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Switzer WM, Shankar A, Jia H, Knyazev S, Ambrosio F, Kelly R, Zheng H, Campbell EM, Cintron R, Pan Y, Saduvala N, Panneer N, Richman R, Singh MB, Thoroughman DA, Blau EF, Khalil GM, Lyss S, Heneine W. High HIV diversity, recombination, and superinfection revealed in a large outbreak among persons who inject drugs in Kentucky and Ohio, USA. Virus Evol 2024; 10:veae015. [PMID: 38510920 PMCID: PMC10953796 DOI: 10.1093/ve/veae015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 01/30/2024] [Accepted: 02/05/2024] [Indexed: 03/22/2024] Open
Abstract
We investigated transmission dynamics of a large human immunodeficiency virus (HIV) outbreak among persons who inject drugs (PWID) in KY and OH during 2017-20 by using detailed phylogenetic, network, recombination, and cluster dating analyses. Using polymerase (pol) sequences from 193 people associated with the investigation, we document high HIV-1 diversity, including Subtype B (44.6 per cent); numerous circulating recombinant forms (CRFs) including CRF02_AG (2.5 per cent) and CRF02_AG-like (21.8 per cent); and many unique recombinant forms composed of CRFs with major subtypes and sub-subtypes [CRF02_AG/B (24.3 per cent), B/CRF02_AG/B (0.5 per cent), and A6/D/B (6.4 per cent)]. Cluster analysis of sequences using a 1.5 per cent genetic distance identified thirteen clusters, including a seventy-five-member cluster composed of CRF02_AG-like and CRF02_AG/B, an eighteen-member CRF02_AG/B cluster, Subtype B clusters of sizes ranging from two to twenty-three, and a nine-member A6/D and A6/D/B cluster. Recombination and phylogenetic analyses identified CRF02_AG/B variants with ten unique breakpoints likely originating from Subtype B and CRF02_AG-like viruses in the largest clusters. The addition of contact tracing results from OH to the genetic networks identified linkage between persons with Subtype B, CRF02_AG, and CRF02_AG/B sequences in the clusters supporting de novo recombinant generation. Superinfection prevalence was 13.3 per cent (8/60) in persons with multiple specimens and included infection with B and CRF02_AG; B and CRF02_AG/B; or B and A6/D/B. In addition to the presence of multiple, distinct molecular clusters associated with this outbreak, cluster dating inferred transmission associated with the largest molecular cluster occurred as early as 2006, with high transmission rates during 2017-8 in certain other molecular clusters. This outbreak among PWID in KY and OH was likely driven by rapid transmission of multiple HIV-1 variants including de novo viral recombinants from circulating viruses within the community. Our findings documenting the high HIV-1 transmission rate and clustering through partner services and molecular clusters emphasize the importance of leveraging multiple different data sources and analyses, including those from disease intervention specialist investigations, to better understand outbreak dynamics and interrupt HIV spread.
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Affiliation(s)
- William M Switzer
- Division of HIV Prevention, CDC, 1600 Clifton Rd, Atlanta, GA 30329, USA
| | - Anupama Shankar
- Division of HIV Prevention, CDC, 1600 Clifton Rd, Atlanta, GA 30329, USA
| | - Hongwei Jia
- Division of HIV Prevention, CDC, 1600 Clifton Rd, Atlanta, GA 30329, USA
| | - Sergey Knyazev
- Division of HIV Prevention, CDC, 1600 Clifton Rd, Atlanta, GA 30329, USA
- Oak Ridge Institute for Science and Education, 1299 Bethel Valley Rd, Oak Ridge, TN 37830, USA
| | - Frank Ambrosio
- Division of HIV Prevention, CDC, 1600 Clifton Rd, Atlanta, GA 30329, USA
| | - Reagan Kelly
- Division of HIV Prevention, CDC, 1600 Clifton Rd, Atlanta, GA 30329, USA
- General Dynamics Information Technology, 3150 Fairview Park Dr, Falls Church, VA 22042, USA
| | - HaoQiang Zheng
- Division of HIV Prevention, CDC, 1600 Clifton Rd, Atlanta, GA 30329, USA
| | | | - Roxana Cintron
- Division of HIV Prevention, CDC, 1600 Clifton Rd, Atlanta, GA 30329, USA
| | - Yi Pan
- Division of HIV Prevention, CDC, 1600 Clifton Rd, Atlanta, GA 30329, USA
| | | | - Nivedha Panneer
- Division of HIV Prevention, CDC, 1600 Clifton Rd, Atlanta, GA 30329, USA
| | - Rhiannon Richman
- HIV Surveillance Program, Bureau of HIV/STI/Viral Hepatitis, Ohio Department of Health, 246 North High Street, Colombus, OH 43215, USA
| | - Manny B Singh
- Division of Epidemiology and Health Planning, Kentucky Department for Public Health, Frankfort, KY 40621, USA
| | - Douglas A Thoroughman
- Division of Epidemiology and Health Planning, Kentucky Department for Public Health, Frankfort, KY 40621, USA
- ORR/Division of State and Local Readiness/Field Services Branch/CEFO Program, CDC, 1600 Clifton Rd, Atlanta, GA 30329, USA
| | - Erin F Blau
- Division of Epidemiology and Health Planning, Kentucky Department for Public Health, Frankfort, KY 40621, USA
- Epidemic Intelligence Service, CDC, 1600 Clifton Rd, Atlanta, GA 30329, USA
| | - George M Khalil
- Division of HIV Prevention, CDC, 1600 Clifton Rd, Atlanta, GA 30329, USA
| | - Sheryl Lyss
- Division of HIV Prevention, CDC, 1600 Clifton Rd, Atlanta, GA 30329, USA
- HIV Surveillance Program, Bureau of HIV/STI/Viral Hepatitis, Ohio Department of Health, 246 North High Street, Colombus, OH 43215, USA
- Division of Epidemiology and Health Planning, Kentucky Department for Public Health, Frankfort, KY 40621, USA
- Hamilton County Public Health, 250 William Howard Taft Rd, Cincinnati, OH 45219, USA
- Northern Kentucky Health Department, 8001 Veterans Memorial Drive, Florence, KY 41042, USA
| | - Walid Heneine
- Division of HIV Prevention, CDC, 1600 Clifton Rd, Atlanta, GA 30329, USA
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Dean LS, SahBandar IN, Shikuma CM. Identification and Implications of HIV-1 CRF01_AE Subtype in Hawai'i. HAWAI'I JOURNAL OF HEALTH & SOCIAL WELFARE 2022; 81:215-217. [PMID: 35923383 PMCID: PMC9344534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Human Immunodeficiency Virus has a high propensity for genetic variation, demonstrated by its complex phylogeny and multiplicity of subtypes. Subtype B is predominant in North America as well as in Hawai'i while CRF01_AE is found in over 50% of cases in the Philippines and Southeast Asia. In a small collaborative study between the Hawai'i Center for AIDS and Philippines General Hospital, molecular phylogenetic subtyping was conducted on HIV+ participants. Two of 15 (13%) participants from the Hawai'i cohort and 12 of 21 (57%) participants from the Philippines cohort were identified as having CRF01_AE subtype of HIV-1, with remaining participants identified as subtype B. While one individual in Hawai'i with CRF01_AE had emigrated from the Philippines, the other participant from Hawai'i with CRF01_AE subtype was a local individual, born and raised in Hawai'i. The authors report that HIV subtype diversity may be increased in Hawai'i and discuss its potential clinical and public health implications.
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Affiliation(s)
- Logan S. Dean
- John A. Burns School of Medicine, University of Hawai‘i, Honolulu, HI (LSD, INS, CMS)
| | | | - Cecilia M. Shikuma
- John A. Burns School of Medicine, University of Hawai‘i, Honolulu, HI (LSD, INS, CMS)
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HIV-1 Drug Resistance Assay Using Ion Torrent Next Generation Sequencing and On-Instrument End-to-End Analysis Software. J Clin Microbiol 2022; 60:e0025322. [PMID: 35699434 DOI: 10.1128/jcm.00253-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
HIV-1 antiretroviral therapy management requires sequencing the protease, reverse transcriptase, and integrase portions of the HIV-1 pol gene. Most resistance testing is performed with Sanger sequencing, which has limited ability to detect minor variants. Next generation sequencing (NGS) platforms enable variant detection at frequencies as low as 1% allowing for earlier detection of resistance and modification of therapy. Implementation of NGS assays in the clinical laboratory is hindered by complicated assay design, cumbersome wet bench procedures, and the complexity of data analysis and bioinformatics. We developed a complete NGS protocol and companion analysis and reporting pipeline using AmpliSeq multiplex PCR, Ion Torrent S5 XL sequencing, and Stanford's HIVdb resistance algorithm. Implemented as a Torrent Suite software plugin, the pipeline runs automatically after sequencing. An optimum variant frequency threshold of 10% was determined by comparing Sanger sequences of archived samples from ViroSeq testing, resulting in a sensitivity of 98.2% and specificity of 99.0%. The majority (91%) of drug resistance mutations were detected by both Sanger and NGS, with 1.7% only by Sanger and 7.3% only by NGS. Variant calls were highly reproducible and there was no cross-reactivity to VZV, HBV, CMV, EBV, and HCV. The limit of detection was 500 copies/mL. The NGS assay performance was comparable to ViroSeq Sanger sequencing and has several advantages, including a publicly available end-to-end analysis and reporting plugin. The assay provides a straightforward path for implementation of NGS for HIV drug resistance testing in the laboratory setting without additional investment in bioinformatics infrastructure and resources.
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Qiu X, Sokoll L, Duong Ly T, Coignard C, Eshleman SH, Mohr P, Huizenga C, Swanson P, Cloherty G, Hackett J. An improved HIV antigen/antibody prototype assay for earlier detection of acute HIV infection. J Clin Virol 2021; 145:105022. [PMID: 34739837 DOI: 10.1016/j.jcv.2021.105022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 09/21/2021] [Accepted: 10/19/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND Early detection of acute HIV infection by HIV antigen/antibody assays depends on antigen sensitivity. Maintaining consistently high sensitivity across diverse HIV strains is critical to ensure equal detection. OBJECTIVES The performance of an improved HIV antigen/antibody prototype, HIV Combo Next, was evaluated for detection of genetically-diverse HIV strains and seroconversion samples. STUDY DESIGN Antigen sensitivity of the prototype was evaluated and compared to five FDA-approved HIV antigen/antibody assays using World Health Organization (WHO) HIV p24 antigen standard and reference panels, 17 virus isolates and 9 seroconversion panels. Antibody sensitivity and assay specificity of the prototype were also assessed with 1062 disease-staged and genotyped samples, and samples from 3000 blood donors and 955 individuals with low-risk for HIV infection. RESULTS Compared with other assays evaluated, the prototype demonstrated the best analytical sensitivity for WHO antigen standard, reference panels including 12 HIV-1 variants (0.04 - 0.25 IU/ml) and one HIV-2 variant, and 17 HIV virus isolates including HIV-1 group M, N, P and O and HIV-2 (0.3 -16 pg/ml). The enhanced sensitivity was also observed for seroconversion samples, detecting more PCR-positive samples with detection up to 7 days earlier than the other assays. Improvement in antigen sensitivity did not compromise antibody sensitivity or assay specificity, detecting all HIV disease-staged and genotyped samples, with assay specificity of 99.97% for blood donors and 99.68% for the low-risk population. CONCLUSIONS These data indicate that the new prototype HIV Combo Next assay will be of diagnostic value, providing improved early detection for acute HIV infection from divergent HIV strains.
