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Rashid A, Kang L, Yi F, Getaneh Y, Chu Q, Shah SA, Abidi SH, Shao Y. Identification of a novel first-generation HIV-1 circulating recombinant form (CRF152_DG) among people living with HIV in Karachi, Pakistan. Microbiol Spectr 2024; 12:e0052924. [PMID: 38771033 PMCID: PMC11218485 DOI: 10.1128/spectrum.00529-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 04/18/2024] [Indexed: 05/22/2024] Open
Abstract
The objective of this study was to characterize a novel circulating recombinant form of human immunodeficiency virus type 1 (HIV-1) among people living with HIV in Karachi, Pakistan. We conducted near-full-length genome (NFLG) sequencing on eight samples exhibiting D/G recombination signals in the pol gene region. We successfully obtained NFLG sequences (790-9,614; with reference to the HXB2 genome) from four of the eight samples and then conducted phylogenetic and recombination analyses on them. The four NFLG sequences from our study and one DG unique recombinant form previously identified in the United Kingdom (GenBank accession: MF109700) formed a distinct monophyletic cluster with an Shimodaira-Hasegawa approximate likelihood ratio test node support value of 100%. Bootscan analyses of the five NFLG sequences of DG recombinants showed that all five NFLGs shared the same unique mosaic pattern of recombination breakpoints between D and G clades, with two D fragments in the pol and vif regions inserted into a G backbone. Subregion phylogenetic analyses confirmed these sequences to be a novel circulating recombinant form (CRF) composed of subtypes D and G. The DG recombinant sequences were eventually designated as CRF152_DG by the Los Alamos HIV Sequence Database staff. IMPORTANCE In Pakistan, the genetic diversity of human immunodeficiency virus type 1 (HIV-1) is becoming increasingly complex, compared to the early years of the epidemic that started after the detection of the first cases of HIV-1 in 1987 in Karachi. Based on the available molecular studies, two dominant HIV-1 clades, sub-subtype A1 and CRF02_AG, have been found to co-circulate with other clades, namely B, C, D, G, CRF01_AE, CRF35_A1D, and CRF56_cpx, in various urban areas of Pakistan. Several novel recombinant forms have also been detected. This first report of CRF152_DG highlights the complex nature of the HIV epidemic in Pakistan and emphasizes the importance of continual molecular surveillance (ideally based on whole-genome sequences) of HIV.
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Affiliation(s)
- Abdur Rashid
- School of Medicine, Nankai University, Tianjin, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Li Kang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing, China
- College of Life Sciences, Nankai University, Tianjin, China
| | - Feng Yi
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yimam Getaneh
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Qingfei Chu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing, China
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | | | - Syed Hani Abidi
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi, Pakistan
- Department of Biomedical Sciences, School of Medicine, Nazarbayev University, Astana, Kazakhstan
| | - Yiming Shao
- School of Medicine, Nankai University, Tianjin, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing, China
- College of Life Sciences, Nankai University, Tianjin, China
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Changping Laboratory, Beijing, China
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Choy CY, Wong CS, Kumar PA, Olszyna DP, Teh YE, Chien MFJ, Kurup A, Koh YL, Ho LP, Law HL, Chua NGS, Yong HYJ, Archuleta S. Recommendations for the use of antiretroviral therapy in adults living with human immunodeficiency virus in Singapore. Singapore Med J 2024; 65:259-273. [PMID: 35366662 PMCID: PMC11182460 DOI: 10.11622/smedj.2021174] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 07/06/2021] [Indexed: 11/18/2022]
Abstract
ABSTRACT Since the advent of combination antiretroviral therapy (ART), the mortality attributable to human immunodeficiency virus (HIV) infection has decreased by 80%. Newer antiretroviral agents are highly efficacious, have minimal side effects as compared to older drugs, and can be formulated as combination tablets to reduce patients' pill burden. Despite these advances, 680,000 people worldwide died of acquired immunodeficiency syndrome-related illnesses in 2020. The National ART and Monitoring Recommendations by the National HIV Programme have been created to guide physicians on the prescribing of ART based on the patients' needs. These recommendations are based on international guidelines and tailored to the local context and unique domestic considerations. We hoped that with the publication of these recommendations, the care of people living with HIV can be enhanced, bringing us closer to ending HIV in our lifetime.
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Affiliation(s)
- Chiaw Yee Choy
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore
- National Centre for Infectious Diseases, Singapore
| | - Chen Seong Wong
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore
- National Centre for Infectious Diseases, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - P Arun Kumar
- National Centre for Infectious Diseases, Singapore
| | - Dariusz Piotr Olszyna
- Division of Infectious Diseases, University Medicine Cluster, National University Hospital, Singapore
| | - Yii Ean Teh
- Department of Infectious Diseases, Singapore General Hospital, Singapore
| | | | - Asok Kurup
- Infectious Diseases Care Pte Ltd, Mount Elizabeth Medical Centre, Singapore
| | - Yin Ling Koh
- The Novena Medical Specialists, Mount Elizabeth Novena Specialist Centre, Singapore
| | - Lai Peng Ho
- Department of Care and Counselling, Tan Tock Seng Hospital, Singapore
| | - Hwa Lin Law
- Department of Pharmacy, Tan Tock Seng Hospital, Singapore
| | | | | | - Sophia Archuleta
- National Centre for Infectious Diseases, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Division of Infectious Diseases, University Medicine Cluster, National University Hospital, Singapore
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Lopez-Rios J, Frasca T, Kindlon MJ, Exner TM, Norcini Pala A, Wainberg ML, Calderon Y, Cotroneo R, Jiménez AA, Remien RH. Limited Knowledge and Lack of Screening for Acute HIV Infection at Primary Care Clinics in High-Prevalence Communities of New York City. AIDS Behav 2019; 23:2870-2878. [PMID: 31054030 DOI: 10.1007/s10461-019-02527-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Diagnosis and treatment of acute HIV infection (AHI) is crucial for ending the HIV epidemic. Individuals with AHI, who have high viral loads and often are unaware of their infection, are more likely to transmit HIV to others than those with chronic infection. In preparation for an educational intervention on AHI in primary health care settings in high HIV-prevalence areas of New York City, 22 clinic directors, 313 clinic providers, and 220 patients were surveyed on their knowledge and awareness of the topic from 2012-2015. Basic HIV knowledge was high among all groups while knowledge of AHI was partial among providers and virtually absent among patients. Inadequate knowledge about this crucial phase of HIV may be impeding timely identification of cases in the primary care setting.
