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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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Rashid A, Kang L, Yi F, Chu Q, Shah SA, Mahmood SF, Getaneh Y, Wei M, Chang S, Abidi SH, Shao Y. Human Immunodeficiency Virus Type-1 Genetic Diversity and Drugs Resistance Mutations among People Living with HIV in Karachi, Pakistan. Viruses 2024; 16:962. [PMID: 38932254 PMCID: PMC11209141 DOI: 10.3390/v16060962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 06/07/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024] Open
Abstract
The human immunodeficiency virus type-1 epidemic in Pakistan has significantly increased over the last two decades. In Karachi, Pakistan, there is a lack of updated information on the complexity of HIV-1 genetic diversity and the burden of drug resistance mutations (DRMs) that can contribute to ART failure and poor treatment outcomes. This study aimed to determine HIV-1 genetic diversity and identify drug-resistance mutations among people living with HIV in Karachi. A total of 364 HIV-positive individuals, with a median age of 36 years, were enrolled in the study. The HIV-1 partial pol gene was successfully sequenced from 268 individuals. The sequences were used to generate phylogenetic trees to determine clade diversity and also to assess the burden of DRMs. Based on the partial pol sequences, 13 distinct HIV-1 subtypes and recombinant forms were identified. Subtype A1 was the most common clade (40%), followed by CRF02_AG (33.2%). Acquired DRMs were found in 30.6% of the ART-experienced patients, of whom 70.7%, 20.7%, and 8.5% were associated with resistance to NNRTIs, NRTIs, and PIs, respectively. Transmitted DRMs were found in 5.6% of the ART-naïve patients, of whom 93% were associated with resistance against NNRTIs and 7% to PIs. The high prevalence of DRMs in ART-experienced patients poses significant challenges to the long-term benefits and sustainability of the ART program. This study emphasizes the importance of continuous HIV molecular epidemiology and drug resistance surveillance to support evidence-based HIV prevention, precise ART, and targeted AIDS care.
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Affiliation(s)
- Abdur Rashid
- School of Medicine, Nankai University, Tianjin 300071, China; (A.R.); (M.W.)
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (L.K.); (Q.C.); (S.C.)
| | - Li Kang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (L.K.); (Q.C.); (S.C.)
- College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Feng Yi
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (L.K.); (Q.C.); (S.C.)
| | - Qingfei Chu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (L.K.); (Q.C.); (S.C.)
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China;
| | | | | | - Yimam Getaneh
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China;
- Ethiopian Public Health Institute, Addis Ababa P.O. Box 1242, Ethiopia
| | - Min Wei
- School of Medicine, Nankai University, Tianjin 300071, China; (A.R.); (M.W.)
| | - Song Chang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (L.K.); (Q.C.); (S.C.)
| | - Syed Hani Abidi
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi 74800, Pakistan
- Department of Biomedical Sciences, School of Medicine, Nazarbayev University, Astana 010000, Kazakhstan
| | - Yiming Shao
- School of Medicine, Nankai University, Tianjin 300071, China; (A.R.); (M.W.)
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (L.K.); (Q.C.); (S.C.)