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Affiliation(s)
- Xiaoxing Qiu
- Infectious Disease Research, Abbott, Core Diagnostics, Abbott Park, IL, United States.
| | - Lori Sokoll
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | | | | | - Susan H Eshleman
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Phaedre Mohr
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Clinton Huizenga
- Infectious Disease Research, Abbott, Core Diagnostics, Abbott Park, IL, United States
| | - Priscilla Swanson
- Infectious Disease Research, Abbott, Core Diagnostics, Abbott Park, IL, United States
| | - Gavin Cloherty
- Infectious Disease Research, Abbott, Core Diagnostics, Abbott Park, IL, United States
| | - John Hackett
- Infectious Disease Research, Abbott, Core Diagnostics, Abbott Park, IL, United States
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Zhao J, Huang H, Lee S, Ragupathy V, Biswas S, Mbondji-wonje C, Wang X, Jiang A, Hewlett I. Identification, Genetic Characterization and Validation of Highly Diverse HIV-1 Viruses for Reference Panel Development. Viruses 2021; 13:v13071417. [PMID: 34372623 PMCID: PMC8310377 DOI: 10.3390/v13071417] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 07/02/2021] [Accepted: 07/15/2021] [Indexed: 11/16/2022] Open
Abstract
The continued diversification of HIV poses potentially significant challenges to HIV diagnostics and therapeutics. The dynamic evolution of emerging variants is highlighted in countries such as Cameroon in West Central Africa, where all known subtypes and circulating recombinant forms (CRFs) have been shown to be prevalent. We obtained several hundred HIV-positive plasma and viruses from this region for characterization and identification of highly divergent HIV strains. A total of 163 viral strains were cultured to high titers and high volumes using donor peripheral blood mononuclear cells (PBMCs). Initially, 101 viruses representing 59 strains were well characterized and categorized. Results showed that the viral load (VL) range was 0.36–398.9 × 107 copies/mL, p24 values was 0.2–1134 ng/mL. Phylogenetic analysis of thirty-six near full-length HIV-1 genomic sequences demonstrated that most recombinants were highly diverse CRF02 containing unique recombinant forms (URFs). There were seven viral isolates identified as pure subtype/sub-subtypes (F2, A1, G, and D), six as CRFs (CRF06, CRF18, and CRF22), and ten as URFs. These extensively characterized reagents reflect the current dynamic and complex HIV epidemic in Cameroon and provide valuable insights into the potential phylogenetic evolutionary trend of global HIV molecular epidemiology in the future. These materials may be useful for development of HIV validation and reference panels to evaluate the performance of serologic antigen and nucleic acid assays for their ability to detect and quantitate highly divergent HIV strains.
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Affiliation(s)
- Jiangqin Zhao
- Correspondence: (J.Z.); (I.H.); Tel.: +1-240-402-6746 (J.Z.); +1-240-402-9587 (I.H.)
| | | | | | | | | | | | | | | | - Indira Hewlett
- Correspondence: (J.Z.); (I.H.); Tel.: +1-240-402-6746 (J.Z.); +1-240-402-9587 (I.H.)
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O'Keefe KJ, Pipkin S, Fatch R, Scheer S, Liegler T, McFarland W, Grant RM, Truong HHM. Non-B variants of HIV-1 in San Francisco, California. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2021; 90:104677. [PMID: 33321227 PMCID: PMC10686190 DOI: 10.1016/j.meegid.2020.104677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 12/07/2020] [Accepted: 12/10/2020] [Indexed: 11/26/2022]
Abstract
The HIV-1 epidemic in the US has historically been dominated by subtype B. HIV subtype diversity has not been extensively examined in most US cities to determine whether non-B variants have become established, as has been observed in many other global regions. We describe the diversity of non-B variants and present evidence of local transmission of non-B HIV in San Francisco. Viral sequences collected from patients between 2000 and 2016 were matched to the San Francisco HIV/AIDS case registry. HIV subtype was determined using COMET. Phylogenies were reconstructed using the pol region of subtypes A, C, D, G, CRF01_AE, CRF02_AG, and CRF07_BC, with reference sequences from the LANL HIV database. Associations of non-B subtypes and circulating recombinant forms (CRFs) with patient characteristics were assessed using multivariable logistic regression. Out of 11,381 sequences, 10,669 were from 7235 registry cases, of which 141 (2%) had non-B subtypes and CRFs and 72 (1%) had unique recombinant forms. CRF01_AE (0.8%) and subtype C (0.5%) were the most prevalent non-B forms. The frequency of non-B subtypes and CRFs increased in San Francisco during years 2000-2016. Out of 146 transmission events involving non-B study sequences, 18% indicated local transmission within the study population and 74% appeared to be inward migration of the virus. Compared to 7016 cases with only subtype B, 141 cases with non-B sequences were more likely to be of non-US country of birth (aOR = 11.02; p < 0.001), of Asian/Pacific-Islander race/ethnicity (aOR = 3.17; p < 0.001), and diagnosed after 2009 (aOR = 4.81; p < 0.001). Results suggest that most non-B infections were likely acquired outside the US and that local transmission of non-B forms has occurred but so far has not produced extensive transmission networks. Thus, non-B variants were not widely established in San Francisco, an observation that differs from cities worldwide with more diverse epidemics.
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Affiliation(s)
- Kara J O'Keefe
- Department of Medicine, University of California, San Francisco, CA 94158, USA.
| | - Sharon Pipkin
- Department of Public Health, San Francisco, CA 94102, USA.
| | - Robin Fatch
- Department of Epidemiology and Biostatistics, University of California, San Francisco 94158, USA.
| | - Susan Scheer
- Department of Public Health, San Francisco, CA 94102, USA.
| | - Teri Liegler
- Department of Medicine, University of California, San Francisco, CA 94158, USA
| | - Willi McFarland
- Department of Public Health, San Francisco, CA 94102, USA; Department of Epidemiology and Biostatistics, University of California, San Francisco 94158, USA.
| | - Robert M Grant
- Department of Medicine, University of California, San Francisco, CA 94158, USA.
| | - Hong-Ha M Truong
- Department of Medicine, University of California, San Francisco, CA 94158, USA.
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Singh R, Chakraborty M, Gautam A, Roy SK, Halder I, Barber J, Garg A. Residual immune activation in HIV-Infected individuals expands monocytic-myeloid derived suppressor cells. Cell Immunol 2021; 362:104304. [PMID: 33610024 DOI: 10.1016/j.cellimm.2021.104304] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 01/28/2021] [Accepted: 01/28/2021] [Indexed: 12/30/2022]
Abstract
HIV-infected individuals on combined antiretroviral therapy (ART) with virologic suppression exhibit sustained immune dysfunction. Our recent work has highlighted that monocytic myeloid derived suppressor cells (M-MDSC) are elevated in these individuals and suppress immune responses. Factors responsible for M-MDSC expansion in vivo are unknown. Here we compared circulating frequency of M-MDSC in HIV-infected persons from the US and India where HIV subtype-B or -C predominate, respectively. We further investigated soluble mediators of residual immune activation in two cohorts and determined their correlation with M-MDSC expansion. Our findings show that M-MDSC are elevated and correlate with plasma levels of IL-6 in both cohorts. Chemokines CXCL10, CCL4 and CXCL8 were also elevated in HIV-infected individuals, but did not correlate with M-MDSC. These findings support that IL-6 is important in M-MDSC expansion which is independent of HIV subtype.
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Affiliation(s)
- Ritesh Singh
- Department of Community and Family Medicine, All India Institute of Medical Sciences, India
| | - Mouli Chakraborty
- National Institute of Biomedical Genomics, Departments of Chest andRespiratory Diseases JN Medical College and Hospital, Kalyani West Bengal, India
| | - Anuradha Gautam
- National Institute of Biomedical Genomics, Departments of Chest andRespiratory Diseases JN Medical College and Hospital, Kalyani West Bengal, India
| | - Suman K Roy
- Community Medicine and Chest andRespiratory Diseases JN Medical College and Hospital, Kalyani West Bengal, India
| | - Indranil Halder
- Chest andRespiratory Diseases JN Medical College and Hospital, Kalyani West Bengal, India
| | - Jamie Barber
- Department of Infectious Diseases, College of Veterinary Medicine University of Georgia, Athens, GA 30606, USA
| | - Ankita Garg
- Department of Infectious Diseases, College of Veterinary Medicine University of Georgia, Athens, GA 30606, USA.
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Leung KSS, To SWC, Chen JHK, Siu GKH, Chan KCW, Yam WC. Molecular Characterization of HIV-1 Minority Subtypes in Hong Kong: A Recent Epidemic of CRF07_BC among the Men who have Sex with Men Population. Curr HIV Res 2020; 17:53-64. [PMID: 31142258 DOI: 10.2174/1570162x17666190530081355] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 05/03/2019] [Accepted: 05/11/2019] [Indexed: 01/29/2023]
Abstract
BACKGROUND Over the past years, an increasing trend was noticed for non-B and non- CRF01_AE HIV-1 strains prevalence in Hong Kong. OBJECTIVE In this study, we aimed at using the available HIV-1 pol sequences collected from 1994 to 2013 through our local antiretroviral resistance surveillance program to investigate the molecular epidemiology and evolution of HIV-1 minority subtypes in Hong Kong. We also aimed at investigating their potential association and impact of those transmission risk groups. METHODS A total of 2,315 HIV-1 partial pol sequences were included. HIV-1 genotypes were determined by REGA Genotyping Tool and phylogenetic analysis with reference sequences. The viral evolutionary rates and time of the most common ancestor (tMRCA) were estimated by Bayesian Markov Chain Monte Carlo (MCMC) interference. RESULTS Apart from the two prevalent HIV-1 genotypes in Hong Kong (subtype B,41.6%, CRF01_AE,40.5%), phylogenetic analysis revealed a broad viral diversity including CRF07_BC(5.1%), subtype C(4.5%), CRF02_AG(1.1%), CRF08_BC(0.8%), subtype A1(0.8%), subtype G(0.4%), subtype D(0.4%), CRF06_cpx(0.4%), subtype F(0.1%), CRF12_BF(0·04%) and other recombinants(4.5%). The top five minority subtypes were further analyzed which demonstrated distinct epidemiological and phylogenetic patterns. Over 70% of subtypes A1, C and CRF02_AG infections were circulated among non-Chinese Asians or African community in Hong Kong and were mainly transmitted between heterosexual regular partners. Instead, over 90% of CRF07_BC and CRF08_BC patients were Chinese. An epidemic cluster was identified in CRF07_BC and estimated to expand from 2002 onwards based on skyline plot and molecular clock analysis. CONCLUSION Our results highlighted the emergence of CRF07_BC epidemic in local MSM community, public health interventions targeting the community should be further enhanced to tackle the epidemic.
