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Gulinaizhaer A, Zou M, Ma S, Yao Y, Fan X, Wu G. Isothermal nucleic acid amplification technology in HIV detection. Analyst 2023; 148:1189-1208. [PMID: 36825492 DOI: 10.1039/d2an01813f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Nucleic acid testing for HIV plays an important role in the early diagnosis and monitoring of antiretroviral therapy outcomes in HIV patients and HIV-infected infants. Currently, the main molecular diagnostic methods employed are complex, time-consuming, and expensive to operate in resource-limited areas. Isothermal nucleic acid amplification technology overcomes some of the shortcomings of traditional assays and makes it possible to use point-of-care tests for molecular HIV detection. Here, we summarize and discuss the latest technological advances in isothermal nucleic acid amplification for HIV detection, with the intent of providing guidance for the development of subsequent HIV assays with high sensitivity and specificity.
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Affiliation(s)
- Abudushalamu Gulinaizhaer
- Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing 210009, Jiangsu, China.,Department of Laboratory Medicine, Medical School of Southeast University, Nanjing 210009, Jiangsu, China.
| | - Mingyuan Zou
- Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing 210009, Jiangsu, China.,Department of Laboratory Medicine, Medical School of Southeast University, Nanjing 210009, Jiangsu, China.
| | - Shuo Ma
- Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing 210009, Jiangsu, China.,Department of Laboratory Medicine, Medical School of Southeast University, Nanjing 210009, Jiangsu, China.
| | - Yuming Yao
- Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing 210009, Jiangsu, China.,Department of Laboratory Medicine, Medical School of Southeast University, Nanjing 210009, Jiangsu, China.
| | - Xiaobo Fan
- Department of Laboratory Medicine, Medical School of Southeast University, Nanjing 210009, Jiangsu, China.
| | - Guoqiu Wu
- Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing 210009, Jiangsu, China.,Department of Laboratory Medicine, Medical School of Southeast University, Nanjing 210009, Jiangsu, China. .,Jiangsu Provincial Key Laboratory of Critical Care Medicine, Southeast University, Nanjing 210009, Jiangsu, China
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Novitsky V, Steingrimsson J, Howison M, Dunn CW, Gillani FS, Fulton J, Bertrand T, Howe K, Bhattarai L, Ronquillo G, MacAskill M, Bandy U, Hogan J, Kantor R. Not all clusters are equal: dynamics of molecular HIV-1 clusters in a statewide Rhode Island epidemic. AIDS 2023; 37:389-399. [PMID: 36695355 PMCID: PMC9881752 DOI: 10.1097/qad.0000000000003426] [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: 01/26/2023]
Abstract
OBJECTIVES Molecular epidemiology is a powerful tool to characterize HIV epidemics and prioritize public health interventions. Typically, HIV clusters are assumed to have uniform patterns over time. We hypothesized that assessment of cluster evolution would reveal distinct cluster behavior, possibly improving molecular epidemic characterization, towards disrupting HIV transmission. DESIGN Retrospective cohort. METHODS Annual phylogenies were inferred by cumulative aggregation of all available HIV-1 pol sequences of individuals with HIV-1 in Rhode Island (RI) between 1990 and 2020, representing a statewide epidemic. Molecular clusters were detected in annual phylogenies by strict and relaxed cluster definition criteria, and the impact of annual newly-diagnosed HIV-1 cases to the structure of individual clusters was examined over time. RESULTS Of 2153 individuals, 31% (strict criteria) - 47% (relaxed criteria) clustered. Longitudinal tracking of individual clusters identified three cluster types: normal, semi-normal and abnormal. Normal clusters (83-87% of all identified clusters) showed predicted growing/plateauing dynamics, with approximately three-fold higher growth rates in large (15-18%) vs. small (∼5%) clusters. Semi-normal clusters (1-2% of all clusters) temporarily fluctuated in size and composition. Abnormal clusters (11-16% of all clusters) demonstrated collapses and re-arrangements over time. Borderline values of cluster-defining parameters explained dynamics of non-normal clusters. CONCLUSIONS Comprehensive tracing of molecular HIV clusters over time in a statewide epidemic identified distinct cluster types, likely missed in cross-sectional analyses, demonstrating that not all clusters are equal. This knowledge challenges current perceptions of consistent cluster behavior over time and could improve molecular surveillance of local HIV epidemics to better inform public health strategies.
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Affiliation(s)
| | | | - Mark Howison
- Research Improving People’s Lives, Providence, RI, USA
| | | | | | | | | | | | | | | | | | - Utpala Bandy
- Rhode Island Department of Health, Providence, RI, USA
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Zhang D, Li H, Zheng C, Han J, Li H, Liu Y, Wang X, Jia L, Li S, Li T, Zhang B, Chen L, Yang Z, Gan Y, Zhong Y, Li J, Zhao J, Li L. Analysis of HIV-1 molecular transmission network reveals the prevalence characteristics of three main HIV-1 subtypes in Shenzhen, China. J Infect 2022; 85:e190-e192. [PMID: 36031153 DOI: 10.1016/j.jinf.2022.08.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 08/19/2022] [Indexed: 11/25/2022]
Affiliation(s)
- Dong Zhang
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Hanping Li
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Chenli Zheng
- Shenzhen Center for Disease Control and Prevention, Shenzhen, Guangdong 518055, China
| | - Jingwan Han
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Hao Li
- Shenzhen Center for Disease Control and Prevention, Shenzhen, Guangdong 518055, China
| | - Yongjian Liu
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Xiaolin Wang
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Lei Jia
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Siqi Li
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Tianyi Li
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Bohan Zhang
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Lin Chen
- Shenzhen Center for Disease Control and Prevention, Shenzhen, Guangdong 518055, China
| | - Zhengrong Yang
- Shenzhen Center for Disease Control and Prevention, Shenzhen, Guangdong 518055, China
| | - Yongxia Gan
- Shenzhen Center for Disease Control and Prevention, Shenzhen, Guangdong 518055, China
| | - Yifan Zhong
- Shenzhen Center for Disease Control and Prevention, Shenzhen, Guangdong 518055, China
| | - Jingyun Li
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China.
| | - Jin Zhao
- Shenzhen Center for Disease Control and Prevention, Shenzhen, Guangdong 518055, China.
| | - Lin Li
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China.