- College of Life Sciences, Nankai University, Tianjin 300071, China
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China;
- Changping Laboratory, Yard 28, Science Park Road, Changping District, Beijing 102206, China
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Shah SA, Abidi SH, Soomro AA, Farooqui N, Ansari T, Khanani R. Evaluation of the Training Program to Train HIV Treatment Center Staff in Pakistan. Cureus 2024; 16:e61972. [PMID: 38855485 PMCID: PMC11162296 DOI: 10.7759/cureus.61972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/08/2024] [Indexed: 06/11/2024] Open
Abstract
Introduction In Pakistan, HIV training programs, especially for health professionals working in HIV treatment centers, are limited. Consequently, there is little data about HIV awareness among physicians and allied health workers and how it may affect their care for people living with HIV (PLWH). Recently, the Global Fund to Fight AIDS, Tuberculosis, and Malaria (GFATM) grant Principal Recipient UNDP engaged an NGO experienced in HIV/AIDS training, on a competitive basis, to develop a training manual and conduct training of all categories of HIV treatment centers staff. The goal of this study was to assess the training program's influence on trainees' (both physicians and allied health staff) knowledge and abilities and describe its major lessons. Methodology This was a one-group pre-post test study, carried out between January 17 and February 22, 2023. The study was carried out in three phases. In the first phase, a team of experts developed an antiretroviral treatment (ART) training manual. In the second phase, 9- and three-day training workshops were conducted in six different cities of Pakistan, which were attended by physicians and allied health staff working in different HIV treatment centers across Pakistan. The workshops had plenary lectures, discussions, role plays, video cases, and case studies. In the third phase, a quiz, comprising multiple/best choice questions (MCQs/BCQs) and true and false questions, was administered before (pre) and after the workshop (post) to assess the impact of these training sessions in enhancing the level of HIV knowledge, especially related to ART. The workshop was attended by a total of 256 health workers from different cities in Pakistan. The participants had backgrounds in medical science, psychology, laboratory science, nursing, and computer science. Pre-and post-test responses were statistically analyzed to determine the impact of the training program on participant's knowledge. For this, the Shapiro-Wilk test was applied to test data normality, followed by the application of paired t-test or Wilcoxon Signed Rank Test for normally and non-normally distributed data, respectively. Finally, a chi-square test was applied to examine the significant (p<0.05) association between training workshops and improvement in the participant's level of understanding of HIV. In all statistical tests, p<0.05 was considered significant. Results The results from our study showed that before the training session, both physicians and allied staff possessed limited knowledge about HIV-related domains. After the workshops, participants from all cities demonstrated a uniform enhancement of knowledge related to different HIV-related domains, evident from the improvement in post-test scores compared to pre-test scores (p<0.0001). The chi-square test showed a significant association between training workshops and improvement in the participant's level of understanding about HIV (p-values for BCQ, MCQ, and true and false: 0.001, 0.0047, and 0.0024, respectively). Conclusions Pre- and post-test evaluation provides an objective, data-driven method for measuring the impact of educational interventions in improving healthcare workers' awareness about HIV. The results emphasize the role of continuous workshops and training programs in enhancing the knowledge and understanding of healthcare and allied health workers regarding HIV.
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Affiliation(s)
- Sharaf A Shah
- Infectious Disease, Bridge Consultant Foundation, Karachi, PAK
| | - Syed Hani Abidi
- Biomedical Sciences, Nazarbayev University School of Medicine, Astana, KAZ
- Biological and Biomedical Sciences, Aga Khan University Medical College, Karachi, PAK
| | - Altaf A Soomro
- Infectious Disease, Bridge Consultant Foundation, Karachi, PAK
| | - Nida Farooqui
- Biological and Biomedical Sciences, Aga Khan University Medical College, Karachi, PAK
| | - Tehreem Ansari
- Infectious Diseases, Dow University Hospital, Dow University of Health Sciences, Karachi, PAK
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Rashid A, Kang L, Yi F, Mir F, Getaneh Y, Shao Y, Abidi SH. Characterization of HIV-1 CRF02_AG/A3/G unique recombinant forms identified among children in Larkana, Pakistan. Front Cell Infect Microbiol 2023; 13:1284815. [PMID: 37965253 PMCID: PMC10642767 DOI: 10.3389/fcimb.2023.1284815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 10/16/2023] [Indexed: 11/16/2023] Open
Abstract
Co-circulation of different human immunodeficiency virus type 1 HIV-1 subtypes among infected populations can lead to the generation of new recombinants. In Pakistan, subtype A1 and CRF02_AG are the dominant strains circulating among key populations. The high prevalence of new HIV infections among the key populations highlights the possibility of recombination between the dominant strains, which can lead to the generation of new recombinants. Here, we identified a recombinant cluster composed of CRF02_AG, sub-subtype A3, and subtype G among HIV-infected children in Larkana. For the study, 10 retrospectively collected samples, with recombination signals in the pol gene, were used to perform a near full-length genome NFLG sequencing. Of the 10 samples, NFLG was successfully sequenced from seven samples. Phylogenetic analysis of the seven NFLGs showed that all recombinants formed a distinct monophyletic cluster and were distinct from known HIV-1 circulating recombinant forms CRFs. Recombination analyses showed that all seven NFLGs shared a similar recombinant structure consisting of CRF02_AG, sub-subtype A3, and subtype G, with a sub-subtype A3 fragment inserted into pol and vif regions spanning from (HXB2: 4218-5518), and a subtype G fragment inserted into vpu, rev, tat and env regions spanning from (HXB2: 5957-8250) of the CRF02_AG backbone. The identification of unique recombinant forms may indicate the presence and transmission of several co-circulating lineages in Larkana, giving rise to newer CRFs. This study also highlights the importance of continuous molecular surveillance to fully understand HIV-1 genetic diversity in Pakistan, particularly in Larkana, which is the epicenter of HIV outbreaks.