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Affiliation(s)
- Javier Lopez-Rios
- HIV Center for Clinical & Behavioral Studies, New York State Psychiatric Institute/Columbia University, 1051 Riverside Drive, Unit 15, New York, NY, 10032, USA.
| | - Timothy Frasca
- HIV Center for Clinical & Behavioral Studies, New York State Psychiatric Institute/Columbia University, 1051 Riverside Drive, Unit 15, New York, NY, 10032, USA
| | - Marcia J Kindlon
- New York State Department of Health, AIDS Institute, Albany, NY, USA
| | - Theresa M Exner
- HIV Center for Clinical & Behavioral Studies, New York State Psychiatric Institute/Columbia University, 1051 Riverside Drive, Unit 15, New York, NY, 10032, USA
| | - Andrea Norcini Pala
- HIV Center for Clinical & Behavioral Studies, New York State Psychiatric Institute/Columbia University, 1051 Riverside Drive, Unit 15, New York, NY, 10032, USA
| | - Milton L Wainberg
- HIV Center for Clinical & Behavioral Studies, New York State Psychiatric Institute/Columbia University, 1051 Riverside Drive, Unit 15, New York, NY, 10032, USA
| | - Yvette Calderon
- Department of Emergency Medicine, Icahn School of Medicine, Mount Sinai Beth Israel, New York, NY, USA
| | - Richard Cotroneo
- New York State Department of Health, AIDS Institute, Albany, NY, USA
| | | | - Robert H Remien
- HIV Center for Clinical & Behavioral Studies, New York State Psychiatric Institute/Columbia University, 1051 Riverside Drive, Unit 15, New York, NY, 10032, USA
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4
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Dai D, Shang H, Han XX, Zhao B, Liu J, Ding HB, Xu JJ, Chu ZX. The biological characteristics of predominant strains of HIV-1 genotype: modeling of HIV-1 infection among men who have sex with men. J Med Virol 2015; 87:557-68. [PMID: 25655808 DOI: 10.1002/jmv.24116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/16/2014] [Indexed: 12/29/2022]
Abstract
To investigate the molecular subtypes of prevalent HIV-1 strains and characterize the genetics of dominant strains among men who have sex with men. Molecular epidemiology surveys in this study concentrated on the prevalent HIV-1 strains in Liaoning province by year. 229 adult patients infected with HIV-1 and part of a high-risk group of men who have sex with men were recruited. Reverse transcription and nested PCR amplification were performed. Sequencing reactions were conducted and edited, followed by codon-based alignment. NJ phylogenetic tree analyses detected two distinct CRF01_AE phylogenetic clusters, designated clusters 1 and 2. Clusters 1 and 2 accounted for 12.8% and 84.2% of sequences in the pol gene and 17.6% and 73.1% of sequences in the env gene, respectively. Another six samples were distributed on other phylogenetic clusters. Cluster 1 increased significantly from 5.6% to 20.0%, but cluster 2 decreased from 87.5% to 80.0%. Genetic distance analysis indicated that CRF01_AE cluster 1 in Liaoning was homologous to epidemic CRF01_AE strains, but CRF01_AE cluster 2 was different from other scattered strains. Additionally, significant differences were found in tetra-peptide motifs at the tip of V3 loop between cluster 1 and 2; however, differences in coreceptor usage were not detected. This study shows that subtype CRF01_AE strain may be the most prevalent epidemic strain in the men who have sex with men. Genetic characteristics of the subtype CRF01_AE cluster strain in Liaoning showed homology to the prevalent strains of men who have sex with men in other parts of China.
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Affiliation(s)
- Di Dai
- Key Laboratory of AIDS Immunology of National Health and Family Planning Commission, Department of Laboratory Medicine, The First Affiliated Hospital, China Medical University, Shenyang, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
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Chook JB, Ong LY, Takebe Y, Chan KG, Choo M, Kamarulzaman A, Tee KK. Molecular detection of HIV-1 subtype B, CRF01_AE, CRF33_01B, and newly emerging recombinant lineages in Malaysia. Am J Trop Med Hyg 2014; 92:507-512. [PMID: 25535315 PMCID: PMC4350539 DOI: 10.4269/ajtmh.14-0681] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
A molecular genotyping assay for human immunodeficiency virus type 1 (HIV-1) circulating in Southeast Asia is difficult to design because of the high level of genetic diversity. We developed a multiplex real-time polymerase chain reaction (PCR) assay to detect subtype B, CRF01_AE, CRF33_01B, and three newly described circulating recombinant forms, (CRFs) (CRF53_01B, CRF54_01B, and CRF58_01B). A total of 785 reference genomes were used for subtype-specific primers and TaqMan probes design targeting the gag, pol, and env genes. The performance of this assay was compared and evaluated with direct sequencing and phylogenetic analysis. A total of 180 HIV-infected subjects from Kuala Lumpur, Malaysia were screened and 171 samples were successfully genotyped, in agreement with the phylogenetic data. The HIV-1 genotype distribution was as follows: subtype B (16.7%); CRF01_AE (52.8%); CRF33_01B (24.4%); CRF53_01B (1.1%); CRF54_01B (0.6%); and CRF01_AE/B unique recombinant forms (4.4%). The overall accuracy of the genotyping assay was over 95.0%, in which the sensitivities for subtype B, CRF01_AE, and CRF33_01B detection were 100%, 100%, and 97.7%, respectively. The specificity of genotyping was 100%, inter-subtype specificities were > 95% and the limit of detection of 10(3) copies/mL for plasma. The newly developed real-time PCR assay offers a rapid and cost-effective alternative for large-scale molecular epidemiological surveillance for HIV-1.
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Affiliation(s)
| | | | | | | | | | | | - Kok Keng Tee
- *Address correspondence to Kok Keng Tee, Centre of Excellence for Research in AIDS (CERiA), Department of Medicine, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia. E-mail:
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Kaur P, Khong WX, Wee SY, Tan EL, Pipper J, Koay E, Ng KY, Yap JK, Chew KK, Tan MT, Leo YS, Inoue M, Ng OT. Clinical evaluation of a low cost, in-house developed real-time RT-PCR human immunodeficiency virus type 1 (HIV-1) quantitation assay for HIV-1 infected patients. PLoS One 2014; 9:e89826. [PMID: 24603460 PMCID: PMC3945479 DOI: 10.1371/journal.pone.0089826] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Accepted: 01/26/2014] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVES HIV-1 viral quantitation is essential for treatment monitoring. An in-house assay would decrease financial barriers to access. MATERIALS AND METHODS A real-time competitive RT-PCR in house assay (Sing-IH) was developed in Singapore. Using HXB2 as reference, the assay's primers and probes were designed to generate a 183-bp product that overlaps a portion of the LTR region and gag region. A competitive internal control (IC) was included in each assay to monitor false negative results due to inhibition or human error. Clinical evaluation was performed on 249 HIV-1 positive patient samples in comparison with the commercially available Generic HIV Viral Load assay. Correlation and agreement of results were assessed for plasma HIV-1 quantification with both assays. RESULTS The assay has a lower limit of detection equivalent to 126 copies/mL of HIV-1 RNA and a linear range of detection from 100-1000000 copies/mL. Comparative analysis with reference to the Generic assay demonstrated good agreement between both assays with a mean difference of 0.22 log10 copies/mL and 98.8% of values within 1 log10 copies/mL range. Furthermore, the Sing-IH assay can quantify HIV-1 group M subtypes A-H and group N isolates adequately, making it highly suitable for our region, where subtype B and CRF01_AE predominate. CONCLUSIONS With a significantly lower running cost compared to commercially available assays, the broadly sensitive Sing-IH assay could help to overcome the cost barriers and serve as a useful addition to the currently limited HIV viral load assay options for resource-limited settings.