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Affiliation(s)
| | - Sabrina Wai-Chi To
- Department of Microbiology, Queen Mary Hospital, The University of Hong Kong, Hong Kong
| | | | - Gilman Kit-Hang Siu
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong
| | - Kenny Chi-Wai Chan
- Integrated Treatment Centre, Special Preventive Programme, Centre for Health Protection, Department of Health, Hong Kong
| | - Wing-Cheong Yam
- Department of Microbiology, Queen Mary Hospital, The University of Hong Kong, Hong Kong
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Hong SL, Dellicour S, Vrancken B, Suchard MA, Pyne MT, Hillyard DR, Lemey P, Baele G. In Search of Covariates of HIV-1 Subtype B Spread in the United States-A Cautionary Tale of Large-Scale Bayesian Phylogeography. Viruses 2020; 12:v12020182. [PMID: 32033422 PMCID: PMC7077180 DOI: 10.3390/v12020182] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 01/24/2020] [Accepted: 01/28/2020] [Indexed: 12/21/2022] Open
Abstract
Infections with HIV-1 group M subtype B viruses account for the majority of the HIV epidemic in the Western world. Phylogeographic studies have placed the introduction of subtype B in the United States in New York around 1970, where it grew into a major source of spread. Currently, it is estimated that over one million people are living with HIV in the US and that most are infected with subtype B variants. Here, we aim to identify the drivers of HIV-1 subtype B dispersal in the United States by analyzing a collection of 23,588 pol sequences, collected for drug resistance testing from 45 states during 2004-2011. To this end, we introduce a workflow to reduce this large collection of data to more computationally-manageable sample sizes and apply the BEAST framework to test which covariates associate with the spread of HIV-1 across state borders. Our results show that we are able to consistently identify certain predictors of spread under reasonable run times across datasets of up to 10,000 sequences. However, the general lack of phylogenetic structure and the high uncertainty associated with HIV trees make it difficult to interpret the epidemiological relevance of the drivers of spread we are able to identify. While the workflow we present here could be applied to other virus datasets of a similar scale, the characteristic star-like shape of HIV-1 phylogenies poses a serious obstacle to reconstructing a detailed evolutionary and spatial history for HIV-1 subtype B in the US.
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Affiliation(s)
- Samuel L. Hong
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium; (S.D.); (B.V.); (P.L.); (G.B.)
- Correspondence:
| | - Simon Dellicour
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium; (S.D.); (B.V.); (P.L.); (G.B.)
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, 1050 Brussels, Belgium
| | - Bram Vrancken
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium; (S.D.); (B.V.); (P.L.); (G.B.)
| | - Marc A. Suchard
- Department of Biomathematics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA 90095, USA;
- Department of Human Genetics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA 90095, USA
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, CA 90095, USA
| | - Michael T. Pyne
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT 84108, USA;
| | - David R. Hillyard
- Department of Pathology, University of Utah, Salt Lake City, UT 84112, USA;
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium; (S.D.); (B.V.); (P.L.); (G.B.)
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium; (S.D.); (B.V.); (P.L.); (G.B.)
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Abstract
Human immunodeficiency virus-1 (HIV-1) is characterised by a vast genetic diversity classified into distinct phylogenetic strains and recombinant forms. We describe the HIV-1 molecular epidemiology and evolution of 129 consecutive HIV-1 positive migrants living in Milan (northern Italy). Polymerase gene sequences of 116 HIV-1 subtype-B positive patients were aligned with HIV-1 reference sequences (https://www.ncbi.nlm.nih.gov/) by using MAFFT alignment and edited by using Bioedit software. A maximum likelihood (ML) phylogenetic tree was performed by MEGA7 and was visualised by using FigTree v1.4.3. Of 129 migrants, 35 were born in Europe (28 in Eastern Europe), 70 in the Americas (67 in South America), 15 in Africa and nine in Asia; 76.4% were men who have sex with men (MSM). The serotype HIV-1-B prevailed (89.9%), followed by -C, -F1, -D and -A. Compared with 116 HIV-B patients, the 13 with HIV-non-B showed lower Nadir of CD4+ cell/mmc (P = 0.043), more frequently had sub Saharan origin (38.5 vs. 1.72%, P = 0.0001) and less frequently were MSM (40 vs. 74.5%, P = 0.02). The ML phylogenetic tree of the 116 HIV-1 subtype-B positive patients showed 13 statistically supported nodes (bootstrap > 70%). Most of the sequences included in these nodes have been isolated from male patients from the Americas and the most common risk factor was MSM. The low number of HIV-1 non-B subtype patients did not allow to perform this analysis. These results suggest a shift of HIV-1 prevention projects' focus and a continuous monitoring of HIV-1 molecular epidemiology among entry populations. Prevention efforts based on HIV molecular epidemiology may improve public health surveillance setting.
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HIV-1 Latency and Latency Reversal: Does Subtype Matter? Viruses 2019; 11:v11121104. [PMID: 31795223 PMCID: PMC6950696 DOI: 10.3390/v11121104] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 11/22/2019] [Accepted: 11/27/2019] [Indexed: 02/06/2023] Open
Abstract
Cells that are latently infected with HIV-1 preclude an HIV-1 cure, as antiretroviral therapy does not target this latent population. HIV-1 is highly genetically diverse, with over 10 subtypes and numerous recombinant forms circulating worldwide. In spite of this vast diversity, much of our understanding of latency and latency reversal is largely based on subtype B viruses. As such, most of the development of cure strategies targeting HIV-1 are solely based on subtype B. It is currently assumed that subtype does not influence the establishment or reactivation of latent viruses. However, this has not been conclusively proven one way or the other. A better understanding of the factors that influence HIV-1 latency in all viral subtypes will help develop therapeutic strategies that can be applied worldwide. Here, we review the latest literature on subtype-specific factors that affect viral replication, pathogenesis, and, most importantly, latency and its reversal.
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Rhee SY, Magalis BR, Hurley L, Silverberg MJ, Marcus JL, Slome S, Kosakovsky Pond SL, Shafer RW. National and International Dimensions of Human Immunodeficiency Virus-1 Sequence Clusters in a Northern California Clinical Cohort. Open Forum Infect Dis 2019; 6:ofz135. [PMID: 31041344 PMCID: PMC6483754 DOI: 10.1093/ofid/ofz135] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Accepted: 03/12/2019] [Indexed: 11/14/2022] Open
Abstract
Background Recent advances in high-throughput molecular epidemiology are transforming the analysis of viral infections. Methods Human immunodeficiency virus (HIV)-1 pol sequences from a Northern Californian cohort (NCC) of 4553 antiretroviral-naive individuals sampled between 1998 and 2016 were analyzed together with 140 000 previously published global pol sequences. The HIV-TRAnsmission Cluster Engine (HIV-TRACE) was used to infer a transmission network comprising links between NCC and previously published sequences having a genetic distance ≤1.5%. Results Twenty-five percent of NCC sequences were included in 264 clusters linked to a published sequence, and approximately one third of these (8.0% of the total) were linked to 1 or more non-US sequences. The largest cluster, containing 512 NCC sequences (11.2% of the total), comprised the subtype B lineage that traced its origin to the earliest North American sequences. Approximately 5 percent of NCC sequences belonged to a non-B subtype, and these were more likely to cluster with a non-US sequence. Twenty-two NCC sequences belonged to 1 of 4 large clusters containing sequences from rapidly growing regional epidemics: CRF07_BC (East Asia), subtype A6 (former Soviet Union), a Japanese subtype B lineage, and an East/Southeast Asian CRF01_AE lineage. Bayesian phylogenetics suggested that most non-B sequences resulted from separate introductions but that local spread within the largest CRF01_AE cluster occurred twice. Conclusions The NCC contains national and international links to previously published sequences including many to the subtype B strain that originated in North America and several to rapidly growing Asian epidemics. Despite their rapid regional growth, the Asian epidemic strains demonstrated limited NCC spread.
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Affiliation(s)
- Soo-Yon Rhee
- Division of Infectious Diseases, Department of Medicine, Stanford University, California
| | | | - Leo Hurley
- Division of Research, Kaiser Permanente Northern California, Oakland
| | | | - Julia L Marcus
- Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, Massachusetts
| | - Sally Slome
- Department of Infectious Diseases, Kaiser Permanente Northern California, Oakland
| | | | - Robert W Shafer
- Division of Infectious Diseases, Department of Medicine, Stanford University, California
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13
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Kline RL, Saduvala N, Zhang T, Oster AM. Diversity and characterization of HIV-1 subtypes in the United States, 2008-2016. Ann Epidemiol 2019; 33:84-88. [PMID: 30961993 DOI: 10.1016/j.annepidem.2019.02.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 02/05/2019] [Accepted: 02/28/2019] [Indexed: 11/27/2022]
Abstract
PURPOSE This article describes subtype diversity among diagnosed HIV-1 infections in the United States during 2008-2016 by demographic or risk group and over time. METHODS HIV-1 polymerase sequences reported to the National HIV Surveillance System for persons in 17 U.S. states with HIV infection diagnosed during 2008-2016 were subtyped using COMET, an automated subtyping tool, and National HIV Surveillance System demographic data were analyzed. RESULTS Subtype B was identified in 93.6% of 121,793 reported sequences. The most common non-B subtypes and circulating recombinant forms (CRFs) were C, CRF02_AG, A, CRF01_AE, and G. Elevated percentages of non-B subtypes or CRFs were found in persons who were female, aged less than 13 years at diagnosis, Asian, or had transmission attributable to heterosexual contact (females only) or perinatal exposure. Foreign-born persons had a higher percentage of non-B subtypes. The prevalence of non-B subtypes and CRFs increased from 5.0% in 2008 to 8.5% in 2016; among specific subtypes and CRFs, subtype G and CRF01_AE increased. CONCLUSIONS Subtype B remains the predominant strain in the United States. Non-B subtypes and CRFs were not widespread, but diversity and numbers increased from 2008 through 2016, which could have consequences for clinical management, diagnostic testing, and vaccine development.
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Affiliation(s)
- Richard L Kline
- Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, GA
| | | | | | - Alexandra M Oster
- Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, GA.
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14
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Yamaguchi J, Olivo A, Laeyendecker O, Forberg K, Ndembi N, Mbanya D, Kaptue L, Quinn TC, Cloherty GA, Rodgers MA, Berg MG. Universal Target Capture of HIV Sequences From NGS Libraries. Front Microbiol 2018; 9:2150. [PMID: 30271393 PMCID: PMC6146096 DOI: 10.3389/fmicb.2018.02150] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 08/22/2018] [Indexed: 11/13/2022] Open
Abstract
Background: Global surveillance of viral sequence diversity is needed to keep pace with the constant evolution of HIV. Recent next generation sequencing (NGS) methods have realized the goal of sequencing circulating virus directly from patient specimens. Yet, a simple, universal approach that maximizes sensitivity and sequencing capacity remains elusive. Here we present a novel HIV enrichment strategy to yield near complete genomes from low viral load specimens. Methodology: A non-redundant biotin-labeled probe set (HIV-xGen; n = 652) was synthesized to tile all HIV-1 (groups M, N, O, and P) and HIV-2 (A and B) strains. Illumina Nextera barcoded libraries of either gene-specific or randomly primed cDNA derived from infected plasma were hybridized to probes in a single pool and unbound sequences were washed away. Captured viral cDNA was amplified by Illumina adaptor primers, sequenced on a MiSeq, and NGS reads were demultiplexed for alignment with CLC Bio software. Results: HIV-xGen probes selectively captured and amplified reads spanning the entirety of the HIV phylogenetic tree. HIV sequences clearly present in unenriched libraries of specimens but previously not observed due to high host background levels, insufficient sequencing depth or the extent of multiplexing, were now enriched by >1,000-fold. Thus, xGen selection not only substantially increased the depth of existing sequence, but also extended overall genome coverage by an average of 40%. We characterized 50 new, diverse HIV strains from clinical specimens and demonstrated a viral load cutoff of approximately log 3.5 copies/ml for full length coverage. Genome coverage was <20% for 5/10 samples with viral loads <log 3.5 copies/ml and >90% for 35/40 samples with higher viral loads. Conclusions: Characterization of >20 complete genomes at a time is now possible from a single probe hybridization and MiSeq run. With the versatility to capture all HIV strains and the sensitivity to detect low titer specimens, HIV-xGen will serve as an important tool for monitoring HIV sequence diversity.
