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1038496752"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/molbev/msi103", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1039084795"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1097/00002030-200403260-00002", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1041123329"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1097/00002030-200403260-00002", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1041123329"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/srep16897", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1041228005", 
          "https://doi.org/10.1038/srep16897"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/btr481", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1041395816"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.epidem.2015.07.002", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1041981698"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1371/journal.pcbi.1000520", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1046736048"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/molbev/msu300", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1052964628"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1089/aid.1995.11.1423", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1059224057"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1097/qad.0000000000001340", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1060343999"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1097/qad.0000000000001340", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1060343999"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.2471/blt.12.106807", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1070838064"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://app.dimensions.ai/details/publication/pub.1075091356", 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/oxfordjournals.molbev.a040082", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1082735188"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nmeth.4285", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1085213801", 
          "https://doi.org/10.1038/nmeth.4285"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nmeth.4285", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1085213801", 
          "https://doi.org/10.1038/nmeth.4285"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.4102/sajhivmed.v18i1.694", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1090978307"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1136/jech-2017-209713", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1092973512"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/molbev/msy016", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1100728362"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/molbev/msy016", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1100728362"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/s41586-018-0043-0", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1103449745", 
          "https://doi.org/10.1038/s41586-018-0043-0"
        ], 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2019-12", 
    "datePublishedReg": "2019-12-01", 
    "description": "The epidemic in South Africa is characterized by high genetic diversity driven by multiple independent introductions. The bulk of these introductions occurred between 1985-2000 during which time HIV prevalence increased exponentially. Epidemic growth has stabilized in recent years with the implementation of several interventions. Here we identified distinct HIV clades from a large sequence dataset of southern African HIV sequences (n\u2009=\u200915,332). Each clade was characterized using phylodynamic and phylogeographic methods to infer their growth through time and space. The estimated date of origin for the 18 clades that were found, fell between 1979-1992 with strong growth during the 1990's. Phylogeographic reconstruction revealed wide dispersal of clades throughout the country with the city of Johannesburg as the focal point of viral dispersal. We found clear signs of decreasing growth rate in four of the clades since the advent of interventions, while other clades have continued to growth and expand. Our results demonstrate that interventions do not affect the HIV epidemic universally with major difference between different clades over time and space. Here we demonstrate the utility and flexibility of molecular epidemiological methods and demonstrate how they can potentially be a powerful tool in HIV epidemic monitoring in South Africa.", 
    "genre": "research_article", 
    "id": "sg:pub.10.1038/s41598-018-37749-3", 
    "inLanguage": [
      "en"
    ], 
    "isAccessibleForFree": true, 
    "isFundedItemOf": [
      {
        "id": "sg:grant.7439652", 
        "type": "MonetaryGrant"
      }
    ], 
    "isPartOf": [
      {
        "id": "sg:journal.1045337", 
        "issn": [
          "2045-2322"
        ], 
        "name": "Scientific Reports", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "1", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "9"
      }
    ], 
    "name": "The effect of interventions on the transmission and spread of HIV in South Africa: a phylodynamic analysis", 
    "pagination": "2640", 
    "productId": [
      {
        "name": "readcube_id", 
        "type": "PropertyValue", 
        "value": [
          "11cf836b686055aee948b47d826878f39395e1f5344c83ef944c46b133e7fa85"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "30804361"
        ]
      }, 
      {
        "name": "nlm_unique_id", 
        "type": "PropertyValue", 
        "value": [
          "101563288"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1038/s41598-018-37749-3"
        ]
      }, 
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1112362803"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1038/s41598-018-37749-3", 
      "https://app.dimensions.ai/details/publication/pub.1112362803"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2019-04-11T10:36", 
    "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
    "sdPublisher": {
      "name": "Springer Nature - SN SciGraph project", 
      "type": "Organization"
    }, 
    "sdSource": "s3://com-uberresearch-data-dimensions-target-20181106-alternative/cleanup/v134/2549eaecd7973599484d7c17b260dba0a4ecb94b/merge/v9/a6c9fde33151104705d4d7ff012ea9563521a3ce/jats-lookup/v90/0000000349_0000000349/records_113670_00000005.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "https://www.nature.com/articles/s41598-018-37749-3"
  }
]
 

Download the RDF metadata as:  json-ld nt turtle xml License info

HOW TO GET THIS DATA PROGRAMMATICALLY:

JSON-LD is a popular format for linked data which is fully compatible with JSON.

curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1038/s41598-018-37749-3'

N-Triples is a line-based linked data format ideal for batch operations.

