publication . Article . 2017

HIV-1 envelope sequence-based diversity measures for identifying recent infections.

Alexis Kafando; Eric Fournier; Bouchra Serhir; Christine Martineau; Florence Doualla-Bell; Mohamed Ndongo Sangaré; Mohamed Sylla; Annie Chamberland; Mohamed El-Far; Hugues Charest; ...
Open Access
  • Published: 01 Dec 2017 Journal: PLOS ONE, volume 12, page e0189999 (eissn: 1932-6203, Copyright policy)
  • Publisher: Public Library of Science (PLoS)
Abstract
: Identifying recent HIV-1 infections is crucial for monitoring HIV-1 incidence and optimizing public health prevention efforts. To identify recent HIV-1 infections, we evaluated and compared the performance of 4 sequence-based diversity measures including percent diversity, percent complexity, Shannon entropy and number of haplotypes targeting 13 genetic segments within the env gene of HIV-1. A total of 597 diagnostic samples obtained in 2013 and 2015 from recently and chronically HIV-1 infected individuals were selected. From the selected samples, 249 (134 from recent versus 115 from chronic infections) env coding regions, including V1-C5 of gp120 and the gp41...
Subjects
Medical Subject Headings: virus diseases
free text keywords: General Biochemistry, Genetics and Molecular Biology, General Agricultural and Biological Sciences, General Medicine, Research Article, Biology and Life Sciences, Microbiology, Medical Microbiology, Microbial Pathogens, Viral Pathogens, Immunodeficiency Viruses, HIV, HIV-1, Medicine and Health Sciences, Pathology and Laboratory Medicine, Pathogens, Organisms, Viruses, RNA viruses, Retroviruses, Lentivirus, Ecology, Ecological Metrics, Species Diversity, Shannon Index, Ecology and Environmental Sciences, Research and Analysis Methods, Database and Informatics Methods, Bioinformatics, Sequence Analysis, Genetics, Heredity, Genetic Mapping, Haplotypes, Molecular biology, Molecular biology techniques, Sequencing techniques, DNA sequencing, Next-Generation Sequencing, Computational Biology, Genome Analysis, Transcriptome Analysis, Genomics, Physical Sciences, Mathematics, Probability Theory, Statistical Distributions, Distribution Curves, DNA sequence analysis, Medicine, R, Science, Q
75 references, page 1 of 5

1 Public Health agency of Canada. HIV and AIDS in Canada, surveillance report to December 31, 2014. http://healthycanadians.gc.ca/publications/diseases-conditions-maladies-affections/hiv-aids-surveillance-2014-vih-sida/index-eng.php?page=6.

2 Hollingsworth TD, Anderson RM, Fraser C. HIV-1 transmission, by stage of infection. Journal of Infectious Diseases. 2008;198(5):687–93. doi: 10.1086/590501 18662132 [PubMed]

3 van Sighem A, Nakagawa F, De Angelis D, Quinten C, Bezemer D, de Coul EO, et al Estimating HIV Incidence, Time to Diagnosis, and the Undiagnosed HIV Epidemic Using Routine Surveillance Data. Epidemiology. 2015;26(5):653–60. doi: 10.1097/EDE.0000000000000324 26214334 [OpenAIRE] [PubMed]

4 Mastro TD. Determining HIV Incidence in Populations: Moving in the Right Direction. Journal of Infectious Diseases. 2013;207(2):204–6. doi: 10.1093/infdis/jis661 23129757 [PubMed]

5 Smith MK, Rutstein SE, Powers KA, Fidler S, Miller WC, Eron JJ Jr., et al The Detection and Management of Early HIV Infection: A Clinical and Public Health Emergency. Jaids-Journal of Acquired Immune Deficiency Syndromes. 2013;63:S187–S99.

6 Sharma UK, Schito M, Welte A, Rousseau C, Fitzgibbon J, Keele B, et al Workshop summary: Novel biomarkers for HIV incidence assay development. AIDS research and human retroviruses. 2012;28(6):532–9. doi: 10.1089/AID.2011.0332 22206265 [OpenAIRE] [PubMed]

7 Quinn TC, Wawer MJ, Sewankambo N, Serwadda D, Li CJ, Wabwire-Mangen F, et al Viral load and heterosexual transmission of human immunodeficiency virus type 1. N Engl J Med. 2000;342(13):921–9. doi: 10.1056/NEJM200003303421303 10738050 [OpenAIRE] [PubMed]

8 Hall HI, Green TA, Wolitski RJ, Holtgrave DR, Rhodes P, Lehman JS, et al Estimated Future HIV Prevalence, Incidence, and Potential Infections Averted in the United States: A Multiple Scenario Analysis. Jaids-Journal of Acquired Immune Deficiency Syndromes. 2010;55(2):271–6.