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Affiliation(s)
- Julie Yamaguchi
- Infectious Diseases Research, Abbott Diagnostics, Chicago, IL, United States
| | - Ana Olivo
- Infectious Diseases Research, Abbott Diagnostics, Chicago, IL, United States
| | - Oliver Laeyendecker
- National Institute of Allergy and Infectious Diseases, NIH, Baltimore, MD, United States
| | - Kenn Forberg
- Infectious Diseases Research, Abbott Diagnostics, Chicago, IL, United States
| | | | - Dora Mbanya
- Université de Yaoundé 1, Yaoundé, Cameroon.,University of Bamenda, Bamenda, Cameroon
| | | | - Thomas C Quinn
- National Institute of Allergy and Infectious Diseases, NIH, Baltimore, MD, United States
| | - Gavin A Cloherty
- Infectious Diseases Research, Abbott Diagnostics, Chicago, IL, United States
| | - Mary A Rodgers
- Infectious Diseases Research, Abbott Diagnostics, Chicago, IL, United States
| | - Michael G Berg
- Infectious Diseases Research, Abbott Diagnostics, Chicago, IL, United States
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15
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Grossman Z, Rico SV, Cone K, Shao W, Rehm C, Jones S, Bozzi G, Dean S, Dewar R, Rehman T, Purdy J, Hadigan C, Pau AK, Maldarelli F. Early Presence of HIV-1 Subtype C in Washington, D.C. AIDS Res Hum Retroviruses 2018; 34:680-684. [PMID: 29936863 DOI: 10.1089/aid.2018.0041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The presence of non-B HIV subtypes in the USA has been documented during the epidemic, although the timing of early introductions of different subtypes remains uncertain. Subtype C, the most common HIV variant worldwide, was first reported in the USA in 1996-97, after subtype C had expanded greatly in sub-Saharan Africa. In this study, we report a patient with subtype C infection acquired by mother-to-child transmission, born in the USA in 1990 to a Washington, D.C. resident who never traveled outside the USA, demonstrating that subtype C was present in the USA much earlier. Comparative analysis of the sequence from this patient and subtype C sequences in the USA and elsewhere suggest multiple independent introductions of this subtype into the USA have taken place, many of which are traced to sub-Saharan or East Africa. These data indicate subtype C HIV was already present in the USA years earlier than previously reported, and during the early period of subtype C expansion.
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Affiliation(s)
- Zehava Grossman
- HIV Dynamics and Replication Program, NCI, NIH, Frederick, Maryland
- Sackler Faculty of Medicine, School of Public Health, Tel Aviv University, Tel Aviv, Israel
| | - Sheryl-vi Rico
- Intramural Clinical Management & Operations Branch, NIAID, NIH, Bethesda, Maryland
| | - Katherine Cone
- Intramural Clinical Management & Operations Branch, NIAID, NIH, Bethesda, Maryland
- Department of Social Work, NIH Clinical Center, Bethesda, Maryland
| | - Wei Shao
- Leidos Biomedical Research, Inc., Frederick, National Laboratory for Cancer Research, Frederick, Maryland
| | - Catherine Rehm
- Intramural Clinical Management & Operations Branch, NIAID, NIH, Bethesda, Maryland
| | - Sara Jones
- Clinical Research Directorate/Clinical Monitoring Research Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, Maryland
| | - Giorgio Bozzi
- HIV Dynamics and Replication Program, NCI, NIH, Frederick, Maryland
| | - Sophie Dean
- HIV Dynamics and Replication Program, NCI, NIH, Frederick, Maryland
| | - Robin Dewar
- Leidos Biomedical Research, Inc., Frederick, National Laboratory for Cancer Research, Frederick, Maryland
| | - Tauseef Rehman
- Leidos Biomedical Research, Inc., Frederick, National Laboratory for Cancer Research, Frederick, Maryland
| | - Julia Purdy
- Critical Care Medicine Department, NIH Clinical Center, NIH, Bethesda, Maryland
| | - Colleen Hadigan
- Intramural Clinical Management & Operations Branch, NIAID, NIH, Bethesda, Maryland
| | - Alice K. Pau
- Intramural Clinical Management & Operations Branch, NIAID, NIH, Bethesda, Maryland
| | - Frank Maldarelli
- HIV Dynamics and Replication Program, NCI, NIH, Frederick, Maryland
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16
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Hernandez-Sanchez PG, Guerra-Palomares SE, Ramirez-GarciaLuna JL, Arguello JR, Noyola DE, Garcia-Sepulveda CA. Prevalence of Drug Resistance Mutations in Protease, Reverse Transcriptase, and Integrase Genes of North Central Mexico HIV Isolates. AIDS Res Hum Retroviruses 2018; 34:498-506. [PMID: 29620931 DOI: 10.1089/aid.2017.0257] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
This study set out to determine the frequency of antiretroviral drug resistance mutations in treatment-naive subjects of the north central Mexican state of San Luis Potosí. Mexican studies of antiretroviral drug resistance mutations have focused mainly on large metropolitan areas and border towns subjected to intense international migrations. This study set forth to describe the frequency of these mutations in a Mexican region less subjected to such migratory influences and more representative of smaller Mexican cities. Thirty-eight full-length pol sequences spanning the protease, reverse-transcriptase, and integrase-encoding regions were obtained from 42 treatment-naive human immunodeficiency virus (HIV)-infected subjects. Most exhibited subtype B homology, but CRF02_AG was also detected. Evidence of APOBEC3 hypermutation was seen in two samples. Calibrated population analysis revealed a surveillance drug resistance mutation prevalence of 4.9% for protease inhibitors, of 2.7% for nucleoside reverse transcriptase inhibitors, of 8.1% for non-nucleoside reverse transcriptase inhibitors, and an overall prevalence of 9.5%. This corresponds to an intermediate level of transmitted drug resistance according to the World Health Organization. The identification of integrase mutations suggests that transmitted drug mutations are being imported, as inhibitors targeting integrase have not been widely used in Mexico. Our results provide a greater understanding of HIV diversity in Mexico and highlight the way internal migrations allow HIV mutations and genetic features to permeate regions less subjected to international migrations. The implications of these findings will become more evident as Mexico hosts increased repatriations of migrants in the coming years.
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Affiliation(s)
- Pedro Gerardo Hernandez-Sanchez
- Laboratorio de Genómica Viral y Humana, Facultad de Medicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí, México
| | | | - Jose Luis Ramirez-GarciaLuna
- Laboratorio de Genómica Viral y Humana, Facultad de Medicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí, México
| | - Jesus Rafael Arguello
- Departamento de Inmunobiología Molecular, Centro de Investigación Biomédica, Universidad Autónoma de Coahuila, Torreón, México
| | - Daniel Ernesto Noyola
- Departamento de Microbiología, Facultad de Medicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí, México
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Human Genomic Loci Important in Common Infectious Diseases: Role of High-Throughput Sequencing and Genome-Wide Association Studies. CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY 2018; 2018:1875217. [PMID: 29755620 PMCID: PMC5884297 DOI: 10.1155/2018/1875217] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Accepted: 03/07/2018] [Indexed: 12/27/2022]
Abstract
HIV/AIDS, tuberculosis (TB), and malaria are 3 major global public health threats that undermine development in many resource-poor settings. Recently, the notion that positive selection during epidemics or longer periods of exposure to common infectious diseases may have had a major effect in modifying the constitution of the human genome is being interrogated at a large scale in many populations around the world. This positive selection from infectious diseases increases power to detect associations in genome-wide association studies (GWASs). High-throughput sequencing (HTS) has transformed both the management of infectious diseases and continues to enable large-scale functional characterization of host resistance/susceptibility alleles and loci; a paradigm shift from single candidate gene studies. Application of genome sequencing technologies and genomics has enabled us to interrogate the host-pathogen interface for improving human health. Human populations are constantly locked in evolutionary arms races with pathogens; therefore, identification of common infectious disease-associated genomic variants/markers is important in therapeutic, vaccine development, and screening susceptible individuals in a population. This review describes a range of host-pathogen genomic loci that have been associated with disease susceptibility and resistant patterns in the era of HTS. We further highlight potential opportunities for these genetic markers.
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18
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Pérez-Losada M, Castel AD, Lewis B, Kharfen M, Cartwright CP, Huang B, Maxwell T, Greenberg AE, Crandall KA. Characterization of HIV diversity, phylodynamics and drug resistance in Washington, DC. PLoS One 2017; 12:e0185644. [PMID: 28961263 PMCID: PMC5621693 DOI: 10.1371/journal.pone.0185644] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 09/16/2017] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Washington DC has a high burden of HIV with a 2.0% HIV prevalence. The city is a national and international hub potentially containing a broad diversity of HIV variants; yet few sequences from DC are available on GenBank to assess the evolutionary history of HIV in the US capital. Towards this general goal, here we analyze extensive sequence data and investigate HIV diversity, phylodynamics, and drug resistant mutations (DRM) in DC. METHODS Molecular HIV-1 sequences were collected from participants infected through 2015 as part of the DC Cohort, a longitudinal observational study of HIV+ patients receiving care at 13 DC clinics. Sequences were paired with Cohort demographic, risk, and clinical data and analyzed using maximum likelihood, Bayesian and coalescent approaches of phylogenetic, network and population genetic inference. We analyzed 601 sequences from 223 participants for int (~864 bp) and 2,810 sequences from 1,659 participants for PR/RT (~1497 bp). RESULTS Ninety-nine and 94% of the int and PR/RT sequences, respectively, were identified as subtype B, with 14 non-B subtypes also detected. Phylodynamic analyses of US born infected individuals showed that HIV population size varied little over time with no significant decline in diversity. Phylogenetic analyses grouped 13.5% of the int sequences into 14 clusters of 2 or 3 sequences, and 39.0% of the PR/RT sequences into 203 clusters of 2-32 sequences. Network analyses grouped 3.6% of the int sequences into 4 clusters of 2 sequences, and 10.6% of the PR/RT sequences into 76 clusters of 2-7 sequences. All network clusters were detected in our phylogenetic analyses. Higher proportions of clustered sequences were found in zip codes where HIV prevalence is highest (r = 0.607; P<0.00001). We detected a high prevalence of DRM for both int (17.1%) and PR/RT (39.1%), but only 8 int and 12 PR/RT amino acids were identified as under adaptive selection. We observed a significant (P<0.0001) association between main risk factors (men who have sex with men and heterosexuals) and genotypes in the five well-supported clusters with sufficient sample size for testing. DISCUSSION Pairing molecular data with clinical and demographic data provided novel insights into HIV population dynamics in Washington, DC. Identification of populations and geographic locations where clustering occurs can inform and complement active surveillance efforts to interrupt HIV transmission.