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1038/s41598-018-37749-3'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1038/s41598-018-37749-3'

RDF/XML is a standard XML format for linked data.

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1038/s41598-018-37749-3'


 

This table displays all metadata directly associated to this object as RDF triples.

226 TRIPLES      21 PREDICATES      65 URIs      21 LITERALS      9 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1038/s41598-018-37749-3 schema:about anzsrc-for:01
2 anzsrc-for:0102
3 schema:author N47c418344f9d47fb91cfa99662ebf5a5
4 schema:citation sg:pub.10.1038/313277a0
5 sg:pub.10.1038/nmeth.4285
6 sg:pub.10.1038/s41586-018-0043-0
7 sg:pub.10.1038/srep16897
8 sg:pub.10.1186/1471-2105-14-317
9 https://app.dimensions.ai/details/publication/pub.1075091356
10 https://doi.org/10.1016/j.epidem.2015.07.002
11 https://doi.org/10.1016/j.meegid.2013.04.032
12 https://doi.org/10.1016/j.meegid.2016.07.008
13 https://doi.org/10.1016/s2352-3018(16)30186-2
14 https://doi.org/10.1073/pnas.1207965110
15 https://doi.org/10.1073/pnas.241370698
16 https://doi.org/10.1089/aid.1995.11.1423
17 https://doi.org/10.1093/bioinformatics/16.6.562
18 https://doi.org/10.1093/bioinformatics/16.7.573
19 https://doi.org/10.1093/bioinformatics/btr481
20 https://doi.org/10.1093/bioinformatics/btt010
21 https://doi.org/10.1093/molbev/msi103
22 https://doi.org/10.1093/molbev/msn090
23 https://doi.org/10.1093/molbev/mss075
24 https://doi.org/10.1093/molbev/mss265
25 https://doi.org/10.1093/molbev/msu300
26 https://doi.org/10.1093/molbev/msy016
27 https://doi.org/10.1093/nar/gkh340
28 https://doi.org/10.1093/nar/gks414
29 https://doi.org/10.1093/oxfordjournals.molbev.a040082
30 https://doi.org/10.1093/ve/vev003
31 https://doi.org/10.1097/00002030-200403260-00002
32 https://doi.org/10.1097/qad.0000000000001340
33 https://doi.org/10.1128/jvi.01556-08
34 https://doi.org/10.1136/jech-2017-209713
35 https://doi.org/10.1371/journal.pbio.0040088
36 https://doi.org/10.1371/journal.pcbi.1000520
37 https://doi.org/10.1534/genetics.106.068874
38 https://doi.org/10.2471/blt.12.106807
39 https://doi.org/10.4102/sajhivmed.v18i1.694
40 schema:datePublished 2019-12
41 schema:datePublishedReg 2019-12-01
42 schema:description The epidemic in South Africa is characterized by high genetic diversity driven by multiple independent introductions. The bulk of these introductions occurred between 1985-2000 during which time HIV prevalence increased exponentially. Epidemic growth has stabilized in recent years with the implementation of several interventions. Here we identified distinct HIV clades from a large sequence dataset of southern African HIV sequences (n = 15,332). Each clade was characterized using phylodynamic and phylogeographic methods to infer their growth through time and space. The estimated date of origin for the 18 clades that were found, fell between 1979-1992 with strong growth during the 1990's. Phylogeographic reconstruction revealed wide dispersal of clades throughout the country with the city of Johannesburg as the focal point of viral dispersal. We found clear signs of decreasing growth rate in four of the clades since the advent of interventions, while other clades have continued to growth and expand. Our results demonstrate that interventions do not affect the HIV epidemic universally with major difference between different clades over time and space. Here we demonstrate the utility and flexibility of molecular epidemiological methods and demonstrate how they can potentially be a powerful tool in HIV epidemic monitoring in South Africa.
43 schema:genre research_article
44 schema:inLanguage en
45 schema:isAccessibleForFree true