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Affiliation(s)
- Palvinder Kaur
- Institute of Infectious Disease and Epidemiology, Communicable Disease Centre, Tan Tock Seng Hospital, Singapore, Singapore
| | - Wei Xin Khong
- Institute of Infectious Disease and Epidemiology, Communicable Disease Centre, Tan Tock Seng Hospital, Singapore, Singapore
| | - Sue Yuen Wee
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos #03-01, Singapore, Singapore
| | - Eng Lee Tan
- Centre for Biomedical and Life Sciences, Singapore Polytechnic, Singapore, Singapore
- Department of Paediatrics, University Children's Medical Institute, National University Hospital, Singapore
| | - Juergen Pipper
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, Singapore, Singapore
| | - Evelyn Koay
- Molecular Diagnosis Centre, Department of Laboratory Medicine, National University Hospital, Singapore
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Kah Ying Ng
- Institute of Infectious Disease and Epidemiology, Communicable Disease Centre, Tan Tock Seng Hospital, Singapore, Singapore
| | - Joe Kwan Yap
- Institute of Infectious Disease and Epidemiology, Communicable Disease Centre, Tan Tock Seng Hospital, Singapore, Singapore
| | - Kuan Kiat Chew
- Institute of Infectious Disease and Epidemiology, Communicable Disease Centre, Tan Tock Seng Hospital, Singapore, Singapore
| | - Mei Ting Tan
- Institute of Infectious Disease and Epidemiology, Communicable Disease Centre, Tan Tock Seng Hospital, Singapore, Singapore
| | - Yee Sin Leo
- Institute of Infectious Disease and Epidemiology, Communicable Disease Centre, Tan Tock Seng Hospital, Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Lee Kong Chian School Of Medicine, Nanyang Technological University, Singapore
| | - Masafumi Inoue
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos #03-01, Singapore, Singapore
| | - Oon Tek Ng
- Institute of Infectious Disease and Epidemiology, Communicable Disease Centre, Tan Tock Seng Hospital, Singapore, Singapore
- * E-mail:
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Chow WZ, Takebe Y, Syafina NE, Prakasa MS, Chan KG, Al-Darraji HAA, Koh C, Kamarulzaman A, Tee KK. A newly emerging HIV-1 recombinant lineage (CRF58_01B) disseminating among people who inject drugs in Malaysia. PLoS One 2014; 9:e85250. [PMID: 24465513 PMCID: PMC3898983 DOI: 10.1371/journal.pone.0085250] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Accepted: 11/24/2013] [Indexed: 11/19/2022] Open
Abstract
The HIV epidemic is primarily characterised by the circulation of HIV-1 group M (main) comprising of 11 subtypes and sub-subtypes (A1, A2, B-D, F1, F2, G, H, J, and K) and to date 55 circulating recombinant forms (CRFs). In Southeast Asia, active inter-subtype recombination involving three main circulating genotypes--subtype B (including subtype B', the Thai variant of subtype B), CRF01_AE, and CRF33_01B--have contributed to the emergence of novel unique recombinant forms. In the present study, we conducted the molecular epidemiological surveillance of HIV-1 gag-RT genes among 258 people who inject drugs (PWIDs) in Kuala Lumpur, Malaysia, between 2009 and 2011 whereby a novel CRF candidate was recently identified. The near full-length genome sequences obtained from six epidemiologically unlinked individuals showed identical mosaic structures consisting of subtype B' and CRF01_AE, with six unique recombination breakpoints in the gag-RT, pol, and env regions. Among the high-risk population of PWIDs in Malaysia, which was predominantly infected by CRF33_01B (>70%), CRF58_01B circulated at a low but significant prevalence (2.3%, 6/258). Interestingly, the CRF58_01B shared two unique recombination breakpoints with other established CRFs in the region: CRF33_01B, CRF48_01B, and CRF53_01B in the gag gene, and CRF15_01B (from Thailand) in the env gene. Extended Bayesian Markov chain Monte Carlo sampling analysis showed that CRF58_01B and other recently discovered CRFs were most likely to have originated in Malaysia, and that the recent spread of recombinant lineages in the country had little influence from neighbouring countries. The isolation, genetic characterization, and evolutionary features of CRF58_01B among PWIDs in Malaysia signify the increasingly complex HIV-1 diversity in Southeast Asia that may hold an implication on disease treatment, control, and prevention.
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Affiliation(s)
- Wei Zhen Chow
- Centre of Excellence for Research in AIDS (CERiA), Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Yutaka Takebe
- Centre of Excellence for Research in AIDS (CERiA), Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
- AIDS Research Center, National Institute of Infectious Diseases, Toyama, Shinjuku-ku, Tokyo, Japan
| | - Nur Ezreen Syafina
- Centre of Excellence for Research in AIDS (CERiA), Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Malarvelli Soorya Prakasa
- Centre of Excellence for Research in AIDS (CERiA), Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Kok Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Haider Abdulrazzaq Abed Al-Darraji
- Centre of Excellence for Research in AIDS (CERiA), Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Clayton Koh
- Centre of Excellence for Research in AIDS (CERiA), Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Adeeba Kamarulzaman
- Centre of Excellence for Research in AIDS (CERiA), Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Kok Keng Tee
- Centre of Excellence for Research in AIDS (CERiA), Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
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Wertheim JO, Leigh Brown AJ, Hepler NL, Mehta SR, Richman DD, Smith DM, Kosakovsky Pond SL. The global transmission network of HIV-1. J Infect Dis 2013; 209:304-13. [PMID: 24151309 DOI: 10.1093/infdis/jit524] [Citation(s) in RCA: 166] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) is pandemic, but its contemporary global transmission network has not been characterized. A better understanding of the properties and dynamics of this network is essential for surveillance, prevention, and eventual eradication of HIV. Here, we apply a simple and computationally efficient network-based approach to all publicly available HIV polymerase sequences in the global database, revealing a contemporary picture of the spread of HIV-1 within and between countries. This approach automatically recovered well-characterized transmission clusters and extended other clusters thought to be contained within a single country across international borders. In addition, previously undescribed transmission clusters were discovered. Together, these clusters represent all known modes of HIV transmission. The extent of international linkage revealed by our comprehensive approach demonstrates the need to consider the global diversity of HIV, even when describing local epidemics. Finally, the speed of this method allows for near-real-time surveillance of the pandemic's progression.