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Affiliation(s)
- Marcos Pérez-Losada
- Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Ashburn, VA, United States of America
- CIBIO-InBIO, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
- Milken Institute School of Public Health, Department of Epidemiology and Biostatistics, The George Washington University, Washington, DC, United States of America
| | - Amanda D. Castel
- Milken Institute School of Public Health, Department of Epidemiology and Biostatistics, The George Washington University, Washington, DC, United States of America
| | - Brittany Lewis
- Milken Institute School of Public Health, Department of Epidemiology and Biostatistics, The George Washington University, Washington, DC, United States of America
| | - Michael Kharfen
- District of Columbia Department of Health, Washington, DC, United States of America
| | | | - Bruce Huang
- Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Ashburn, VA, United States of America
| | - Taylor Maxwell
- Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Ashburn, VA, United States of America
| | - Alan E. Greenberg
- Milken Institute School of Public Health, Department of Epidemiology and Biostatistics, The George Washington University, Washington, DC, United States of America
| | - Keith A. Crandall
- Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Ashburn, VA, United States of America
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19
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López SN, Rodríguez-Valentín M, Rivera M, Rodríguez M, Babu M, Cubano LA, Xiong H, Wang G, Kucheryavykh L, Boukli NM. HIV-1 Gp120 clade B/C induces a GRP78 driven cytoprotective mechanism in astrocytoma. Oncotarget 2017; 8:68415-68438. [PMID: 28978127 PMCID: PMC5620267 DOI: 10.18632/oncotarget.19474] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 06/28/2017] [Indexed: 01/20/2023] Open
Abstract
HIV-1 clades are known to be one of the key factors implicated in modulating HIV-associated neurocognitive disorders. HIV-1 B and C clades account for the majority of HIV-1 infections, clade B being the most neuropathogenic. The mechanisms behind HIV-mediated neuropathogenesis remain the subject of active research. We hypothesized that HIV-1 gp120 clade B and C proteins may exert differential proliferation, cell survival and NeuroAIDS effects in human astrocytoma cells via the Unfolded Protein Response, an endoplasmic reticulum- based cytoprotective mechanism. The differential effect of gp120 clade B and C was evaluated using for the first time a Tandem Mass Tag isobaric labeling quantitative proteomic approach. Flow cytometry analyses were performed for cell cycle and cell death identification. Among the proteins differentiated by HIV-1 gp120 proteins figure cytoskeleton, oxidative stress, UPR markers and numerous glycolytic metabolism enzymes. Our results demonstrate that HIV-1 gp120 B induced migration, proliferative and protective responses granted by the expression of GRP78, while HIV-1 gp120 C induced the expression of key inflammatory and pro-apoptotic markers. These novel findings put forward the first evidence that GRP78 is a key player in HIV-1 clade B and C neuropathogenic discrepancies and can be used as a novel target for immunotherapies.
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Affiliation(s)
- Sheila N López
- Biomedical Proteomics Facility, Department of Microbiology and Immunology, Universidad Central del Caribe, School of Medicine, Bayamón, PR, USA
| | - Madeline Rodríguez-Valentín
- Biomedical Proteomics Facility, Department of Microbiology and Immunology, Universidad Central del Caribe, School of Medicine, Bayamón, PR, USA
| | - Mariela Rivera
- Biomedical Proteomics Facility, Department of Microbiology and Immunology, Universidad Central del Caribe, School of Medicine, Bayamón, PR, USA
| | - Maridaliz Rodríguez
- Biomedical Proteomics Facility, Department of Microbiology and Immunology, Universidad Central del Caribe, School of Medicine, Bayamón, PR, USA
| | - Mohan Babu
- Department of Biochemistry, Research and Innovation Center, University of Regina, Saskatchewan, Canada
| | - Luis A Cubano
- Biomedical Proteomics Facility, Department of Microbiology and Immunology, Universidad Central del Caribe, School of Medicine, Bayamón, PR, USA
| | - Huangui Xiong
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
| | - Guangdi Wang
- RCMI Cancer Research Center, Xavier University of Louisiana, New Orleans, LA, USA
| | - Lilia Kucheryavykh
- Department of Biochemistry, Universidad Central del Caribe, School of Medicine, Bayamón, PR, USA
| | - Nawal M Boukli
- Biomedical Proteomics Facility, Department of Microbiology and Immunology, Universidad Central del Caribe, School of Medicine, Bayamón, PR, USA
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20
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Dennis AM, Hué S, Learner E, Sebastian J, Miller WC, Eron JJ. Rising prevalence of non-B HIV-1 subtypes in North Carolina and evidence for local onward transmission. Virus Evol 2017; 3:vex013. [PMID: 28567304 PMCID: PMC5442504 DOI: 10.1093/ve/vex013] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
HIV-1 diversity is increasing in North American and European cohorts which may have public health implications. However, little is known about non-B subtype diversity in the southern United States, despite the region being the epicenter of the nation's epidemic. We characterized HIV-1 diversity and transmission clusters to identify the extent to which non-B strains are transmitted locally. We conducted cross-sectional analyses of HIV-1 partial pol sequences collected from 1997 to 2014 from adults accessing routine clinical care in North Carolina (NC). Subtypes were evaluated using COMET and phylogenetic analysis. Putative transmission clusters were identified using maximum-likelihood trees. Clusters involving non-B strains were confirmed and their dates of origin were estimated using Bayesian phylogenetics. Data were combined with demographic information collected at the time of sample collection and country of origin for a subset of patients. Among 24,972 sequences from 15,246 persons, the non-B subtype prevalence increased from 0% to 3.46% over the study period. Of 325 persons with non-B subtypes, diversity was high with over 15 pure subtypes and recombinants; subtype C (28.9%) and CRF02_AG (24.0%) were most common. While identification of transmission clusters was lower for persons with non-B versus B subtypes, several local transmission clusters (≥3 persons) involving non-B subtypes were identified and all were presumably due to heterosexual transmission. Prevalence of non-B subtype diversity remains low in NC but a statistically significant rise was identified over time which likely reflects multiple importation. However, the combined phylogenetic clustering analysis reveals evidence for local onward transmission. Detection of these non-B clusters suggests heterosexual transmission and may guide diagnostic and prevention interventions.
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Affiliation(s)
- Ann M Dennis
- Division of Infectious Diseases, University of North Carolina, Chapel Hill, NC, USA
| | - Stephane Hué
- London School of Hygiene & Tropical Medicine, London, UK
| | - Emily Learner
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Joseph Sebastian
- Laboratory Corporation of America, Research Triangle Park, NC, USA
| | - William C Miller
- Department of Epidemiology, Ohio State University, Columbus, OH, USA
| | - Joseph J Eron
- Division of Infectious Diseases, University of North Carolina, Chapel Hill, NC, USA.,Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
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21
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Qiu X, Sokoll L, Yip P, Elliott DJ, Dua R, Mohr P, Wang XY, Spencer M, Swanson P, Dawson GJ, Hackett J. Comparative evaluation of three FDA-approved HIV Ag/Ab combination tests using a genetically diverse HIV panel and diagnostic specimens. J Clin Virol 2017; 92:62-68. [PMID: 28535437 DOI: 10.1016/j.jcv.2017.05.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 05/03/2017] [Accepted: 05/06/2017] [Indexed: 11/19/2022]
Abstract
BACKGROUND HIV Ag/Ab combination assays are recommended by CDC for routine screening and several HIV Ag/Ab combination tests are now FDA-approved. Maintaining high specificity and consistent sensitivity across diverse HIV strains is critical for these assays to accurately detect HIV infection and expedite delivery of patient results. OBJECTIVES To evaluate performance of three FDA-approved HIV tests: ARCHITECT HIV Combo (Abbott), ADVIA Centaur HIV Combo (Siemens) and BioPlex HIV Ag-Ab (Bio-Rad). STUDY DESIGN Sensitivity and specificity were evaluated using an extensive panel of 28 HIV infected human specimens and 17 cultured virus isolates representing multiple genotypes, 6 seroconversion panels, 4 human samples with acute infection, WHO p24 standard and 4020 clinical specimens. RESULTS The p24 limit of detection (LOD) for the WHO standard was 0.19IU/ml, 0.70IU/ml, and 1.77IU/ml in BioPlex, ARCHITECT, and Centaur respectively. The distribution of LODs across 15 HIV-1 isolates was substantially narrower in ARCHITECT (5-33pg/ml) than in BioPlex (11-198pg/ml) and Centaur (6-384pg/ml). All assays detected antibodies to the majority of HIV-1 and HIV-2 variants. However, reduced sensitivity was observed for Centaur in detection of antibodies to HIV-1 group M (CRF02_AG), O and N variants. BioPlex and ARCHITECT showed better seroconversion sensitivity than Centaur, detecting one bleed (3-7 days) earlier in 4 (BioPlex) and 3 (ARCHITECT) of 6 seroconversion panels. ARCHITECT demonstrated the highest specificity (99.90-100%) compared to BioPlex (99.80%) and Centaur (99.42%). CONCLUSIONS The overall performance of ARCHITECT and BioPlex was superior to Centaur, especially for detection of acute HIV infection.
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Affiliation(s)
- Xiaoxing Qiu
- Infectious Disease Research, Abbott, Diagnostics, Abbott Park, IL, United States.
| | - Lori Sokoll
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD, United States
| | - Paul Yip
- Department of Laboratory Medicine and Pathobiology, University of Toronto and University Health Network, Toronto, ON, Canada
| | - Debra J Elliott
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD, United States
| | - Renu Dua
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD, United States
| | - Phaedre Mohr
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD, United States
| | - Xiao Yan Wang
- Department of Laboratory Medicine and Pathobiology, University of Toronto and University Health Network, Toronto, ON, Canada
| | - Megan Spencer
- Department of Laboratory Medicine and Pathobiology, University of Toronto and University Health Network, Toronto, ON, Canada
| | - Priscilla Swanson
- Infectious Disease Research, Abbott, Diagnostics, Abbott Park, IL, United States
| | - George J Dawson
- Infectious Disease Research, Abbott, Diagnostics, Abbott Park, IL, United States
| | - John Hackett
- Infectious Disease Research, Abbott, Diagnostics, Abbott Park, IL, United States
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Sallam M, Esbjörnsson J, Baldvinsdóttir G, Indriðason H, Björnsdóttir TB, Widell A, Gottfreðsson M, Löve A, Medstrand P. Molecular epidemiology of HIV-1 in Iceland: Early introductions, transmission dynamics and recent outbreaks among injection drug users. INFECTION GENETICS AND EVOLUTION 2017; 49:157-163. [DOI: 10.1016/j.meegid.2017.01.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 12/19/2016] [Accepted: 01/02/2017] [Indexed: 10/20/2022]
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Oster AM, Switzer WM, Hernandez AL, Saduvala N, Wertheim JO, Nwangwu-Ike N, Ocfemia MC, Campbell E, Hall HI. Increasing HIV-1 subtype diversity in seven states, United States, 2006-2013. Ann Epidemiol 2017; 27:244-251.e1. [PMID: 28318764 DOI: 10.1016/j.annepidem.2017.02.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 01/19/2017] [Accepted: 02/07/2017] [Indexed: 11/24/2022]
Abstract
PURPOSE The aim of the analysis was to explore HIV-1 subtype diversity in the United States and understand differences in prevalence of non-B subtypes and circulating recombinant forms (CRFs) between demographic/risk groups and over time. METHODS We included HIV-1 polymerase sequences reported to the National HIV Surveillance System for HIV infections diagnosed during 2006-2013 in seven states. We assigned subtype or CRF using the automated subtyping tool COMET, assessed subtype/CRF prevalence by demographic characteristics and country of birth, and determined changes in subtype/CRF by HIV diagnosis year. RESULTS Of 32,968 sequences, 30,757 (93.3%) were subtype B. The most common non-B subtypes and CRFs were C (1.6%), CRF02_AG (1.4%), A (0.6%), CRF01_AE (0.5%), and G (0.3%). Elevated percentages of non-B infections occurred among persons aged <13 years at diagnosis (40.9%), Asians (32.1%), persons born outside the United States (22.6%), and persons with infection attributable to heterosexual contact (12.0%-15.0%). Prevalence of non-B infections increased from 5.9% in 2006 to 8.5% in 2013. CONCLUSIONS Subtype B continues to predominate in the United States. However, the percentage of non-B infections has grown in recent years, and numerous demographic subgroups have much higher prevalence. Subgroups and areas with high prevalence of non-B infections might represent sub-epidemics meriting further investigation.