46 schema:isPartOf N84a0e429d9f74fb19a96b07025dd58c1
47 N9707ba07e0bb465ab3210148032c4f85
48 sg:journal.1045337
49 schema:name The effect of interventions on the transmission and spread of HIV in South Africa: a phylodynamic analysis
50 schema:pagination 2640
51 schema:productId N296efc37849a48618b22e457c196a5a3
52 N6a6236b6582542a38ea2026752e077c8
53 N8ac41897429e429b8ebc8f820f4d75d9
54 N9a0f8278dff84325b8686837328f37e5
55 Na610765bddbe4c348c1e745899379cde
56 schema:sameAs https://app.dimensions.ai/details/publication/pub.1112362803
57 https://doi.org/10.1038/s41598-018-37749-3
58 schema:sdDatePublished 2019-04-11T10:36
59 schema:sdLicense https://scigraph.springernature.com/explorer/license/
60 schema:sdPublisher N21bd2ef8d3634b9f8b1163ed82f834c4
61 schema:url https://www.nature.com/articles/s41598-018-37749-3
62 sgo:license sg:explorer/license/
63 sgo:sdDataset articles
64 rdf:type schema:ScholarlyArticle
65 N06d7fe523b834fb882cf25f9fbcabcc5 schema:affiliation https://www.grid.ac/institutes/grid.11956.3a
66 schema:familyName van Zyl
67 schema:givenName Gert
68 rdf:type schema:Person
69 N1a21f3c6b9514cab99cdc5f277f1a18a rdf:first N1d30cb8f8dc84f5299848c14d6e3a460
70 rdf:rest N6f0c9dee0d5445e7b107f1852cd713e3
71 N1d30cb8f8dc84f5299848c14d6e3a460 schema:affiliation https://www.grid.ac/institutes/grid.11956.3a
72 schema:familyName Engelbrecht
73 schema:givenName Susan
74 rdf:type schema:Person
75 N21bd2ef8d3634b9f8b1163ed82f834c4 schema:name Springer Nature - SN SciGraph project
76 rdf:type schema:Organization
77 N296efc37849a48618b22e457c196a5a3 schema:name pubmed_id
78 schema:value 30804361
79 rdf:type schema:PropertyValue
80 N4320859f10af49e688bb34045aef62f8 schema:affiliation https://www.grid.ac/institutes/grid.16463.36
81 schema:familyName Junqueira
82 schema:givenName Dennis Maletich
83 rdf:type schema:Person
84 N47c418344f9d47fb91cfa99662ebf5a5 rdf:first Nfcce02361fd94189b9a4ced1d0e61d3d
85 rdf:rest N801e381e44c540228c6e54a4d3c0db3c
86 N5b09647a42524869abf120e23a2c03cb schema:affiliation https://www.grid.ac/institutes/grid.15276.37
87 schema:familyName Salemi
88 schema:givenName Marco
89 rdf:type schema:Person
90 N5cce9f97c9a348839dc75e6e9911fa6b schema:affiliation https://www.grid.ac/institutes/grid.16463.36
91 schema:familyName de Oliveira
92 schema:givenName Tulio
93 rdf:type schema:Person
94 N60d5733b0ed44c5b8430b4072df38822 rdf:first N95daec4f0bff48c5964aad36bb488404
95 rdf:rest N1a21f3c6b9514cab99cdc5f277f1a18a
96 N6a6236b6582542a38ea2026752e077c8 schema:name doi
97 schema:value 10.1038/s41598-018-37749-3
98 rdf:type schema:PropertyValue
99 N6f0c9dee0d5445e7b107f1852cd713e3 rdf:first N06d7fe523b834fb882cf25f9fbcabcc5
100 rdf:rest Nc4309ff2f8e34aa4ae299426a1e8a49e
101 N801e381e44c540228c6e54a4d3c0db3c rdf:first N4320859f10af49e688bb34045aef62f8
102 rdf:rest N60d5733b0ed44c5b8430b4072df38822
103 N84a0e429d9f74fb19a96b07025dd58c1 schema:issueNumber 1
104 rdf:type schema:PublicationIssue
105 N8ac41897429e429b8ebc8f820f4d75d9 schema:name readcube_id
106 schema:value 11cf836b686055aee948b47d826878f39395e1f5344c83ef944c46b133e7fa85
107 rdf:type schema:PropertyValue
108 N95daec4f0bff48c5964aad36bb488404 schema:affiliation https://www.grid.ac/institutes/grid.16463.36
109 schema:familyName Lessells
110 schema:givenName Richard
111 rdf:type schema:Person
112 N9707ba07e0bb465ab3210148032c4f85 schema:volumeNumber 9
113 rdf:type schema:PublicationVolume
114 N9a0f8278dff84325b8686837328f37e5 schema:name nlm_unique_id
115 schema:value 101563288
116 rdf:type schema:PropertyValue
117 Na610765bddbe4c348c1e745899379cde schema:name dimensions_id
118 schema:value pub.1112362803
119 rdf:type schema:PropertyValue
120 Nc4309ff2f8e34aa4ae299426a1e8a49e rdf:first N5cce9f97c9a348839dc75e6e9911fa6b