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Brenner BG, Ibanescu RI, Osman N, Cuadra-Foy E, Oliveira M, Chaillon A, Stephens D, Hardy I, Routy JP, Thomas R, Baril JG, Leblanc R, Tremblay C, Roger M. The Role of Phylogenetics in Unravelling Patterns of HIV Transmission towards Epidemic Control: The Quebec Experience (2002-2020). Viruses 2021; 13:1643. [PMID: 34452506 PMCID: PMC8402830 DOI: 10.3390/v13081643] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/09/2021] [Accepted: 08/11/2021] [Indexed: 01/23/2023] Open
Abstract
Phylogenetics has been advanced as a structural framework to infer evolving trends in the regional spread of HIV-1 and guide public health interventions. In Quebec, molecular network analyses tracked HIV transmission dynamics from 2002-2020 using MEGA10-Neighbour-joining, HIV-TRACE, and MicrobeTrace methodologies. Phylogenetics revealed three patterns of viral spread among Men having Sex with Men (MSM, n = 5024) and heterosexuals (HET, n = 1345) harbouring subtype B epidemics as well as B and non-B subtype epidemics (n = 1848) introduced through migration. Notably, half of new subtype B infections amongst MSM and HET segregating as solitary transmissions or small cluster networks (2-5 members) declined by 70% from 2006-2020, concomitant to advances in treatment-as-prevention. Nonetheless, subtype B epidemic control amongst MSM was thwarted by the ongoing genesis and expansion of super-spreader large cluster variants leading to micro-epidemics, averaging 49 members/cluster at the end of 2020. The growth of large clusters was related to forward transmission cascades of untreated early-stage infections, younger at-risk populations, more transmissible/replicative-competent strains, and changing demographics. Subtype B and non-B subtype infections introduced through recent migration now surpass the domestic epidemic amongst MSM. Phylodynamics can assist in predicting and responding to active, recurrent, and newly emergent large cluster networks, as well as the cryptic spread of HIV introduced through migration.
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Affiliation(s)
- Bluma G. Brenner
- McGill Centre for Viral Diseases, Lady Davis Institute for Medical Research, Montréal, QC H3T 1E2, Canada; (R.-I.I.); (N.O.); (E.C.-F.); (M.O.)
- Department of Microbiology and Immunology, McGill University, Montréal, QC H4A 3J1, Canada
- Department of Medicine (Surgery, Infectious Disease), McGill University, Montréal, QC H3A 2M7, Canada
| | - Ruxandra-Ilinca Ibanescu
- McGill Centre for Viral Diseases, Lady Davis Institute for Medical Research, Montréal, QC H3T 1E2, Canada; (R.-I.I.); (N.O.); (E.C.-F.); (M.O.)
| | - Nathan Osman
- McGill Centre for Viral Diseases, Lady Davis Institute for Medical Research, Montréal, QC H3T 1E2, Canada; (R.-I.I.); (N.O.); (E.C.-F.); (M.O.)
- Department of Microbiology and Immunology, McGill University, Montréal, QC H4A 3J1, Canada
| | - Ernesto Cuadra-Foy
- McGill Centre for Viral Diseases, Lady Davis Institute for Medical Research, Montréal, QC H3T 1E2, Canada; (R.-I.I.); (N.O.); (E.C.-F.); (M.O.)
- Department of Microbiology and Immunology, McGill University, Montréal, QC H4A 3J1, Canada
| | - Maureen Oliveira
- McGill Centre for Viral Diseases, Lady Davis Institute for Medical Research, Montréal, QC H3T 1E2, Canada; (R.-I.I.); (N.O.); (E.C.-F.); (M.O.)
| | - Antoine Chaillon
- Department of Medicine, University of California, San Diego, CA 93903, USA;
| | - David Stephens
- Department of Mathematics and Statistics, McGill University, Montréal, QC H3A 0B9, Canada;
| | - Isabelle Hardy
- Département de Microbiologie et d’Immunologie et Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CHUM), Montréal, QC H2X 0C1, Canada; (I.H.); (C.T.); (M.R.)
| | - Jean-Pierre Routy
- Chronic Viral Illness Service, McGill University Health Centre, Montréal, QC H3A 3J1, Canada;
| | - Réjean Thomas
- Clinique Médicale l’Actuel, Montréal, QC H2L 4P9, Canada;
| | - Jean-Guy Baril
- Clinique Médicale Urbaine du Quartier Latin, Montréal, QC H2L 4E9, Canada;
| | - Roger Leblanc
- Clinique Médicale OPUS, Montréal, QC H3A 1T1, Canada;
| | - Cecile Tremblay
- Département de Microbiologie et d’Immunologie et Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CHUM), Montréal, QC H2X 0C1, Canada; (I.H.); (C.T.); (M.R.)
| | - Michel Roger
- Département de Microbiologie et d’Immunologie et Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CHUM), Montréal, QC H2X 0C1, Canada; (I.H.); (C.T.); (M.R.)
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