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Affiliation(s)
- Alexandra M Oster
- Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, GA.
| | - William M Switzer
- Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, GA
| | - Angela L Hernandez
- Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, GA
| | | | - Joel O Wertheim
- ICF International, Atlanta, GA; Department of Medicine, University of California, San Diego
| | - Ndidi Nwangwu-Ike
- Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, GA
| | - M Cheryl Ocfemia
- Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, GA
| | - Ellsworth Campbell
- Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, GA
| | - H Irene Hall
- Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, GA
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A Highly Conserved Residue in HIV-1 Nef Alpha Helix 2 Modulates Protein Expression. mSphere 2016; 1:mSphere00288-16. [PMID: 27840851 PMCID: PMC5103047 DOI: 10.1128/msphere.00288-16] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 10/21/2016] [Indexed: 01/22/2023] Open
Abstract
The HIV-1 Nef protein has been established as a key pathogenic determinant of HIV/AIDS, but there is little knowledge of how the extensive genetic diversity of HIV-1 affects Nef function. Upon compiling a set of subtype-specific reference strains, we identified a subtype C reference strain, C.BR92025, that contained natural polymorphisms at otherwise highly conserved residues 13, 84, and 92. Interestingly, strain C.BR92025 Nef displayed impaired Nef function and had decreased protein expression. We have demonstrated that strain C.BR92025 Nef has a higher rate of protein turnover than highly expressed Nef proteins and that this higher rate of protein turnover is due to an alanine-to-valine substitution at Nef residue 84. These findings highlight residue A84 as a major determinant of HIV-1 Nef expression. Extensive genetic diversity is a defining characteristic of human immunodeficiency virus type 1 (HIV-1) and poses a significant barrier to the development of an effective vaccine. To better understand the impact of this genetic diversity on the HIV-1 pathogenic factor Nef, we compiled a panel of reference strains from the NIH Los Alamos HIV Database. Initial sequence analysis identified point mutations at Nef residues 13, 84, and 92 in subtype C reference strain C.BR92025 from Brazil. Functional analysis revealed impaired major histocompatibility complex class I and CD4 downregulation of strain C.BR92025 Nef, which corresponded to decreased protein expression. Metabolic labeling demonstrated that strain C.BR92025 Nef has a greater rate of protein turnover than subtype B reference strain B.JRFL that, on the basis of mutational analysis, is related to Nef residue A84. An alanine-to-valine substitution at position 84, located in alpha helix 2 of Nef, was sufficient to alter the rate of turnover of an otherwise highly expressed Nef protein. In conclusion, these findings highlight HIV-1 Nef residue A84 as a major determinant of protein expression that may offer an additional avenue to disrupt or mediate the effects of this key HIV-1 pathogenic factor. IMPORTANCE The HIV-1 Nef protein has been established as a key pathogenic determinant of HIV/AIDS, but there is little knowledge of how the extensive genetic diversity of HIV-1 affects Nef function. Upon compiling a set of subtype-specific reference strains, we identified a subtype C reference strain, C.BR92025, that contained natural polymorphisms at otherwise highly conserved residues 13, 84, and 92. Interestingly, strain C.BR92025 Nef displayed impaired Nef function and had decreased protein expression. We have demonstrated that strain C.BR92025 Nef has a higher rate of protein turnover than highly expressed Nef proteins and that this higher rate of protein turnover is due to an alanine-to-valine substitution at Nef residue 84. These findings highlight residue A84 as a major determinant of HIV-1 Nef expression.
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Delaney KP, Hanson DL, Masciotra S, Ethridge SF, Wesolowski L, Owen SM. Time Until Emergence of HIV Test Reactivity Following Infection With HIV-1: Implications for Interpreting Test Results and Retesting After Exposure. Clin Infect Dis 2016; 64:53-59. [PMID: 27737954 DOI: 10.1093/cid/ciw666] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 09/16/2016] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Understanding the period of time between an exposure resulting in infection with human immunodeficiency virus (HIV) and when a test can reliably detect the presence of that infection, that is, the test window period, may benefit testing programs and clinicians in counseling patients about when the clinician and the patient can be confident a suspected exposure did not result in HIV infection. METHODS We evaluated the intervals between reactivity of the Aptima HIV-1 RNA test (Aptima) and 20 US Food and Drug Administration-approved HIV immunoassays using 222 longitudinally collected plasma specimens from HIV-1 seroconverters from the United States. Using interval-censored survival and binomial regression approaches a multi-model framework was implemented to estimate the relative emergence of test reactivity, referred to here as an inter-test reactivity interval (ITRI). We then combined ITRI results with simulated data for the eclipse period, the time between exposure and detection of HIV virus by Aptima, to estimate the window period for each test. RESULTS The estimated ITRIs were shorter with each new class of HIV tests, ranging from 5.9 to 24.8 days. The 99th percentiles of the window period probability distribution ranged from 44 days for laboratory screening tests that detect both antigen and antibody to 65 days for the Western blot test. CONCLUSIONS Our directly comparable estimates of the emergence of reactivity for 20 immunoassays are valuable to testing providers for interpreting negative HIV test results obtained shortly after exposure, and for counseling individuals on when to retest after an exposure.
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Affiliation(s)
| | | | | | | | | | - Sherry Michele Owen
- Office of the Director, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia
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Multiple introductions and onward transmission of non-pandemic HIV-1 subtype B strains in North America and Europe. Sci Rep 2016; 6:33971. [PMID: 27653834 PMCID: PMC5032033 DOI: 10.1038/srep33971] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 09/06/2016] [Indexed: 12/28/2022] Open
Abstract
Most HIV-1 subtype B infections in North America and Europe seem to have resulted from the expansion of a single pandemic lineage (BPANDEMIC) disseminated from the United States (US). Some non-pandemic subtype B strains of Caribbean origin (BCAR) may have also reached North America and Europe, but their epidemiological relevance in those regions remains largely unknown. Here we analyze a total of 20,045 HIV-1 subtype B pol sequences from the US, Canada, and Europe, to estimate the prevalence and to reconstruct the spatiotemporal dynamics of dissemination of HIV-1 BCAR strains in those regions. We find that BCAR strains were probably disseminated from the Caribbean into North America and Europe at multiple times since the early 1970s onwards. The BCAR strains reached the US, Canada and at least 16 different European countries, where they account for a very low fraction (<5%) of subtype B infections, with exception of the Czech Republic (7.7%). We also find evidence of the onward transmission of BCAR clades in the US, Canada, the Czech Republic, Germany, Italy, Spain and the UK, as well as short-distance spreading of BCAR lineages between neighboring European countries from Central and Western Europe, and long-distance dissemination between the US and Europe.
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Eybpoosh S, Bahrampour A, Karamouzian M, Azadmanesh K, Jahanbakhsh F, Mostafavi E, Zolala F, Haghdoost AA. Spatio-Temporal History of HIV-1 CRF35_AD in Afghanistan and Iran. PLoS One 2016; 11:e0156499. [PMID: 27280293 PMCID: PMC4900578 DOI: 10.1371/journal.pone.0156499] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 05/16/2016] [Indexed: 01/28/2023] Open
Abstract
HIV-1 Circulating Recombinant Form 35_AD (CRF35_AD) has an important position in the epidemiological profile of Afghanistan and Iran. Despite the presence of this clade in Afghanistan and Iran for over a decade, our understanding of its origin and dissemination patterns is limited. In this study, we performed a Bayesian phylogeographic analysis to reconstruct the spatio-temporal dispersion pattern of this clade using eligible CRF35_AD gag and pol sequences available in the Los Alamos HIV database (432 sequences available from Iran, 16 sequences available from Afghanistan, and a single CRF35_AD-like pol sequence available from USA). Bayesian Markov Chain Monte Carlo algorithm was implemented in BEAST v1.8.1. Between-country dispersion rates were tested with Bayesian stochastic search variable selection method and were considered significant where Bayes factor values were greater than three. The findings suggested that CRF35_AD sequences were genetically similar to parental sequences from Kenya and Uganda, and to a set of subtype A1 sequences available from Afghan refugees living in Pakistan. Our results also showed that across all phylogenies, Afghan and Iranian CRF35_AD sequences formed a monophyletic cluster (posterior clade credibility> 0.7). The divergence date of this cluster was estimated to be between 1990 and 1992. Within this cluster, a bidirectional dispersion of the virus was observed across Afghanistan and Iran. We could not clearly identify if Afghanistan or Iran first established or received this epidemic, as the root location of this cluster could not be robustly estimated. Three CRF35_AD sequences from Afghan refugees living in Pakistan nested among Afghan and Iranian CRF35_AD branches. However, the CRF35_AD-like sequence available from USA diverged independently from Kenyan subtype A1 sequences, suggesting it not to be a true CRF35_AD lineage. Potential factors contributing to viral exchange between Afghanistan and Iran could be injection drug networks and mass migration of Afghan refugees and labours to Iran, which calls for extensive preventive efforts.
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Affiliation(s)
- Sana Eybpoosh
- Regional Knowledge Hub, and WHO Collaborating Centre for HIV Surveillance, Institute for Futures Studies in Health, Kerman University of Medical Sciences, Kerman, Iran
| | - Abbas Bahrampour
- Modeling in Health Research Centre, Institute for Futures Studies in Health, Kerman University of Medical Sciences, Kerman, Iran
| | - Mohammad Karamouzian
- Regional Knowledge Hub, and WHO Collaborating Centre for HIV Surveillance, Institute for Futures Studies in Health, Kerman University of Medical Sciences, Kerman, Iran
- School of Population and Public Health, Faculty of Medicine, University of British Colombia, Vancouver, BC, Canada
| | | | | | - Ehsan Mostafavi
- Epidemiology Department, Pasteur Institute of Iran, Tehran, Iran
- Emerging and Reemerging Infectious Diseases Research Centre, Pasteur Institute of Iran, Akanlu, Kabudar Ahang, Hamadan, Iran
| | - Farzaneh Zolala
- Modeling in Health Research Centre, Institute for Futures Studies in Health, Kerman University of Medical Sciences, Kerman, Iran
| | - Ali Akbar Haghdoost
- Regional Knowledge Hub, and WHO Collaborating Centre for HIV Surveillance, Institute for Futures Studies in Health, Kerman University of Medical Sciences, Kerman, Iran
- * E-mail:
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Delatorre E, de Azevedo SSD, Rodrigues-Pedro A, Velasco-de-Castro CA, Couto-Fernandez JC, Pilotto JH, Morgado MG. Tracing the origin of a singular HIV-1 CRF45_cpx clade identified in Brazil. INFECTION GENETICS AND EVOLUTION 2016; 46:223-232. [PMID: 27259365 DOI: 10.1016/j.meegid.2016.05.040] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Revised: 05/26/2016] [Accepted: 05/30/2016] [Indexed: 01/10/2023]
Abstract
The HIV-1 epidemiology has changed over the past decade toward a marked increase in the circulation of strains previously restricted to local epidemics. Recent molecular epidemiological surveys identified some HIV-1 strains of probable African origin circulating in Brazil, including the Circulating Recombinant Form (CRF) 45_cpx, a complex A1/K/U recombinant that circulates in Central Africa. Here, we characterize partial genomic sequences and reconstruct the evolutionary history of HIV-1 CRF45_cpx-related recombinant samples identified in independent studies carried out with HIV+ individuals in Brazil. The sequences were obtained by overlapping PCR amplifications followed by direct sequencing. Recombination profiles were determined by phylogenetic and bootscaning analyses. The evolutionary history was estimated by a Bayesian coalescent-based method using datasets representing the gag, pol and env gene fragments. Six of the 10 samples isolated in Rio de Janeiro showed a CRF45_cpx-like pattern throughout the sequenced genome. The remaining were classified as second-generation recombinants, showing the mosaic patterns: CRF45_cpx/B/D/F1/U, CRF45_cpx/B/F1/U, CRF45_cpx/B/U and CRF45_cpx/F1. All Brazilian CRF45_cpx sequences, except one, formed a monophyletic clade (CRF45-BR), which seems to be the result of a single introduction event that has spread to the Rio de Janeiro, São Paulo and Minas Gerais states and is related to sequences from Argentina, Italy and Belgium. The Bayesian analyses pointed out quite consistent onset dates for CRF45-BR clade (~1984: 1976-1996) in the three gene datasets. These results indicate that the CRF45-BR clade has been circulating in the Southeastern Brazilian region for about 30years, although its presence was not detected until recently due to its very low prevalence. This reinforces the relevance of large-scale molecular surveillance data to identify the emergence of new HIV variants and their impact on local epidemics.