9 Gray RH, Li X, Kigozi G, Serwadda D, Nalugoda F, Watya S, et al The impact of male circumcision on HIV incidence and cost per infection prevented: a stochastic simulation model from Rakai, Uganda. Aids. 2007;21(7):845–50. doi: 10.1097/QAD.0b013e3280187544 17415039 [PubMed]

10 Fiamma A, Lissouba P, Amy OE, Singh B, Laeyende cker O, Quinn TC, et al Can HIV incidence testing be used for evaluating HIV intervention programs? A reanalysis of the Orange Farm male circumcision trial (ANRS-1265). Bmc Infectious Diseases. 2010;10.

11 Miller WC, Rosenberg NE, Rutstein SE, Powers KA. Role of acute and early HIV infection in the sexual transmission of HIV. Curr Opin HIV AIDS. 2010;5(4):277–82. doi: 10.1097/COH.0b013e32833a0d3a 20543601 [OpenAIRE] [PubMed]

12 Brenner BG, Roger M, Routy JP, Moisi D, Ntemgwa M, Matte C, et al High rates of forward transmission events after acute/early HIV-1 infection. J Infect Dis. 2007;195(7):951–9. doi: 10.1086/512088 17330784 [PubMed]

13 Brenner BG, Roger M, Stephens D, Moisi D, Hardy I, Weinberg J, et al Transmission Clustering Drives the Onward Spread of the HIV Epidemic Among Men Who Have Sex With Men in Quebec. Journal of Infectious Diseases. 2011;204(7):1115–9. doi: 10.1093/infdis/jir468 21881127 [OpenAIRE] [PubMed]

14 Aghaizu A, Murphy G, Tosswill J, De Angelis D, Charlett A, Gill ON, et al Recent infection testing algorithm (RITA) applied to new HIV diagnoses in England, Wales and Northern Ireland, 2009 to 2011. Eurosurveillance. 2014;19(2):5–11.

15 Murphy G, Parry JV. Assays for the detection of recent infections with human immunodeficiency virus type 1. Euro surveillance: bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin. 2008;13(36).

75 references, page 1 of 5
Abstract
: Identifying recent HIV-1 infections is crucial for monitoring HIV-1 incidence and optimizing public health prevention efforts. To identify recent HIV-1 infections, we evaluated and compared the performance of 4 sequence-based diversity measures including percent diversity, percent complexity, Shannon entropy and number of haplotypes targeting 13 genetic segments within the env gene of HIV-1. A total of 597 diagnostic samples obtained in 2013 and 2015 from recently and chronically HIV-1 infected individuals were selected. From the selected samples, 249 (134 from recent versus 115 from chronic infections) env coding regions, including V1-C5 of gp120 and the gp41...
Subjects
Medical Subject Headings: virus diseases
free text keywords: General Biochemistry, Genetics and Molecular Biology, General Agricultural and Biological Sciences, General Medicine, Research Article, Biology and Life Sciences, Microbiology, Medical Microbiology, Microbial Pathogens, Viral Pathogens, Immunodeficiency Viruses, HIV, HIV-1, Medicine and Health Sciences, Pathology and Laboratory Medicine, Pathogens, Organisms, Viruses, RNA viruses, Retroviruses, Lentivirus, Ecology, Ecological Metrics, Species Diversity, Shannon Index, Ecology and Environmental Sciences, Research and Analysis Methods, Database and Informatics Methods, Bioinformatics, Sequence Analysis, Genetics, Heredity, Genetic Mapping, Haplotypes, Molecular biology, Molecular biology techniques, Sequencing techniques, DNA sequencing, Next-Generation Sequencing, Computational Biology, Genome Analysis, Transcriptome Analysis, Genomics, Physical Sciences, Mathematics, Probability Theory, Statistical Distributions, Distribution Curves, DNA sequence analysis, Medicine, R, Science, Q
75 references, page 1 of 5

1 Public Health agency of Canada. HIV and AIDS in Canada, surveillance report to December 31, 2014. http://healthycanadians.gc.ca/publications/diseases-conditions-maladies-affections/hiv-aids-surveillance-2014-vih-sida/index-eng.php?page=6.