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9
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Ong LY, Razak SNH, Lee YM, Sri La Sri Ponnampalavanar S, Syed Omar SF, Azwa RI, Tee KK, Kamarulzaman A. Molecular diversity of HIV-1 and surveillance of transmitted drug resistance variants among treatment Naïve patients, 5 years after active introduction of HAART in Kuala Lumpur, Malaysia. J Med Virol 2013; 86:38-44. [PMID: 24127302 DOI: 10.1002/jmv.23772] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/09/2013] [Indexed: 12/14/2022]
Abstract
Expansion of antiretroviral treatment programs have led to the growing concern for the development of antiretroviral drug resistance. The aims were to assess the prevalence of drug resistant HIV-1 variants and to identify circulating subtypes among HAART-naïve patients. Plasma specimens from N = 100 HIV+ HAART-naïve adult were collected between March 2008 and August 2010 and viral RNA were extracted for nested PCR and sequenced. PR-RT sequences were protein aligned and checked for transmitted drug resistance mutations. Phylogenetic reconstruction and recombination analysis were performed to determine the genotypes. Based on the WHO consensus guidelines, none of the recruited patients had any transmitted drug resistance mutations. When analyzed against the Stanford guidelines, 35% of patients had at least one reported mutation that may reduce drug susceptibility to PI (24%), NRTI (5%), and NNRTI (14%). The commonly detected mutation that may affect current first line therapy was V179D (3%), which may lead to reduced susceptibility to NNRTI. The predominant circulating HIV-1 genotypes were CRF01_AE (51%) and CRF33_01B (17%). The prevalence of unique recombinant forms (URF) was 7%; five distinct recombinant structures involving CRF01_AE and subtype B' were observed, among them a cluster of three isolates that could form a novel circulating recombinant form (CRF) candidate. Transmitted drug resistance prevalence among HAART-naïve patients was low in this cohort of patients in Kuala Lumpur despite introduction of HAART 5 years ago. Owing to the high genetic diversity, continued molecular surveillance can identify the persistent emergence of HIV-1 URF and novel CRF with significant epidemiological impact.
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Affiliation(s)
- Lai Yee Ong
- Faculty of Medicine, Centre of Excellence for Research in AIDS (CERiA), University of Malaya, Kuala Lumpur, Malaysia
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10
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Azam M, Malik A, Rizvi M, Singh S, Gupta P, Rai A. Emergence of drug resistance-associated mutations in HIV-1 subtype C protease gene in north India. Virus Genes 2013; 47:422-8. [PMID: 23888308 DOI: 10.1007/s11262-013-0961-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2013] [Accepted: 07/12/2013] [Indexed: 10/26/2022]
Abstract
A major cause of anti-retroviral therapy (ART) failure is the drug resistance-associated mutations in polymerase gene of HIV-1. Paucity of data regarding potential drug resistance to protease inhibitors (PIs) prompted us to carry out this study. Drug resistance (DR) genotyping of the entire protease gene was performed in 104 HIV-1 ART-naive and first-line ART-experienced patients. The DR pattern was analyzed using the Stanford HIV-DR database, International AIDS Society-USA mutation list and REGA algorithm version 8.0. Subtyping was done using Mega 4 and REGA HIV-1 subtyping tool-v2.01. Majority of our sequences 98 (96%) were subtype C and remaining four (3.92%) were subtype A1. In three (2.9%) DE patients, major DR-associated mutation at D30 N and M46I positions were detected. Approximately 70% polymorphisms as minor mutations were observed in protease gene, of which 14 distinct amino acids changes were linked to partial DR such as G16E, K20R, M36I, D60E, I62V, L63P, I64M, H69K, T74A/S, V77I, V82I, I85V, L89M, and I93L. The two major and several minor mutations detected in this study confer low/intermediate levels of resistance to most PIs independently or together. Our results conclude that resistance testing in HIV-1-infected patients should be performed before the initiation of PI therapy for better therapeutic outcome in this region. This information not only will shed light on the extent of current DR in HIV strains but also will aid in patient treatment and drug designing.
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Affiliation(s)
- Mohd Azam
- Department of Microbiology, Faculty of Medicine, J.N. Medical College, Aligarh Muslim University, Aligarh, 202002, India
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11
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Kiertiburanakul S, Chaiwarith R, Sirivichayakul S, Ditangco R, Jiamsakul A, Li PCK, Kantipong P, Lee C, Ratanasuwan W, Kamarulzaman A, Sohn AH, Sungkanuparph S. Comparisons of Primary HIV-1 Drug Resistance between Recent and Chronic HIV-1 Infection within a Sub-Regional Cohort of Asian Patients. PLoS One 2013; 8:e62057. [PMID: 23826076 PMCID: PMC3694952 DOI: 10.1371/journal.pone.0062057] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Accepted: 03/17/2013] [Indexed: 12/30/2022] Open
Abstract
Background The emergence and transmission of HIV-1 drug resistance (HIVDR) has raised concerns after rapid global antiretroviral therapy (ART) scale-up. There are limited data on the epidemiology of primary HIVDR in resource-limited settings in Asia. We aimed to determine the prevalence and compare the distribution of HIVDR in a cohort of ART-naïve Asian patients with recent and chronic HIV-1 infection. Methods Multicenter prospective study was conducted in ART-naïve patients between 2007 and 2010. Resistance-associated mutations (RAMs) were assessed using the World Health Organization 2009 list for surveillance of primary HIVDR. Results A total of 458 patients with recent and 1,340 patients with chronic HIV-1 infection were included in the analysis. The overall prevalence of primary HIVDR was 4.6%. Recently infected patients had a higher prevalence of primary HIVDR (6.1% vs. 4.0%, p = 0.065) and frequencies of RAMs to protease inhibitors (PIs; 3.9% vs. 1.0%, p<0.001). Among those with recent infection, the most common RAMs to nucleoside reverse transcriptase inhibitors (NRTIs) were M184I/V and T215D/E/F/I/S/Y (1.1%), to non-NRTIs was Y181C (1.3%), and to PIs was M46I (1.5%). Of patients with chronic infection, T215D/E/F/I/S/Y (0.8%; NRTI), Y181C (0.5%; non-NRTI), and M46I (0.4%; PI) were the most common RAMs. K70R (p = 0.016) and M46I (p = 0.026) were found more frequently among recently infected patients. In multivariate logistic regression analysis in patients with chronic infection, heterosexual contact as a risk factor for HIV-1 infection was less likely to be associated with primary HIVDR compared to other risk categories (odds ratio 0.34, 95% confidence interval 0.20–0.59, p<0.001). Conclusions The prevalence of primary HIVDR was higher among patients with recent than chronic HIV-1 infection in our cohort, but of borderline statistical significance. Chronically infected patients with non-heterosexual risks for HIV were more likely to have primary HIVDR.