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Affiliation(s)
- Abdur Rashid
- School of Medicine, Nankai University, Tianjin, China
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Li Kang
- College of Life Sciences, Nankai University, Tianjin, China
| | - Feng Yi
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Fatima Mir
- Department of Pediatric and Child Health, Aga Khan University, Karachi, Pakistan
| | - Yimam Getaneh
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Yiming Shao
- School of Medicine, Nankai University, Tianjin, China
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Changping Laboratory, Beijing, 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
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Siddiqui D, Badar U, Javaid M, Farooqui N, Shah SA, Iftikhar A, Sultan F, Mir F, Furqan S, Mahmood SF, Abidi SH. Genetic and antiretroviral drug resistance mutations analysis of reverse transcriptase and protease gene from Pakistani people living with HIV-1. PLoS One 2023; 18:e0290425. [PMID: 37616294 PMCID: PMC10449192 DOI: 10.1371/journal.pone.0290425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 08/08/2023] [Indexed: 08/26/2023] Open
Abstract
BACKGROUND Antiretroviral therapy (ART) effectiveness is compromised by the emergence of HIV drug resistance mutations (DRM) and can lead to the failure of ART. Apart from intrinsic viral factors, non-compliance with drugs and/or the use of sub-optimum therapy can lead to the emergence of DRMs. In Pakistan HIV currently exists as a concentrated epidemic, however, ART coverage is very low, and drug adherence is poor. ART is selected assuming without baseline genotyping. Pakistan has recently seen a rise in treatment failures, but the country's actual burden of DRM is still unknown. In this study, we perform the genetic and drug resistance analysis of the pol gene from Pakistani HIV-positive ART-naïve and ART-experienced individuals. METHODS In this study, HIV-1 pol was sequenced from 146 HIV-1 positive individuals, divided into ART-naïve (n = 37) and ART-experienced (n = 109). The sequences were also used to determine HIV-1 subtypes, the prevalence of DRM, and pol genetic variability. RESULTS DRM analysis identified numerous DRMs against reverse transcriptase inhibitors in both ART-naïve and ART-experienced groups, including a few that are classified as rare. Additionally, the ART-experienced group showed mutations associated with resistance to protease inhibitors. Genetic analysis showed negative selection pressure in both groups, but a higher rate of evolution in the ART-naïve group. CONCLUSION High prevalence of DRMs, especially against previous first-line treatment in ART- naïve and the accumulation of DRMs in ART-experienced groups is concerning and warrants that a more extensive DRM survey be carried out to inform first-line and second-line ART regimen recommendations.
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Affiliation(s)
- Dilsha Siddiqui
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi, Pakistan
- Department of Genetics, University of Karachi, Karachi, Pakistan
| | - Uzma Badar
- Department of Genetics, University of Karachi, Karachi, Pakistan
| | | | - Nida Farooqui
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi, Pakistan
| | | | - Ayesha Iftikhar
- Shaukat Khanum Memorial Hospital and Research Centre, Lahore, Pakistan
| | - Faisal Sultan
- Shaukat Khanum Memorial Hospital and Research Centre, Lahore, Pakistan
| | - Fatima Mir
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Sofia Furqan
- National AIDS Control Program, Ministry of Health, Islamabad, Pakistan
| | | | - Syed Hani Abidi
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi, Pakistan
- Department of Biomedical Sciences, Nazarbayev University School of Medicine, Astana, Kazakhstan
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Farooqui N, Mir F, Siddiqui D, Hotwani A, Nathwani AA, Mahmood SF, Sadiq K, Kayani HA, Sheikh SA, Shah SA, Ferrand RA, Abidi SH. Phylogenetic and drug- and vaccine-resistance profiles of Hepatitis B Virus among children with HIV co-infection in Pakistan. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 105:105371. [PMID: 36179949 PMCID: PMC9614405 DOI: 10.1016/j.meegid.2022.105371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 09/25/2022] [Accepted: 09/26/2022] [Indexed: 02/07/2023]
Abstract