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Affiliation(s)
- Edson Delatorre
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil.
| | - Suwellen S D de Azevedo
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Adriana Rodrigues-Pedro
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Carlos Augusto Velasco-de-Castro
- Laboratório de Virologia, Departamento de Patologia Clínica, Instituto Nacional de Saúde da Mulher, da Criança e do Adolescente Fernandes Figueira, FIOCRUZ, Rio de Janeiro, Brazil
| | | | - Jose H Pilotto
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil; Hospital Geral de Nova Iguaçu, Rio de Janeiro, Brazil
| | - Mariza G Morgado
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
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Wertheim JO, Oster AM, Hernandez AL, Saduvala N, Bañez Ocfemia MC, Hall HI. The International Dimension of the U.S. HIV Transmission Network and Onward Transmission of HIV Recently Imported into the United States. AIDS Res Hum Retroviruses 2016; 32:1046-1053. [PMID: 27105549 DOI: 10.1089/aid.2015.0272] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The majority of HIV infections in the United States can be traced back to a single introduction in late 1960s or early 1970s. However, it remains unclear whether subsequent introductions of HIV into the United States have given rise to onward transmission. Genetic transmission networks can aid in understanding HIV transmission. We constructed a genetic distance-based transmission network using HIV-1 pol sequences reported to the U.S. National HIV Surveillance System (n = 41,539) and all publicly available non-U.S. HIV-1 pol sequences (n = 86,215). Of the 13,145 U.S. persons clustered in the network, 457 (3.5%) were genetically linked to a potential transmission partner outside the United States. For internationally connected persons residing in but born outside the United States, 61% had a connection to their country of birth or to another country that shared a language with their country of birth. Bayesian molecular clock phylogenetic analyses indicate that introduced nonsubtype B infections have resulted in onward transmission within the United States.
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Affiliation(s)
- Joel O. Wertheim
- Department of Medicine, University of California, San Diego, San Diego, California
- ICF International, Atlanta, Georgia
| | - Alexandra M. Oster
- Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Angela L. Hernandez
- Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia
| | | | - M. Cheryl Bañez Ocfemia
- Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - H. Irene Hall
- Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia
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Mir D, Jung M, Delatorre E, Vidal N, Peeters M, Bello G. Phylodynamics of the major HIV-1 CRF02_AG African lineages and its global dissemination. INFECTION GENETICS AND EVOLUTION 2016; 46:190-199. [PMID: 27180893 DOI: 10.1016/j.meegid.2016.05.017] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 05/09/2016] [Accepted: 05/11/2016] [Indexed: 12/16/2022]
Abstract
The HIV-1 CRF02_AG clade is the most prevalent HIV variant in West and West-Central Africa and its detection outside Africa is increasingly common. Little is known, however, about the number and phylodynamics of major CRF02_AG lineages circulating worldwide. To this end, a total of 3170 HIV-1 CRF02_AG-like pol sequences isolated around the world, over a period of 25years (1989 to 2013), were analyzed using Maximum Likelihood and Bayesian coalescent-based methods. Our results suggest that most of the current CRF02_AG diversity comes from the dissemination of a few founder strains out of Central Africa into West Africa and Cameroon between the late 1960s and the middle 1980s. The CRF02_AG strain introduced into West Africa established a large regional epidemic with low phylogeographic structure. This strain was also successfully disseminated out of the West African region and originated at least three large secondary outbreaks in Cameroon at around the late 1970s, in the former Soviet Union (FSU) countries at around the late 1990s, and in Bulgaria/Germany at around the early 2000s. The CRF02_AG African lineages introduced into Cameroon remained mostly restricted to this country and its neighbors. Demographic reconstructions indicate that major CRF02_AG clades circulating in Africa exhibited a decline in growth rate since the middle 1980s/1990s, whereas CRF02_AG clades in Europe and the FSU countries continue to grow exponentially until the middle to late 2000s. Substantial differences in the median estimated growth rate of the same CRF02_AG clade circulating in different regions (0.63-2.00year-1), and of different CRF02_AG clades circulating in the same country (0.41-0.75year-1) were observed. Thus, the cause of the epidemic outcome of the different HIV-1 CRF02_AG lineages is probably multifactorial.
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Affiliation(s)
- Daiana Mir
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Matthieu Jung
- Unité Mixte Internationale 233, Institut de Recherche pour le Développement, INSERM U1175, and Université Montpellier, Montpellier, France; Institut de Biologie Computationnelle, LIRMM, UMR 5506 CNRS - Université Montpellier, Montpellier, France
| | - Edson Delatorre
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Nicole Vidal
- Unité Mixte Internationale 233, Institut de Recherche pour le Développement, INSERM U1175, and Université Montpellier, Montpellier, France
| | - Martine Peeters
- Unité Mixte Internationale 233, Institut de Recherche pour le Développement, INSERM U1175, and Université Montpellier, Montpellier, France; Institut de Biologie Computationnelle, LIRMM, UMR 5506 CNRS - Université Montpellier, Montpellier, France
| | - Gonzalo Bello
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil.
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De Luca A, Flandre P, Dunn D, Zazzi M, Wensing A, Santoro MM, Günthard HF, Wittkop L, Kordossis T, Garcia F, Castagna A, Cozzi-Lepri A, Churchill D, De Wit S, Brockmeyer NH, Imaz A, Mussini C, Obel N, Perno CF, Roca B, Reiss P, Schülter E, Torti C, van Sighem A, Zangerle R, Descamps D. Improved darunavir genotypic mutation score predicting treatment response for patients infected with HIV-1 subtype B and non-subtype B receiving a salvage regimen. J Antimicrob Chemother 2016; 71:1352-60. [PMID: 26825119 PMCID: PMC5808835 DOI: 10.1093/jac/dkv465] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 12/03/2015] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES The objective of this study was to improve the prediction of the impact of HIV-1 protease mutations in different viral subtypes on virological response to darunavir. METHODS Darunavir-containing treatment change episodes (TCEs) in patients previously failing PIs were selected from large European databases. HIV-1 subtype B-infected patients were used as the derivation dataset and HIV-1 non-B-infected patients were used as the validation dataset. The adjusted association of each mutation with week 8 HIV RNA change from baseline was analysed by linear regression. A prediction model was derived based on best subset least squares estimation with mutational weights corresponding to regression coefficients. Virological outcome prediction accuracy was compared with that from existing genotypic resistance interpretation systems (GISs) (ANRS 2013, Rega 9.1.0 and HIVdb 7.0). RESULTS TCEs were selected from 681 subtype B-infected and 199 non-B-infected adults. Accompanying drugs were NRTIs in 87%, NNRTIs in 27% and raltegravir or maraviroc or enfuvirtide in 53%. The prediction model included weighted protease mutations, HIV RNA, CD4 and activity of accompanying drugs. The model's association with week 8 HIV RNA change in the subtype B (derivation) set was R(2) = 0.47 [average squared error (ASE) = 0.67, P < 10(-6)]; in the non-B (validation) set, ASE was 0.91. Accuracy investigated by means of area under the receiver operating characteristic curves with a binary response (above the threshold value of HIV RNA reduction) showed that our final model outperformed models with existing interpretation systems in both training and validation sets. CONCLUSIONS A model with a new darunavir-weighted mutation score outperformed existing GISs in both B and non-B subtypes in predicting virological response to darunavir.
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Affiliation(s)
- Andrea De Luca
- Division of Infectious Diseases, Siena University Hospital, Siena, Italy Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | | | - David Dunn
- MRC Clinical Trials Unit at University College London, London, UK
| | - Maurizio Zazzi
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | | | | | - Huldrych F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Switzerland and Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Linda Wittkop
- Inserm U897, ISPED, Université de Bordeaux, CHU Bordeaux, France/Cohere in Eurocoord RCC, Bordeaux, France
| | | | | | | | | | - Duncan Churchill
- Brighton and Sussex University Hospitals NHS Trust, Brighton, UK
| | | | - Norbert H Brockmeyer
- Department of Dermatology and Venereology, Center for Sexual Health and Medicine, Ruhr University Bochum, Bochum, Germany and Competence Network for HIV/AIDS, Ruhr University Bochum, Bochum, Germany
| | - Arkaitz Imaz
- Bellvitge University Hospital, Barcelona, Catalonia, Spain
| | | | - Niels Obel
- Copenhagen University Hospital, Copenhagen, Denmark
| | | | | | - Peter Reiss
- Stichting HIV Monitoring, Amsterdam, The Netherlands, and Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands/Cohere in Eurocoord RCC, Copenhagen, Denmark
| | | | | | | | - Robert Zangerle
- Universitätsklinik für Dermatologie und Venerologie, Innsbruck, Austria
| | - Diane Descamps
- AP-HP, Hôpital Bichat-Claude Bernard, Laboratoire de Virologie, IAME, UMR_1137, INSERM, Univ Paris Diderot, Sorbonne Paris Cité, Paris, France
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A Pan-HIV Strategy for Complete Genome Sequencing. J Clin Microbiol 2015; 54:868-82. [PMID: 26699702 DOI: 10.1128/jcm.02479-15] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 12/16/2015] [Indexed: 01/23/2023] Open
Abstract
Molecular surveillance is essential to monitor HIV diversity and track emerging strains. We have developed a universal library preparation method (HIV-SMART [i.e.,switchingmechanismat 5' end ofRNAtranscript]) for next-generation sequencing that harnesses the specificity of HIV-directed priming to enable full genome characterization of all HIV-1 groups (M, N, O, and P) and HIV-2. Broad application of the HIV-SMART approach was demonstrated using a panel of diverse cell-cultured virus isolates. HIV-1 non-subtype B-infected clinical specimens from Cameroon were then used to optimize the protocol to sequence directly from plasma. When multiplexing 8 or more libraries per MiSeq run, full genome coverage at a median ∼2,000× depth was routinely obtained for either sample type. The method reproducibly generated the same consensus sequence, consistently identified viral sequence heterogeneity present in specimens, and at viral loads of ≤4.5 log copies/ml yielded sufficient coverage to permit strain classification. HIV-SMART provides an unparalleled opportunity to identify diverse HIV strains in patient specimens and to determine phylogenetic classification based on the entire viral genome. Easily adapted to sequence any RNA virus, this technology illustrates the utility of next-generation sequencing (NGS) for viral characterization and surveillance.