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Affiliation(s)
| | - Romanee Chaiwarith
- Research Institute for Health Sciences, Chiang Mai University, Chiang Mai, Thailand
| | - Sunee Sirivichayakul
- Faculty of Medicine, Chulalongkorn University and HIV-NAT/Thai Red Cross AIDS Research Centre, Bangkok, Thailand
| | | | | | | | | | | | - Winai Ratanasuwan
- Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | | | - Annette H. Sohn
- TREAT Asia, amfAR - The Foundation for AIDS Research, Bangkok, Thailand
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12
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Chow WZ, Ong LY, Razak SH, Lee YM, Ng KT, Yong YK, Azmel A, Takebe Y, Al-Darraji HAA, Kamarulzaman A, Tee KK. Molecular diversity of HIV-1 among people who inject drugs in Kuala Lumpur, Malaysia: massive expansion of circulating recombinant form (CRF) 33_01B and emergence of multiple unique recombinant clusters. PLoS One 2013; 8:e62560. [PMID: 23667490 PMCID: PMC3646884 DOI: 10.1371/journal.pone.0062560] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Accepted: 03/22/2013] [Indexed: 11/19/2022] Open
Abstract
Since the discovery of HIV-1 circulating recombinant form (CRF) 33_01B in Malaysia in the early 2000 s, continuous genetic diversification and active recombination involving CRF33_01B and other circulating genotypes in the region including CRF01_AE and subtype B' of Thai origin, have led to the emergence of novel CRFs and unique recombinant forms. The history and magnitude of CRF33_01B transmission among various risk groups including people who inject drugs (PWID) however have not been investigated despite the high epidemiological impact of CRF33_01B in the region. We update the most recent molecular epidemiology of HIV-1 among PWIDs recruited in Malaysia between 2010 and 2011 by population sequencing and phylogenetic analysis of 128 gag-pol sequences. HIV-1 CRF33_01B was circulating among 71% of PWIDs whilst a lower prevalence of other previously dominant HIV-1 genotypes [subtype B' (11%) and CRF01_AE (5%)] and CRF01_AE/B' unique recombinants (13%) were detected, indicating a significant shift in genotype replacement in this population. Three clusters of CRF01_AE/B' recombinants displaying divergent yet phylogenetically-related mosaic genomes to CRF33_01B were identified and characterized, suggestive of an abrupt emergence of multiple novel CRF clades. Using rigorous maximum likelihood approach and the Bayesian Markov chain Monte Carlo (MCMC) sampling of CRF33_01Bpol sequences to elucidate the past population dynamics, we found that the founder lineages of CRF33_01B were likely to have first emerged among PWIDs in the early 1990 s before spreading exponentially to various high and low-risk populations (including children who acquired infections from their mothers) and later on became endemic around the early 2000 s. Taken together, our findings provide notable genetic evidence indicating the widespread expansion of CRF33_01B among PWIDs and into the general population. The emergence of numerous previously unknown recombinant clades highlights the escalating genetic complexity of HIV-1 in the Southeast Asian region.
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Affiliation(s)
- Wei Zhen Chow
- Centre of Excellence for Research in AIDS (CERiA), Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Lai Yee Ong
- Centre of Excellence for Research in AIDS (CERiA), Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Siti Humaira Razak
- Centre of Excellence for Research in AIDS (CERiA), Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Yeat Mei Lee
- Centre of Excellence for Research in AIDS (CERiA), Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Kim Tien Ng
- Centre of Excellence for Research in AIDS (CERiA), Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Yean Kong Yong
- Centre of Excellence for Research in AIDS (CERiA), Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Azureen Azmel
- Centre of Excellence for Research in AIDS (CERiA), Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Yutaka Takebe
- Centre of Excellence for Research in AIDS (CERiA), Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
- AIDS Research Center, National Institute of Infectious Diseases, Toyama, Shinjuku-ku, Tokyo, Japan
| | - Haider Abdulrazzaq Abed Al-Darraji
- Centre of Excellence for Research in AIDS (CERiA), Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Adeeba Kamarulzaman
- Centre of Excellence for Research in AIDS (CERiA), Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Kok Keng Tee
- Centre of Excellence for Research in AIDS (CERiA), Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
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13
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Emergence in Japan of an HIV-1 variant associated with transmission among men who have sex with men (MSM) in China: first indication of the International Dissemination of the Chinese MSM lineage. J Virol 2013; 87:5351-61. [PMID: 23365432 DOI: 10.1128/jvi.02370-12] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A survey of HIV-1 strains circulating in the Tokyo-Kanagawa metropolitan area of Japan during 2004 to 2011 (n = 477) identified six Japanese males (patients 1 to 6), who harbored viruses with genome segments derived from a distinct CRF01_AE variant uniquely found among men who have sex with men (MSM) in China (designated CN.MSM.01-1). These six HIV infections were diagnosed in 2010 and 2011 among MSM (3 of 75) and men with unknown risk factors (3 of 63) and differed from the vast majority of HIV infections among MSM in Japan, which are overwhelmingly characterized by subtype B (239 of 246 [97.2%]). Approximately one-third (91 of 239 [38.1%]) of subtype B strains from MSM in Japan belong to a large monophyletic cluster (designated JP.MSM.B-1). In addition, we identified a smaller subtype B cluster (n = 8) (designated JP.MSM.B-2) that also contains strains from two Chinese MSM living in Japan. Interestingly, patients 5 and 6 were found to be coinfected with CRF01_AE (CN.MSM.01-1) and subtype B (JP.MSM.B-2 or JP.MSM.B-1) variants that are unique to the HIV-1 epidemics among MSM in China and Japan, respectively. Our study demonstrates for the first time the effect of the expanding HIV epidemic among MSM in China on transmission in neighboring countries and shows the ongoing mixing of CRF01_AE and subtype B lineages unique to HIV-1 that cocirculate in MSM populations in East Asia. This finding highlights the importance of strengthening epidemiological surveillance in the region and the need for effective measures to limit transmission among MSM in East Asia.
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14
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Rutvisuttinunt W, Sirivichayakul S, Oota S, Assawadarachai V, Poltavee K, Savadsuk H, Pattanachaiwit S, Chaemchuen S, Arroyo MA, Paris RM, Michael NL, Kim JH, Ruxrungtham K, de Souza M, Phanuphak P, Tovanabutra S. Two unique recombinant forms identified in incident HIV type 1 infections in Thai blood donors. AIDS Res Hum Retroviruses 2012; 28:1703-11. [PMID: 22587412 DOI: 10.1089/aid.2011.0339] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
HIV-1 genetic diversity of recently seroconverting (<12 months) Thai repeated blood donors attending the National Blood Centre, Thai Red Cross Society (NBC, TRCS) from September 2007 until March 2008 was assessed. Ten HIV-1 recent seroconvertors (10/239,134 donations) were identified during the study period. The estimated median time to seroconversion was 67.3 days (range: 45.5-102.0 days), and viral load ranged from 307 to 341,805 copies HIV-1 RNA/ml. MHAbce, a real-time-based PCR genotyping assay, identified six CRF01_AE, two CRF01_AE/B recombinants, one subtype B, and one CRF01_AE/B dual infection. Nine samples were further characterized by full genome sequencing, identifying CRF01_AE (N=6), unique CRF01_AE/B recombinants (N=2), and subtype B (N=1). One recombinant contained 13 breakpoints located in gag, pol, vif, vpr, env, and nef while the other recombinant contained 10 breakpoints located in pol, vif, env, and nef. This study found two unique CRF01B recombinants circulating in 10 recent HIV-1-positive subjects from a blood donor population in Thailand.