2 Hollingsworth TD, Anderson RM, Fraser C. HIV-1 transmission, by stage of infection. Journal of Infectious Diseases. 2008;198(5):687–93. doi: 10.1086/590501 18662132 [PubMed]

3 van Sighem A, Nakagawa F, De Angelis D, Quinten C, Bezemer D, de Coul EO, et al Estimating HIV Incidence, Time to Diagnosis, and the Undiagnosed HIV Epidemic Using Routine Surveillance Data. Epidemiology. 2015;26(5):653–60. doi: 10.1097/EDE.0000000000000324 26214334 [OpenAIRE] [PubMed]

4 Mastro TD. Determining HIV Incidence in Populations: Moving in the Right Direction. Journal of Infectious Diseases. 2013;207(2):204–6. doi: 10.1093/infdis/jis661 23129757 [PubMed]

5 Smith MK, Rutstein SE, Powers KA, Fidler S, Miller WC, Eron JJ Jr., et al The Detection and Management of Early HIV Infection: A Clinical and Public Health Emergency. Jaids-Journal of Acquired Immune Deficiency Syndromes. 2013;63:S187–S99.

6 Sharma UK, Schito M, Welte A, Rousseau C, Fitzgibbon J, Keele B, et al Workshop summary: Novel biomarkers for HIV incidence assay development. AIDS research and human retroviruses. 2012;28(6):532–9. doi: 10.1089/AID.2011.0332 22206265 [OpenAIRE] [PubMed]

7 Quinn TC, Wawer MJ, Sewankambo N, Serwadda D, Li CJ, Wabwire-Mangen F, et al Viral load and heterosexual transmission of human immunodeficiency virus type 1. N Engl J Med. 2000;342(13):921–9. doi: 10.1056/NEJM200003303421303 10738050 [OpenAIRE] [PubMed]

8 Hall HI, Green TA, Wolitski RJ, Holtgrave DR, Rhodes P, Lehman JS, et al Estimated Future HIV Prevalence, Incidence, and Potential Infections Averted in the United States: A Multiple Scenario Analysis. Jaids-Journal of Acquired Immune Deficiency Syndromes. 2010;55(2):271–6.

9 Gray RH, Li X, Kigozi G, Serwadda D, Nalugoda F, Watya S, et al The impact of male circumcision on HIV incidence and cost per infection prevented: a stochastic simulation model from Rakai, Uganda. Aids. 2007;21(7):845–50. doi: 10.1097/QAD.0b013e3280187544 17415039 [PubMed]

10 Fiamma A, Lissouba P, Amy OE, Singh B, Laeyende cker O, Quinn TC, et al Can HIV incidence testing be used for evaluating HIV intervention programs? A reanalysis of the Orange Farm male circumcision trial (ANRS-1265). Bmc Infectious Diseases. 2010;10.

11 Miller WC, Rosenberg NE, Rutstein SE, Powers KA. Role of acute and early HIV infection in the sexual transmission of HIV. Curr Opin HIV AIDS. 2010;5(4):277–82. doi: 10.1097/COH.0b013e32833a0d3a 20543601 [OpenAIRE] [PubMed]

12 Brenner BG, Roger M, Routy JP, Moisi D, Ntemgwa M, Matte C, et al High rates of forward transmission events after acute/early HIV-1 infection. J Infect Dis. 2007;195(7):951–9. doi: 10.1086/512088 17330784 [PubMed]

13 Brenner BG, Roger M, Stephens D, Moisi D, Hardy I, Weinberg J, et al Transmission Clustering Drives the Onward Spread of the HIV Epidemic Among Men Who Have Sex With Men in Quebec. Journal of Infectious Diseases. 2011;204(7):1115–9. doi: 10.1093/infdis/jir468 21881127 [OpenAIRE] [PubMed]

14 Aghaizu A, Murphy G, Tosswill J, De Angelis D, Charlett A, Gill ON, et al Recent infection testing algorithm (RITA) applied to new HIV diagnoses in England, Wales and Northern Ireland, 2009 to 2011. Eurosurveillance. 2014;19(2):5–11.

15 Murphy G, Parry JV. Assays for the detection of recent infections with human immunodeficiency virus type 1. Euro surveillance: bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin. 2008;13(36).

75 references, page 1 of 5
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