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Ragonnet-Cronin M, Lycett SJ, Hodcroft EB, Hué S, Fearnhill E, Brown AE, Delpech V, Dunn D, Leigh Brown AJ. Transmission of Non-B HIV Subtypes in the United Kingdom Is Increasingly Driven by Large Non-Heterosexual Transmission Clusters. J Infect Dis 2015; 213:1410-8. [PMID: 26704616 PMCID: PMC4813743 DOI: 10.1093/infdis/jiv758] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 12/10/2015] [Indexed: 12/02/2022] Open
Abstract
Background. The United Kingdom human immunodeficiency virus (HIV) epidemic was historically dominated by HIV subtype B transmission among men who have sex with men (MSM). Now 50% of diagnoses and prevalent infections are among heterosexual individuals and mainly involve non-B subtypes. Between 2002 and 2010, the prevalence of non-B diagnoses among MSM increased from 5.4% to 17%, and this study focused on the drivers of this change. Methods. Growth between 2007 and 2009 in transmission clusters among 14 000 subtype A1, C, D, and G sequences from the United Kingdom HIV Drug Resistance Database was analysed by risk group. Results. Of 1148 clusters containing at least 2 sequences in 2007, >75% were pairs and >90% were heterosexual. Most clusters (71.4%) did not grow during the study period. Growth was significantly lower for small clusters and higher for clusters of ≥7 sequences, with the highest growth observed for clusters comprising sequences from MSM and people who inject drugs (PWID). Risk group (P < .0001), cluster size (P < .0001), and subtype (P < .01) were predictive of growth in a generalized linear model. Discussion. Despite the increase in non-B subtypes associated with heterosexual transmission, MSM and PWID are at risk for non-B infections. Crossover of subtype C from heterosexuals to MSM has led to the expansion of this subtype within the United Kingdom.
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Affiliation(s)
| | | | | | | | | | | | | | - David Dunn
- MRC Clinical Trials Unit at University College London
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Luk KC, Berg MG, Naccache SN, Kabre B, Federman S, Mbanya D, Kaptué L, Chiu CY, Brennan CA, Hackett J. Utility of Metagenomic Next-Generation Sequencing for Characterization of HIV and Human Pegivirus Diversity. PLoS One 2015; 10:e0141723. [PMID: 26599538 PMCID: PMC4658132 DOI: 10.1371/journal.pone.0141723] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 10/12/2015] [Indexed: 02/06/2023] Open
Abstract
Given the dynamic changes in HIV-1 complexity and diversity, next-generation sequencing (NGS) has the potential to revolutionize strategies for effective HIV global surveillance. In this study, we explore the utility of metagenomic NGS to characterize divergent strains of HIV-1 and to simultaneously screen for other co-infecting viruses. Thirty-five HIV-1-infected Cameroonian blood donor specimens with viral loads of >4.4 log10 copies/ml were selected to include a diverse representation of group M strains. Random-primed NGS libraries, prepared from plasma specimens, resulted in greater than 90% genome coverage for 88% of specimens. Correct subtype designations based on NGS were concordant with sub-region PCR data in 31 of 35 (89%) cases. Complete genomes were assembled for 25 strains, including circulating recombinant forms with relatively limited data available (7 CRF11_cpx, 2 CRF13_cpx, 1 CRF18_cpx, and 1 CRF37_cpx), as well as 9 unique recombinant forms. HPgV (formerly designated GBV-C) co-infection was detected in 9 of 35 (25%) specimens, of which eight specimens yielded complete genomes. The recovered HPgV genomes formed a diverse cluster with genotype 1 sequences previously reported from Ghana, Uganda, and Japan. The extensive genome coverage obtained by NGS improved accuracy and confidence in phylogenetic classification of the HIV-1 strains present in the study population relative to conventional sub-region PCR. In addition, these data demonstrate the potential for metagenomic analysis to be used for routine characterization of HIV-1 and identification of other viral co-infections.
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Affiliation(s)
- Ka-Cheung Luk
- Abbott Diagnostics, Infectious Disease Research, Abbott Park, Illinois, United States of America
| | - Michael G Berg
- Abbott Diagnostics, Infectious Disease Research, Abbott Park, Illinois, United States of America
| | - Samia N Naccache
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, United States of America
| | - Beniwende Kabre
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, United States of America
| | - Scot Federman
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, United States of America
| | | | | | - Charles Y Chiu
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, United States of America.,Department of Medicine, Division of Infectious Diseases, University of California San Francisco, San Francisco, California, United States of America
| | - Catherine A Brennan
- Abbott Diagnostics, Infectious Disease Research, Abbott Park, Illinois, United States of America
| | - John Hackett
- Abbott Diagnostics, Infectious Disease Research, Abbott Park, Illinois, United States of America
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Germer JJ, Wu P, Soderberg JD, Mandrekar JN, Yao JD. HIV-1 subtype diversity among clinical specimens submitted for routine antiviral drug resistance testing in the United States. Diagn Microbiol Infect Dis 2015; 83:257-60. [PMID: 26302855 DOI: 10.1016/j.diagmicrobio.2015.07.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 07/14/2015] [Accepted: 07/20/2015] [Indexed: 11/24/2022]
Abstract
Diversity of human immunodeficiency virus type 1 (HIV-1) has important implications for the diagnosis, treatment, and management of HIV-1-infected individuals. HIV-1 pol sequences from 3895 clinical plasma specimens collected in the United States over a 1-year period and submitted for routine HIV-1 genotypic drug resistance testing were retrospectively analyzed for HIV-1 subtype. Of these 3895 HIV-1 sequences, 207 (5.31%) were determined to be non-B subtypes (including recombinant forms). Among individual states, the percentage of non-B subtypes ranged from 0% (12 states) to 28.57% in South Dakota, with 7 states having percentages of >10%. All 4 states with the highest percentages of non-B subtypes were located within the US West North Central region: Minnesota, 11.82%; Iowa, 15.38%; North Dakota, 25.00%; and South Dakota, 28.57%. Reasons for the unexpectedly wide diversity of HIV-1 subtypes present in multiple states located in the West North Central region of the United States remain to be determined.
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Affiliation(s)
- Jeffrey J Germer
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Puqiang Wu
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Jason D Soderberg
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Jayawant N Mandrekar
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Joseph D Yao
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.
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36
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Neogi U, Häggblom A, Santacatterina M, Bratt G, Gisslén M, Albert J, Sonnerborg A. Temporal trends in the Swedish HIV-1 epidemic: increase in non-B subtypes and recombinant forms over three decades. PLoS One 2014; 9:e99390. [PMID: 24922326 PMCID: PMC4055746 DOI: 10.1371/journal.pone.0099390] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Accepted: 05/13/2014] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND HIV-1 subtype B (HIV-1B) still dominates in resource-rich countries but increased migration contributes to changes in the global subtype distribution. Also, spread of non-B subtypes within such countries occurs. The trend of the subtype distribution from the beginning of the epidemic in the country has earlier not been reported in detail. Thus the primary objective of this study is to describe the temporal trend of the subtype distribution from the beginning of the HIV-1 epidemic in Sweden over three decades. METHODS HIV-1 pol sequences from patients (n = 3967) diagnosed in Sweden 1983-2012, corresponding to >40% of patients ever diagnosed, were re-subtyped using several automated bioinformatics tools. The temporal trends of subtypes and recombinants during three decades were described by a multinomial logistic regression model. RESULTS All eleven group M HIV-1 subtypes and sub-subtypes (78%), 17 circulating recombinant forms (CRFs) (19%) and 32 unique recombinants forms (URF) (3%) were identified. When all patients were analysed, there was an increase of newly diagnosed HIV-1C (RR, 95%CI: 1.10, 1.06-1.14), recombinants (1.20, 1.17-1.24) and other pure subtypes (1.11, 1.07-1.16) over time compared to HIV-1B. The same pattern was found when all patients infected in Sweden (n = 1165) were analysed. Also, for MSM patients infected in Sweden (n = 921), recombinant forms and other pure subtypes increased. SIGNIFICANCE Sweden exhibits one of the most diverse subtype epidemics outside Africa. The increase of non-B subtypes is due to migration and to a spread among heterosexually infected patients and MSM within the country. This viral heterogeneity may become a hotspot for development of more diverse and complex recombinant forms if the epidemics converge.
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Affiliation(s)
- Ujjwal Neogi
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
- * E-mail:
| | - Amanda Häggblom
- Unit of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
- Department of Infectious Diseases, County Council of Gävleborg, Gävle, Sweden
| | - Michele Santacatterina
- Unit of Biostatistics, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Göran Bratt
- Department of Clinical Science and Education, Venhälsan, Stockholm South General Hospital, Stockholm, Sweden
| | - Magnus Gisslén
- Department of Infectious Diseases, University of Gothenburg, Gothenburg, Sweden
| | - Jan Albert
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Anders Sonnerborg
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
- Unit of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
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Chan PA, Reitsma MB, DeLong A, Boucek B, Nunn A, Salemi M, Kantor R. Phylogenetic and geospatial evaluation of HIV-1 subtype diversity at the largest HIV center in Rhode Island. INFECTION GENETICS AND EVOLUTION 2014; 28:358-66. [PMID: 24721515 DOI: 10.1016/j.meegid.2014.03.027] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Revised: 03/17/2014] [Accepted: 03/24/2014] [Indexed: 12/01/2022]
Abstract
Individuals infected with HIV-1 non-B subtypes are understudied in the United States. Their characterization may augment prevention and treatment interventions. We examined the regional molecular epidemiology of non-B subtypes using a combined phylogenetic and geospatial approach. HIV-1 pol sequences and clinical data obtained for routine clinical care were aggregated from 2004 to 2011 at the largest HIV center in Rhode Island. Subtyping was performed by neighbor-joining and maximum-likelihood phylogeny and compared across eight commonly used tools (HIVdb, REGA, RIP, NCBI, Geno2Pheno, EuResist, jpHMM and STAR) using proportional odds ordinal regression. Individuals with non-B subtypes were characterized according to demographics and risk factors for infection, intra-subtype clustering by maximum-likelihood phylogeny, and geospatial hotspot analysis using Getis-Ord Gi(∗) statistics. Of 1277 unique sequences, phylogenetic subtyping demonstrated 8.3% (N=106, 95% CI 6.8-10%) non-B subtypes and circulating recombinant forms (CRFs): CRF02_AG=46; A=15; C=15; CRF01_AE=6; CRF06_CPX=5; CRF14_BG=5; G=3; CRF43_02G=3; D=3; CRF24_BG=3; CRF11_CPX=1; F1=1. Compared to phylogeny, Geno2Pheno was the most concordant (86% exact match) followed by REGA (85%), EuResist (85%) and STAR (82%). Of 106 individuals with non-B subtypes, 50% were male, 71% acquired infection through heterosexual transmission; 76%, were born in Africa, 6% Southeast Asia, 5% the United States, 3% Central America, 1% Europe, and 9% unknown. Eighty percent of CRF02_AG, 93% of A and 87% of C sequences were from African-born individuals. Twenty-two percent of non-B subtypes formed transmission clusters, including a significant number of younger individuals with perinatally-acquired infection. Geospatial analyses revealed hotspots of B and non-B subtypes in the state capital with a more concentrated focus among non-B subtypes. Molecular examination of regional HIV diversity revealed a larger than expected non-subtype B infected population, mostly born in Africa, with low ongoing regional transmission. Phylogenetic and geospatial characterization of infection clusters is helpful to identify targets for treatment and prevention interventions.
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Affiliation(s)
- Philip A Chan
- Division of Infectious Diseases, Department of Medicine, Alpert Medical School of Brown University, Providence, RI, USA.
| | - Marissa B Reitsma
- Division of Infectious Diseases, Department of Medicine, Alpert Medical School of Brown University, Providence, RI, USA
| | - Allison DeLong
- Center for Statistical Sciences, Brown University, Providence, RI, USA
| | | | - Amy Nunn
- Division of Infectious Diseases, Department of Medicine, Alpert Medical School of Brown University, Providence, RI, USA
| | - Marco Salemi
- Department of Pathology, University of Florida, Gainesville, FL, USA
| | - Rami Kantor
- Division of Infectious Diseases, Department of Medicine, Alpert Medical School of Brown University, Providence, RI, USA
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