INTRODUCTION HIV-1 and hepatitis B virus (HBV) share common routes of transmission and therefore co-infection is common. In 2019, an HIV-1 outbreak that resulted in >1000 children being infected, predominantly through nosocomial transmission, occurred in Sindh, Pakistan. We conducted a phylogenetic and drug resistance analysis of the HBV Reverse Transcriptase (RT) gene in children with HIV-1 and HBV co-infection. METHODOLOGY Blood samples were collected from 321 children with HIV who were recruited as part of a study to investigate the HIV-1 outbreak. All samples were tested for HBV surface antigen (HBsAg) using an ELISA assay, and positive samples were used to amplify and sequence the HBV RT gene. The phylogenetic relationship between sequences was analyzed, and drug- and vaccine- resistance mutations in the RT gene were explored. RESULTS Of 321 samples, 23% (n = 75) were positive for HBsAg on ELISA. Phylogenetic analysis of the sequences revealed that 63.5% of HBV sequences were sub-genotype D1, while the rest were sub-genotype D2. Cluster analysis revealed grouping of sub-genotype D1 sequences exclusively with Pakistani sequences, while clustering of sub-genotypes D2 predominantly with global sequences. The 236Y mutation associated with resistance to tenofovir was observed in 2.8% of HBV sequences. Additionally, seven vaccine escape mutations were observed, the most common being 128 V. CONCLUSION Our study suggests ongoing transmission of HBV D1 and D2 sub-genotypes in the HIV-1 co-infected population, likely nosocomially, given common routes of HVB and HIV-1 transmission. The prevalence of major HBV drug- and vaccine-resistant mutations remains low. Surveillance for further transmissions and the possible emergence of major drug- or vaccine-resistant variants is required.
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Affiliation(s)
- Nida Farooqui
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi, Pakistan; Department of Biosciences, The Shaheed Zulfikar Ali Bhutto Institute of Science and Technology, Karachi, Pakistan
| | - Fatima Mir
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Dilsha Siddiqui
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi, Pakistan
| | - Aneeta Hotwani
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Apsara Ali Nathwani
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | | | - Kamran Sadiq
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Hammad Afzal Kayani
- Department of Biosciences, The Shaheed Zulfikar Ali Bhutto Institute of Science and Technology, Karachi, Pakistan
| | | | | | - Rashida Abbas Ferrand
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan; Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Syed Hani Abidi
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi, Pakistan; Department of Biomedical Sciences, Nazarbayev University School of Medicine, Nur-Sultan, Kazakhstan.
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Abidi SH, Siddiqui D, Mahmood SF, Siddiqui R, Nathwani AA, Hotwani A, Shah SA, Khan P, Ferrand RA, Mir F. Unassigned Complex Unique Recombinant Forms Related to CRF36_cpx in Children Identified in an HIV-1 Outbreak in Pakistan. AIDS Res Hum Retroviruses 2022; 38:806-811. [PMID: 35778855 PMCID: PMC7614887 DOI: 10.1089/aid.2021.0168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
In 2019, an outbreak of HIV infection predominantly affecting children occurred in Larkana district, Pakistan. This is the largest outbreak ever reported in this age group in Pakistan. In this study, we report two HIV-1 unique recombinant forms identified during the outbreak. Blood samples were collected from HIV-positive children as part of a case-control study to investigate the outbreak. The pol gene was sequenced and used to detect HIV subtype/recombinant forms using subtype, recombination, and phylogenetic analyses. Drug resistance mutation (DRM) analysis was performed to characterize the DRMs in each sequence. We observed the emergence of two unassigned unique recombinant forms related to CRF36_cpx in 15 individuals of the 344 samples collected. Genotype analysis revealed the presence of multiple DRMs associated with resistance to reverse transcriptase inhibitors. The discovery of these unassigned unique recombinant forms in our population highlights the need for comprehensive molecular epidemiological studies to fully understand the distribution and drug resistance patterns to aid control efforts.