121 rdf:rest Nfb1b811956864a729d7ac7017410d192
122 Nfb1b811956864a729d7ac7017410d192 rdf:first N5b09647a42524869abf120e23a2c03cb
123 rdf:rest rdf:nil
124 Nfcce02361fd94189b9a4ced1d0e61d3d schema:affiliation https://www.grid.ac/institutes/grid.16463.36
125 schema:familyName Wilkinson
126 schema:givenName Eduan
127 rdf:type schema:Person
128 anzsrc-for:01 schema:inDefinedTermSet anzsrc-for:
129 schema:name Mathematical Sciences
130 rdf:type schema:DefinedTerm
131 anzsrc-for:0102 schema:inDefinedTermSet anzsrc-for:
132 schema:name Applied Mathematics
133 rdf:type schema:DefinedTerm
134 sg:grant.7439652 http://pending.schema.org/fundedItem sg:pub.10.1038/s41598-018-37749-3
135 rdf:type schema:MonetaryGrant
136 sg:journal.1045337 schema:issn 2045-2322
137 schema:name Scientific Reports
138 rdf:type schema:Periodical
139 sg:pub.10.1038/313277a0 schema:sameAs https://app.dimensions.ai/details/publication/pub.1034786339
140 https://doi.org/10.1038/313277a0
141 rdf:type schema:CreativeWork
142 sg:pub.10.1038/nmeth.4285 schema:sameAs https://app.dimensions.ai/details/publication/pub.1085213801
143 https://doi.org/10.1038/nmeth.4285
144 rdf:type schema:CreativeWork
145 sg:pub.10.1038/s41586-018-0043-0 schema:sameAs https://app.dimensions.ai/details/publication/pub.1103449745
146 https://doi.org/10.1038/s41586-018-0043-0
147 rdf:type schema:CreativeWork
148 sg:pub.10.1038/srep16897 schema:sameAs https://app.dimensions.ai/details/publication/pub.1041228005
149 https://doi.org/10.1038/srep16897
150 rdf:type schema:CreativeWork
151 sg:pub.10.1186/1471-2105-14-317 schema:sameAs https://app.dimensions.ai/details/publication/pub.1000087427
152 https://doi.org/10.1186/1471-2105-14-317
153 rdf:type schema:CreativeWork
154 https://app.dimensions.ai/details/publication/pub.1075091356 schema:CreativeWork
155 https://doi.org/10.1016/j.epidem.2015.07.002 schema:sameAs https://app.dimensions.ai/details/publication/pub.1041981698
156 rdf:type schema:CreativeWork
157 https://doi.org/10.1016/j.meegid.2013.04.032 schema:sameAs https://app.dimensions.ai/details/publication/pub.1014275875
158 rdf:type schema:CreativeWork
159 https://doi.org/10.1016/j.meegid.2016.07.008 schema:sameAs https://app.dimensions.ai/details/publication/pub.1038496752
160 rdf:type schema:CreativeWork
161 https://doi.org/10.1016/s2352-3018(16)30186-2 schema:sameAs https://app.dimensions.ai/details/publication/pub.1020680319
162 rdf:type schema:CreativeWork
163 https://doi.org/10.1073/pnas.1207965110 schema:sameAs https://app.dimensions.ai/details/publication/pub.1022732702
164 rdf:type schema:CreativeWork
165 https://doi.org/10.1073/pnas.241370698 schema:sameAs https://app.dimensions.ai/details/publication/pub.1016109150
166 rdf:type schema:CreativeWork
167 https://doi.org/10.1089/aid.1995.11.1423 schema:sameAs https://app.dimensions.ai/details/publication/pub.1059224057
168 rdf:type schema:CreativeWork
169 https://doi.org/10.1093/bioinformatics/16.6.562 schema:sameAs https://app.dimensions.ai/details/publication/pub.1007650275
170 rdf:type schema:CreativeWork
171 https://doi.org/10.1093/bioinformatics/16.7.573 schema:sameAs https://app.dimensions.ai/details/publication/pub.1010590069
172 rdf:type schema:CreativeWork
173 https://doi.org/10.1093/bioinformatics/btr481 schema:sameAs https://app.dimensions.ai/details/publication/pub.1041395816
174 rdf:type schema:CreativeWork
175 https://doi.org/10.1093/bioinformatics/btt010 schema:sameAs https://app.dimensions.ai/details/publication/pub.1036385399
176 rdf:type schema:CreativeWork
177 https://doi.org/10.1093/molbev/msi103 schema:sameAs https://app.dimensions.ai/details/publication/pub.1039084795
178 rdf:type schema:CreativeWork
179 https://doi.org/10.1093/molbev/msn090 schema:sameAs https://app.dimensions.ai/details/publication/pub.1025856837