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Affiliation(s)
- Wiriya Rutvisuttinunt
- Department of Retrovirology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Sunee Sirivichayakul
- Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Sineenart Oota
- National Blood Centre, Thai Red Cross Society, Bangkok, Thailand
| | | | - Kultida Poltavee
- Department of Retrovirology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Hathairat Savadsuk
- Department of Retrovirology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | | | - Suwittra Chaemchuen
- Department of Retrovirology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Miguel A. Arroyo
- Department of Retrovirology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Rockville, Maryland
- Department of Pathology, Walter Reed National Military Medical Center, Bethesda, Maryland
| | - Robert M. Paris
- Department of Retrovirology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
- Department of Infectious Diseases, Walter Reed National Military Medical Center, Bethesda, Maryland
| | - Nelson L. Michael
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Rockville, Maryland
| | - Jerome H. Kim
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Rockville, Maryland
| | - Kiat Ruxrungtham
- Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Thai Red Cross AIDS Research Centre, Bangkok, Thailand
| | - Mark de Souza
- Department of Retrovirology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Rockville, Maryland
| | - Praphan Phanuphak
- Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Thai Red Cross AIDS Research Centre, Bangkok, Thailand
| | - Sodsai Tovanabutra
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Rockville, Maryland
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15
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Transmitted drug resistance and phylogenetic relationships among acute and early HIV-1-infected individuals in New York City. J Acquir Immune Defic Syndr 2012; 61:1-8. [PMID: 22592583 DOI: 10.1097/qai.0b013e31825a289b] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND Transmitted drug resistance (TDR) is critical to managing HIV-1-infected individuals and being a public health concern. We report on TDR prevalence and include analyses of phylogenetic clustering of HIV-1 in a predominantly men who have sex with men cohort diagnosed during acute/recent HIV-1 infection in New York City. METHODS Genotypic resistance testing was conducted on plasma samples of 600 individuals with acute/recent HIV-1 infection (1995-2010). Sequences were used for resistance and phylogenetic analyses. Demographic and clinical data were abstracted from medical records. TDR was defined according to International AIDS Society-USA and Stanford HIV database guidelines. Phylogenetic and other analyses were conducted using PAUP*4.0 and SAS, respectively. RESULTS The mean duration since HIV-1 infection was 66.5 days. TDR prevalence was 14.3% and stably ranged between 10.8% and 21.6% (P(trend) = 0.42). Nucleoside reverse transcriptase inhibitors resistance declined from 15.5% to 2.7% over the study period (P(trend) = 0.005). M41L (3.7%), T215Y (4.0%), and K103N/S (4.7%) were the most common mutations. K103N/S prevalence increased from 1.9% to 8.0% between 1995 and 2010 (P(trend) = 0.04). Using a rigorous definition of clustering, 19.3% (112 of 581) of subtype B viral sequences cosegregated into transmission clusters and clusters increased over time. There were fewer and smaller transmission clusters than had been reported in a similar cohort in Montreal but similar to reports from elsewhere. CONCLUSIONS TDR is stable in this cohort and remains a significant concern to both individual patient management and the public health.
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16
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Beyrer C, Baral SD, van Griensven F, Goodreau SM, Chariyalertsak S, Wirtz AL, Brookmeyer R. Global epidemiology of HIV infection in men who have sex with men. Lancet 2012; 380:367-77. [PMID: 22819660 PMCID: PMC3805037 DOI: 10.1016/s0140-6736(12)60821-6] [Citation(s) in RCA: 1133] [Impact Index Per Article: 94.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Epidemics of HIV in men who have sex with men (MSM) continue to expand in most countries. We sought to understand the epidemiological drivers of the global epidemic in MSM and why it continues unabated. We did a comprehensive review of available data for HIV prevalence, incidence, risk factors, and the molecular epidemiology of HIV in MSM from 2007 to 2011, and modelled the dynamics of HIV transmission with an agent-based simulation. Our findings show that the high probability of transmission per act through receptive anal intercourse has a central role in explaining the disproportionate disease burden in MSM. HIV can be transmitted through large MSM networks at great speed. Molecular epidemiological data show substantial clustering of HIV infections in MSM networks, and higher rates of dual-variant and multiple-variant HIV infection in MSM than in heterosexual people in the same populations. Prevention strategies that lower biological transmission and acquisition risks, such as approaches based on antiretrovirals, offer promise for controlling the expanding epidemic in MSM, but their potential effectiveness is limited by structural factors that contribute to low health-seeking behaviours in populations of MSM in many parts of the world.
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Affiliation(s)
- Chris Beyrer
- Center for Public Health and Human Rights, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA.
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17
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Chibo D, Kaye M, Birch C. HIV transmissions during seroconversion contribute significantly to new infections in men who have sex with men in Australia. AIDS Res Hum Retroviruses 2012; 28:460-4. [PMID: 21806486 DOI: 10.1089/aid.2011.0137] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Transmission of HIV from recently infected individuals contributes to the number of new cases of infection, but the extent to which it occurs from those who are unaware of their infection is not known. Phylogenetic analysis was performed on 209 cases of acute HIV subtype B infection detected between January 2005 and September 2010, most of whom (88%) were men who have sex with men. Only new cases with an evolving Western blot profile confirmed by detection of HIV RNA were included. Subjects whose known dates of seroconversion were within 1 month of at least one other phylogenetically linked case identified during the 6 years of the study were then examined to estimate the prevalence of onward transmission. Almost 30% of cases could have acquired their infection from another person undergoing seroconversion within the same month. Temporal increases in the number of phylogenetically related strains within several clusters were demonstrated during the study, although the rate of increase varied. Transmission of HIV from individuals undergoing seroconversion is an important contributor to the number of new infections identified every year and very likely occurs before they have knowledge of their infection. Clusters of related HIV strains can grow at a disconcerting rate, demonstrating that more focused public health efforts are required to minimize further HIV transmissions within sexual networks.