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Affiliation(s)
- Syed Hani Abidi
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi, Pakistan
- Department of Biomedical Sciences, Nazarbayev University School of Medicine, Nur-Sultan, Kazakhstan
| | - Dilsha Siddiqui
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi, Pakistan
| | | | - Rehana Siddiqui
- Department of Community Health Sciences, Aga Khan University, Karachi, Pakistan
| | - Apsara Ali Nathwani
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Aneeta Hotwani
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | | | - Palwasha Khan
- Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, UK
| | - Rashida Abbas Ferrand
- Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, UK
| | - Fatima Mir
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
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Marfani WB, Khan HA, Sadiq M, Outani O. The rise in HIV cases in Pakistan: Prospective implications and approaches. Ann Med Surg (Lond) 2022; 81:104492. [PMID: 36106067 PMCID: PMC9464852 DOI: 10.1016/j.amsu.2022.104492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 08/19/2022] [Indexed: 11/29/2022] Open
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CMV and EBV Co-Infection in HIV-Infected Children: Infection Rates and Analysis of Differential Expression of Cytokines in HIV Mono- and HIV-CMV-EBV Co-Infected Groups. Viruses 2022; 14:v14081823. [PMID: 36016445 PMCID: PMC9414517 DOI: 10.3390/v14081823] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/25/2022] [Accepted: 08/13/2022] [Indexed: 12/29/2022] Open
Abstract
(1) Background: CMV and EBV co-infections can affect the HIV disease progression by modulating the immune system. The disease dynamics can differ in HIV-positive adults and children. In Pakistan, HIV is rapidly expanding, especially in children; however, the prevalence of CMV and EBV co-infection and the effect on immune modulation in HIV-positive children are not known. This study aimed to bridge this gap by estimating the rate of active CMV and EBV co-infection in HIV-positive children, followed by the analysis of differential expression of cytokines in HIV mono- and HIV/CMV/EBV co-infected children. (2) Methods: DNA samples from 319 HIV-positive children, previously recruited as part of a study to investigate the HIV outbreak in Larkana, Pakistan, in 2019, were screened for CMV and EBV through qPCR. Subsequently, differences in HIV viral loads and CD4 counts were analyzed between the HIV mono- and HIV/CMV/EBV co-infected groups. The RNA samples were used to determine the differential expression of both pro- and anti-inflammatory cytokines in the mono- and co-infected groups using RT-qPCR, while unpaired T-test and Pearson correlation test were applied to, respectively, analyze the differential cytokine expression and correlation between cytokine in the two groups. (3) Results: Of 319 samples, the rate of active EBV and CMV co-infection in HIV-positive children was observed in 79.9% and 38.9%, respectively. A significant difference was observed in HIV viral load between HIV mono- and co-infected groups. IFN-γ expression was found to be lower in the HIV mono-infected group, while higher in all other three co-infected groups. Meanwhile, mRNA expression of TGF-β1 was found to be lower in HIV mono- and HIV–CMV–EBV co-infected groups, while higher in HIV–CMV and HIV–EBV co-infected groups. IFN-γ and IL-2 exhibited a significant positive correlation in all except HIV–CMV co-infected group. (4) Conclusions: The study suggests that the presence of EBV/CMV co-infection can affect the HIV viral loads and expression of certain cytokines (IFN-γ and TGF-β1), which may affect the HIV disease dynamics in infected children.
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Patil A, Patil S, Rao A, Gadhe S, Kurle S, Panda S. Exploring the Evolutionary History and Phylodynamics of Human Immunodeficiency Virus Type 1 Outbreak From Unnao, India Using Phylogenetic Approach. Front Microbiol 2022; 13:848250. [PMID: 35663884 PMCID: PMC9158528 DOI: 10.3389/fmicb.2022.848250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 04/04/2022] [Indexed: 11/13/2022] Open
Abstract
Certain rural and semiurban settings in the Unnao district, Uttar Pradesh, India observed an unprecedented increase in the detection of HIV cases during July 2017. Subsequent investigations through health camps and a follow-up case-control study attributed the outbreak to the unsafe injection exposures during treatment. In this study, we have undertaken a secondary analysis to understand the phylogenetic aspects of the outbreak-associated HIV-1 sequences along with the origin and phylodynamics of these sequences. The initial phylogenetic analysis indicated separate monophyletic grouping and there was no mixing of outbreak-associated sequences with sequences from other parts of India. Transmission network analysis using distance-based and non-distance-based methods revealed the existence of transmission clusters within the monophyletic Unnao clade. The median time to the most recent common ancestor (tMRCA) for sequences from Unnao using the pol gene region was observed to be 2011.87 [95% highest posterior density (HPD): 2010.09–2013.53], while the estimates using envelope (env) gene region sequences traced the tMRCA to 2010.33 (95% HPD: 2007.76–2012.99). Phylodynamics estimates demonstrated that the pace of this local epidemic has slowed down in recent times before the time of sampling, but was certainly on an upward track since its inception till 2014.