180 rdf:type schema:CreativeWork
181 https://doi.org/10.1093/molbev/mss075 schema:sameAs https://app.dimensions.ai/details/publication/pub.1013930907
182 rdf:type schema:CreativeWork
183 https://doi.org/10.1093/molbev/mss265 schema:sameAs https://app.dimensions.ai/details/publication/pub.1004959029
184 rdf:type schema:CreativeWork
185 https://doi.org/10.1093/molbev/msu300 schema:sameAs https://app.dimensions.ai/details/publication/pub.1052964628
186 rdf:type schema:CreativeWork
187 https://doi.org/10.1093/molbev/msy016 schema:sameAs https://app.dimensions.ai/details/publication/pub.1100728362
188 rdf:type schema:CreativeWork
189 https://doi.org/10.1093/nar/gkh340 schema:sameAs https://app.dimensions.ai/details/publication/pub.1025846396
190 rdf:type schema:CreativeWork
191 https://doi.org/10.1093/nar/gks414 schema:sameAs https://app.dimensions.ai/details/publication/pub.1029700001
192 rdf:type schema:CreativeWork
193 https://doi.org/10.1093/oxfordjournals.molbev.a040082 schema:sameAs https://app.dimensions.ai/details/publication/pub.1082735188
194 rdf:type schema:CreativeWork
195 https://doi.org/10.1093/ve/vev003 schema:sameAs https://app.dimensions.ai/details/publication/pub.1034021905
196 rdf:type schema:CreativeWork
197 https://doi.org/10.1097/00002030-200403260-00002 schema:sameAs https://app.dimensions.ai/details/publication/pub.1041123329
198 rdf:type schema:CreativeWork
199 https://doi.org/10.1097/qad.0000000000001340 schema:sameAs https://app.dimensions.ai/details/publication/pub.1060343999
200 rdf:type schema:CreativeWork
201 https://doi.org/10.1128/jvi.01556-08 schema:sameAs https://app.dimensions.ai/details/publication/pub.1028912207
202 rdf:type schema:CreativeWork
203 https://doi.org/10.1136/jech-2017-209713 schema:sameAs https://app.dimensions.ai/details/publication/pub.1092973512
204 rdf:type schema:CreativeWork
205 https://doi.org/10.1371/journal.pbio.0040088 schema:sameAs https://app.dimensions.ai/details/publication/pub.1037373684
206 rdf:type schema:CreativeWork
207 https://doi.org/10.1371/journal.pcbi.1000520 schema:sameAs https://app.dimensions.ai/details/publication/pub.1046736048
208 rdf:type schema:CreativeWork
209 https://doi.org/10.1534/genetics.106.068874 schema:sameAs https://app.dimensions.ai/details/publication/pub.1032068700
210 rdf:type schema:CreativeWork
211 https://doi.org/10.2471/blt.12.106807 schema:sameAs https://app.dimensions.ai/details/publication/pub.1070838064
212 rdf:type schema:CreativeWork
213 https://doi.org/10.4102/sajhivmed.v18i1.694 schema:sameAs https://app.dimensions.ai/details/publication/pub.1090978307
214 rdf:type schema:CreativeWork
215 https://www.grid.ac/institutes/grid.11956.3a schema:alternateName Stellenbosch University
216 schema:name Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
217 National Health Laboratory Services (NHLS), Tygerberg Coastal, Cape Town, South Africa
218 rdf:type schema:Organization
219 https://www.grid.ac/institutes/grid.15276.37 schema:alternateName University of Florida
220 schema:name Emerging Pathogens Institute, University of Florida, 32608, Gainesville, Florida, United States of America
221 rdf:type schema:Organization
222 https://www.grid.ac/institutes/grid.16463.36 schema:alternateName University of KwaZulu-Natal
223 schema:name Emerging Pathogens Institute, University of Florida, 32608, Gainesville, Florida, United States of America
224 KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, 4001, Durban, South Africa
225 School of Laboratory Medicine and Medical Science, Department of Health Sciences, University of KwaZulu-Natal, 4001, Durban, South Africa
226 rdf:type schema:Organization
 




Preview window. Press ESC to close (or click here)


...