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Affiliation(s)
- Doris Chibo
- HIV Characterisation Laboratory, Victorian Infectious Diseases Reference Laboratory, North Melbourne, Victoria, Australia
| | - Matthew Kaye
- HIV Characterisation Laboratory, Victorian Infectious Diseases Reference Laboratory, North Melbourne, Victoria, Australia
| | - Chris Birch
- HIV Characterisation Laboratory, Victorian Infectious Diseases Reference Laboratory, North Melbourne, Victoria, Australia
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18
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Soria J, Bull M, Mitchell C, La Rosa A, Dross S, Kraft K, Coombs R, Ticona E, Frenkel L. Transmitted HIV resistance to first-line antiretroviral therapy in Lima, Peru. AIDS Res Hum Retroviruses 2012; 28:333-8. [PMID: 21819256 DOI: 10.1089/aid.2011.0131] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Transmission of drug-resistant HIV (TDR) has been associated with virologic failure of "first-line," nonnucleoside reverse transcriptase inhibitor (NNRTI)-based antiretroviral therapy (ART). A national ART program began in Peru in 2004. We evaluated the prevalence of TDR in individuals initiating ART and their virologic outcome during 2 years of ART. HIV-infected, ARV-naive subjects who met criteria to start ART in Lima, Peru were enrolled in a longitudinal observational study between July 2007 and February 2009. Blood plasma and cells obtained prior to ART initiation were assessed for antiretroviral (ARV) resistance by an oligonucleotide ligation assay (OLA) sensitive to 2% mutant at reverse transcriptase (RT) codons K103N, Y181C, G190A, and M184V and a subset by consensus sequencing. A total of 112 participants were enrolled; the mean CD4 was 134 ± 89 cells/μl and the median plasma HIV RNA was 93,556 copies/ml (IQR 62,776-291,364). Drug resistance mutations conferring high-level resistance to ARV were rare, detected in one of 96 (1%) evaluable participants. This subject had the Y181C mutation detected in both plasma and peripheral blood mononuclear cells (PBMCs) at a concentration of 100% by OLA and consensus sequencing; nevertheless nevirapine-ART suppressed her viral replication. Consensus sequencing of 37 (19%) participants revealed multiple polymorphisms that occasionally have been associated with low-level reductions in ARV susceptibility. A low prevalence of TDR was detected among Peruvians initiating ART. Given the increasing availability of ART, continuing surveillance is needed to determine if TDR increases and the mutant codons associated with virologic failure.
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Affiliation(s)
- Jaime Soria
- Hospital Nacional Dos de Mayo, Lima, Peru
- Investigaciones Médicas en Salud (INMENSA), Lima, Peru
| | - Marta Bull
- Seattle Children's Hospital Research Institute, Seattle, Washington
| | | | | | - Sandra Dross
- Seattle Children's Hospital Research Institute, Seattle, Washington
| | - Kelli Kraft
- Seattle Children's Hospital Research Institute, Seattle, Washington
| | | | - Eduardo Ticona
- Hospital Nacional Dos de Mayo, Lima, Peru
- Investigaciones Médicas en Salud (INMENSA), Lima, Peru
| | - Lisa Frenkel
- Seattle Children's Hospital Research Institute, Seattle, Washington
- University of Washington, Seattle, Washington
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Ng OT, Munshaw S, Lamers SL, Chew KK, Lin L, Redd AD, Manucci J, Quinn TC, Ray SC, Chua A, Leo YS, Laeyendecker O. Molecular epidemiology of HIV type 1 in Singapore and identification of novel CRF01_AE/B recombinant forms. AIDS Res Hum Retroviruses 2011; 27:1135-7. [PMID: 21235306 DOI: 10.1089/aid.2010.0364] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
To investigate HIV-1 molecular epidemiology in Singapore, we sequenced portions of three regions of the HIV-1 genome (protease HXB2: 2163 to 2620, gp120 HXB2: 6904 to 7628, and gp41 HXB2: 7817 to 8264) from 212 plasma samples collected between February 2008 and August 2009. From these samples, 109 (51.4%) generated interpretable data in all regions. Sixty-one (56.0%) were identified as CRF01_AE, 26 (23.9%) as subtype B and 14 (12.8%) as possible novel recombinant forms. The main novel recombinant pattern, detected in 13 sequences, had subtype B in protease and gp41 and CRF01_AE in gp120. There was intermixing of subtypes within transmission risk groups. However, 85% of subjects infected with the novel recombinant forms self-identified as men who have sex with men or bisexuals compared with only 41% of individuals infected with CRF01_AE and 62% infected with subtype B (p = 0.001).
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Affiliation(s)
- Oon Tek Ng
- Johns Hopkins School of Medicine, Baltimore, Maryland
- Department of Infectious Disease, Tan Tock Seng Hospital, Singapore, Singapore
| | | | | | - Kuan Kiat Chew
- Department of Infectious Disease, Tan Tock Seng Hospital, Singapore, Singapore
| | - Li Lin
- Department of Infectious Disease, Tan Tock Seng Hospital, Singapore, Singapore
| | - Andrew D. Redd
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Baltimore, Maryland
| | - Jordyn Manucci
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Baltimore, Maryland
| | - Thomas C. Quinn
- Johns Hopkins School of Medicine, Baltimore, Maryland
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Baltimore, Maryland
| | - Stuart C. Ray
- Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Arlene Chua
- Department of Infectious Disease, Tan Tock Seng Hospital, Singapore, Singapore
| | - Yee Sin Leo
- Department of Infectious Disease, Tan Tock Seng Hospital, Singapore, Singapore
| | - Oliver Laeyendecker
- Johns Hopkins School of Medicine, Baltimore, Maryland
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Baltimore, Maryland
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Zhao B, Han X, Dai D, Liu J, Ding H, Xu J, Chu Z, Bice T, Diao Y, Shang H. New trends of primary drug resistance among HIV type 1-infected men who have sex with men in Liaoning Province, China. AIDS Res Hum Retroviruses 2011; 27:1047-53. [PMID: 21417755 DOI: 10.1089/aid.2010.0119] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
To elucidate the recent changes in prevalence of HIV-1 primary resistance mutations in men who have sex with men (MSM) in Liaoning province, 217 samples from antiretroviral therapy-naive MSM were collected. For 201 samples, the entire protease gene and 256 amino acids of the reverse transcriptase gene were successfully amplified by reverse transcriptase polymerase chain reaction (RT-PCR) and nested PCR of viral RNA and were sequenced. Among the amplified pol sequences, HIV-1 CRF01_AE accounted for 87.6% (176/201), subtype B accounted for 8.0% (16/201), and subtype CRF07_BC accounted for 4.5% (9/201). The overall prevalence of mutations conferring resistance to any drug was 4.5%, representing 4.5% for protease inhibitor (PI)-related mutations, 0.5% for nucleoside/nucleotide reverse transcriptase inhibitor (NRTI)-related mutations, and 0.5% for nonnucleoside reverse transcriptase inhibitor (NNRTI)-related mutations. Included were V32I (0.5%), M46I (2.0%), L90M (2.0%), T215C (0.5%), and Y188L (0.5%). Only one case carried resistance mutations to all three drug classes (L90M, L10I, and A71T to PI; T215C to NRTI; and Y188L to NNRTI). L10I (4.5%), V118I/IV (17.4%), and K103R/KR (10.0%) were commonly observed mutations, but do not confer any drug resistance to PIs, NRTIs, and NNRTIs. CRF01_AE is becoming a major HIV-1 infection subtype among MSM of Liaoning province. Relatively high rates of HIV drug-resistant mutations to PIs in antiretroviral treatment-naive patients in the study represent a serious challenge for future HIV treatment programs in China.