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Affiliation(s)
- Ajit Patil
- HIV Drug Resistance Laboratory, Indian Council of Medical Research (ICMR)-National AIDS Research Institute, Pune, India
| | - Sandip Patil
- Division of Clinical Sciences, Indian Council of Medical Research (ICMR)-National AIDS Research Institute, Pune, India
| | - Amrita Rao
- Division of Clinical Sciences, Indian Council of Medical Research (ICMR)-National AIDS Research Institute, Pune, India
| | - Sharda Gadhe
- HIV Drug Resistance Laboratory, Indian Council of Medical Research (ICMR)-National AIDS Research Institute, Pune, India
| | - Swarali Kurle
- HIV Drug Resistance Laboratory, Indian Council of Medical Research (ICMR)-National AIDS Research Institute, Pune, India
- *Correspondence: Swarali Kurle
| | - Samiran Panda
- Indian Council of Medical Research Headquarter, New Delhi, India
- Samiran Panda ;
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Nduva GM, Otieno F, Kimani J, McKinnon LR, Cholette F, Sandstrom P, Graham SM, Price MA, Smith AD, Bailey RC, Hassan AS, Esbjörnsson J, Sanders EJ. Phylogeographic Assessment Reveals Geographic Sources of HIV-1 Dissemination Among Men Who Have Sex With Men in Kenya. Front Microbiol 2022; 13:843330. [PMID: 35356525 PMCID: PMC8959701 DOI: 10.3389/fmicb.2022.843330] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Accepted: 01/19/2022] [Indexed: 12/14/2022] Open
Abstract
HIV-1 transmission dynamics involving men who have sex with men (MSM) in Africa are not well understood. We investigated the rates of HIV-1 transmission between MSM across three regions in Kenya: Coast, Nairobi, and Nyanza. We analyzed 372 HIV-1 partial pol sequences sampled during 2006-2019 from MSM in Coast (N = 178, 47.9%), Nairobi (N = 137, 36.8%), and Nyanza (N = 57, 15.3%) provinces in Kenya. Maximum-likelihood (ML) phylogenetics and Bayesian inference were used to determine HIV-1 clusters, evolutionary dynamics, and virus migration rates between geographic regions. HIV-1 sub-subtype A1 (72.0%) was most common followed by subtype D (11.0%), unique recombinant forms (8.9%), subtype C (5.9%), CRF 21A2D (0.8%), subtype G (0.8%), CRF 16A2D (0.3%), and subtype B (0.3%). Forty-six clusters (size range 2-20 sequences) were found-half (50.0%) of which had evidence of extensive HIV-1 mixing among different provinces. Data revealed an exponential increase in infections among MSM during the early-to-mid 2000s and stable or decreasing transmission dynamics in recent years (2017-2019). Phylogeographic inference showed significant (Bayes factor, BF > 3) HIV-1 dissemination from Coast to Nairobi and Nyanza provinces, and from Nairobi to Nyanza province. Strengthening HIV-1 prevention programs to MSM in geographic locations with higher HIV-1 prevalence among MSM (such as Coast and Nairobi) may reduce HIV-1 incidence among MSM in Kenya.
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Affiliation(s)
- George M. Nduva
- Department of Translational Medicine, Lund University, Lund, Sweden
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Joshua Kimani
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
| | - Lyle R. McKinnon
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
| | - Francois Cholette
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
- National Microbiology Laboratory at the JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Paul Sandstrom
- National Microbiology Laboratory at the JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Susan M. Graham
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
- Department of Epidemiology, University of Washington, Seattle, WA, United States
| | - Matt A. Price
- IAVI, San Francisco, CA, United States
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, United States
| | - Adrian D. Smith
- Nuffield Department of Medicine, The University of Oxford, Oxford, United Kingdom
| | - Robert C. Bailey
- Nyanza Reproductive Health Society, Kisumu, Kenya
- Division of Epidemiology and Biostatistics, University of Illinois Chicago, Chicago, IL, United States
| | - Amin S. Hassan
- Department of Translational Medicine, Lund University, Lund, Sweden
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Joakim Esbjörnsson
- Department of Translational Medicine, Lund University, Lund, Sweden
- Nuffield Department of Medicine, The University of Oxford, Oxford, United Kingdom
| | - Eduard J. Sanders
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
- Nuffield Department of Medicine, The University of Oxford, Oxford, United Kingdom
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