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Affiliation(s)
- Bin Zhao
- The Key Laboratory of AIDS Immunology of Ministry of Health, Department of Laboratory Medicine, No. 1 Hospital of China Medical University, Shenyang, China
| | - Xiaoxu Han
- The Key Laboratory of AIDS Immunology of Ministry of Health, Department of Laboratory Medicine, No. 1 Hospital of China Medical University, Shenyang, China
| | - Di Dai
- The Key Laboratory of AIDS Immunology of Ministry of Health, Department of Laboratory Medicine, No. 1 Hospital of China Medical University, Shenyang, China
| | - Jing Liu
- The Key Laboratory of AIDS Immunology of Ministry of Health, Department of Laboratory Medicine, No. 1 Hospital of China Medical University, Shenyang, China
| | - Haibo Ding
- The Key Laboratory of AIDS Immunology of Ministry of Health, Department of Laboratory Medicine, No. 1 Hospital of China Medical University, Shenyang, China
| | - Junjie Xu
- The Key Laboratory of AIDS Immunology of Ministry of Health, Department of Laboratory Medicine, No. 1 Hospital of China Medical University, Shenyang, China
| | - Zhenxing Chu
- The Key Laboratory of AIDS Immunology of Ministry of Health, Department of Laboratory Medicine, No. 1 Hospital of China Medical University, Shenyang, China
| | - Tristan Bice
- The Key Laboratory of AIDS Immunology of Ministry of Health, Department of Laboratory Medicine, No. 1 Hospital of China Medical University, Shenyang, China
| | - Yingying Diao
- The Key Laboratory of AIDS Immunology of Ministry of Health, Department of Laboratory Medicine, No. 1 Hospital of China Medical University, Shenyang, China
| | - Hong Shang
- The Key Laboratory of AIDS Immunology of Ministry of Health, Department of Laboratory Medicine, No. 1 Hospital of China Medical University, Shenyang, China
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Steinberg M, Cook DA, Gilbert M, Krajden M, Haag D, Tsang P, Wong E, Brooks JI, Merks H, Rekart ML. Towards targeted screening for acute HIV infections in British Columbia. J Int AIDS Soc 2011; 14:39. [PMID: 21827673 PMCID: PMC3169441 DOI: 10.1186/1758-2652-14-39] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2010] [Accepted: 08/09/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Our objective was to describe the characteristics of acute and established HIV infections diagnosed in the Canadian province of British Columbia. Province-wide HIV testing and surveillance data were analyzed to inform recommendations for targeted use of screening algorithms to detect acute HIV infections. METHODS Acute HIV infection was defined as a confirmed reactive HIV p24 antigen test (or HIV nucleic acid test), a non-reactive or reactive HIV EIA screening test and a non-reactive or indeterminate Western Blot. Characteristics of unique individuals were identified from the British Columbia HIV/AIDS Surveillance System. Primary drug resistance and HIV subtypes were identified by analyzing HIV pol sequences from residual sera from newly infected individuals. RESULTS From February 2006 to October 2008, 61 individuals met the acute HIV infection case definition, representing 6.2% of the 987 newly diagnosed HIV infections during the analysis period. Acute HIV infection cases were more likely to be men who have sex with men (crude OR 1.71; 95% CI 1.01-2.89], to have had a documented previous negative HIV test result (crude OR 2.89; 95% CI 1.52-5.51), and to have reported a reason for testing due to suspected seroconversion symptoms (crude OR 5.16; 95% CI 2.88-9.23). HIV subtypes and rates of transmitted drug resistance across all classes of drugs were similar in persons with both acute and established HIV infections. CONCLUSIONS Targeted screening to detect acute HIV infection is a logical public health response to the HIV epidemic. Our findings suggest that acute HIV infection screening strategies, in our setting, are helpful for early diagnosis in men who have sex with men, in persons with seroconversion symptoms and in previously negative repeat testers.
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Affiliation(s)
- Malcolm Steinberg
- British Columbia Centre for Disease Control, Vancouver, BC, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Darrel A Cook
- British Columbia Centre for Disease Control, Vancouver, BC, Canada
| | - Mark Gilbert
- British Columbia Centre for Disease Control, Vancouver, BC, Canada
- Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Mel Krajden
- British Columbia Centre for Disease Control, Vancouver, BC, Canada
- Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Devon Haag
- British Columbia Centre for Disease Control, Vancouver, BC, Canada
| | - Peggy Tsang
- British Columbia Centre for Disease Control, Vancouver, BC, Canada
| | - Elsie Wong
- British Columbia Centre for Disease Control, Vancouver, BC, Canada
| | - James I Brooks
- Public Health Agency of Canada, Ottawa, ON, Canada
- Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | | | - Michael L Rekart
- British Columbia Centre for Disease Control, Vancouver, BC, Canada
- Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
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Increased rate of CD4+ T-cell decline and faster time to antiretroviral therapy in HIV-1 subtype CRF01_AE infected seroconverters in Singapore. PLoS One 2011; 6:e15738. [PMID: 21298051 PMCID: PMC3029292 DOI: 10.1371/journal.pone.0015738] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2010] [Accepted: 11/26/2010] [Indexed: 11/23/2022] Open
Abstract
Background It remains controversial as to whether HIV-1 subtypes influence disease progression. Singapore offers a unique opportunity to address this issue due to the presence of co-circulating subtypes. We compared subtype CRF01_AE and non-CRF01_AE infected patients, with regards to estimated annual rate of CD4+ T-cell loss and time from estimated data of seroconversion (EDS) to antiretroviral therapy (ART). Methods We recruited ART-naive patients with known dates of seroconversion between October 2002 and December 2007 at the Singapore Communicable Disease Centre, the national reference treatment centre. Multilevel mixed-effects models were used to analyse the rate of CD4+ T-cell decline. Time from EDS to ART was analyzed with the Kaplan-Meier survival method and compared with Cox proportional hazards models. Results 54 patients with previously assigned HIV-1 subtypes (24 CRF01_AE, 17 B, 8 B', 1 CRF33_01B, 3 CRF34_01B and 1 G) were observed for 89 patient-years. Subtype CRF01_AE and non-CRF01_AE infected patients did not differ in age, gender, risk factor, rate of symptomatic seroconversion, baseline CD4+ T-cell count, log10 viral load or haemoglobin concentration. The estimated annual rate of CD4+ T-cell loss was 58 cells/mm3/year (95% CI: 7 to 109; P = 0.027) greater in subtype CRF01_AE infected patients compared to non-CRF01_AE patients, after adjusting for age, baseline CD4+ T-cell count and baseline log10 viral load. The median time from EDS to ART was 1.8 years faster comparing CRF01_AE to non-CRF01_AE infected patient with a 2.5 times (95% CI: 1.2-5.0; P = 0.013) higher hazard for ART initiation, after controlling for age, baseline CD4+ T-cell count and baseline log10 viral load. Conclusions Infecting subtype significantly impacted the rate of CD4+ T-cell loss and time to treatment in this cohort. Studies to understand the biological basis for this difference could further our understanding of HIV pathogenesis.
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