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Ding Y, Guo H, Hong X, Li Q, Miao Z, Pan Q, Zheng K, Wang W. The distinct spatiotemporal evolutionary landscape of HBV and HDV largely determines the unique epidemic features of HDV globally. Mol Phylogenet Evol 2024; 197:108114. [PMID: 38825156 DOI: 10.1016/j.ympev.2024.108114] [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: 08/21/2023] [Revised: 05/07/2024] [Accepted: 05/26/2024] [Indexed: 06/04/2024]
Abstract
Chronic infection of hepatitis B virus (HBV) and hepatitis D virus (HDV) causes the most severe form of viral hepatitis. Due to the dependence on HBV, HDV was deemed to co-evolve and co-migrate with HBV. However, we previously found that the naturally occurred HDV/HBV combinations do not always reflect the most efficient virological adaptation (Wang et al., 2021). Moreover, regions with heavy HBV burden do not always correlate with high HDV prevalence (e.g., East Asia), and vice versa (e.g., Central Asia). Herein, we systematically elucidated the spatiotemporal evolutionary landscape of HDV to understand the unique epidemic features of HDV. We found that the MRCA of HDV was from South America around the late 13th century, was globally dispersed mainly via Central Asia, and evolved into eight genotypes from the 19th to 20th century. In contrast, the MRCA of HBV was from Europe ∼23.7 thousand years ago (Kya), globally dispersed mainly via Africa and East Asia, and evolved into eight genotypes ∼1100 years ago. When HDV stepped in, all present-day HBV genotypes had already formed and its global genotypic distribution had stayed stable geographically. Nevertheless, regionalized HDV adapted to local HBV genotypes and human lineages, contributing to the global geographical separation of HDV genotypes. Additionally, a sharp increase in HDV infections was observed after the 20th century. In conclusion, HDV exhibited a distinct spatiotemporal distribution path compared with HBV. This unique evolutionary relationship largely fostered the unique epidemic features we observe nowadays. Moreover, HDV infections may continue to ramp up globally, thus more efforts are urgently needed to combat this disease.
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Affiliation(s)
- Yibo Ding
- Department of Pathogen Biology and Immunology, Jiangsu Key Laboratory of Immunity and Metabolism, Jiangsu International Laboratory of Immunity and Metabolism, Xuzhou Medical University, Xuzhou, China
| | - Hongbo Guo
- Department of Pathogen Biology and Immunology, Jiangsu Key Laboratory of Immunity and Metabolism, Jiangsu International Laboratory of Immunity and Metabolism, Xuzhou Medical University, Xuzhou, China.
| | - Xinfang Hong
- Second Medical Center of PLA General Hospital, Beijing, China
| | - Qiudi Li
- Department of Pathogen Biology and Immunology, Jiangsu Key Laboratory of Immunity and Metabolism, Jiangsu International Laboratory of Immunity and Metabolism, Xuzhou Medical University, Xuzhou, China
| | - Zhijiang Miao
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Qiuwei Pan
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam, The Netherlands.
| | - Kuiyang Zheng
- Department of Pathogen Biology and Immunology, Jiangsu Key Laboratory of Immunity and Metabolism, Jiangsu International Laboratory of Immunity and Metabolism, Xuzhou Medical University, Xuzhou, China.
| | - Wenshi Wang
- Department of Pathogen Biology and Immunology, Jiangsu Key Laboratory of Immunity and Metabolism, Jiangsu International Laboratory of Immunity and Metabolism, Xuzhou Medical University, Xuzhou, China.
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Lemée V, Gréaume S, Gautier J, Dzamitika SA, Coignard C, Jortani SA, Grillet B, Badawi M, Plantier JC. Performance evaluation of the new Access HIV Ag/Ab combo assay on the DxI 9000 Access Immunoassay Analyzer. J Clin Virol 2024; 174:105712. [PMID: 39047323 DOI: 10.1016/j.jcv.2024.105712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 07/03/2024] [Accepted: 07/05/2024] [Indexed: 07/27/2024]
Abstract
Fourth-generation HIV immunoassays have been developed to reduce the window period of detection during seroconversion period, allowing for the detection of early and established infections. The aim of this work was to evaluate a newly developed assay, Access HIV Ag/Ab combo on the novel high throughput DxI 9000 Access Immunoassay Analyzer (Beckman Coulter, Inc.). The assay allows for simultaneous qualitative detection and differentiation of HIV-1 p24 antigen and HIV-1/2 antibodies. Assay performance was compared to two gold standard assays, the Abbott Architect HIV Ag/Ab Combo and Roche Elecsys HIV Duo, and assessed in a multicenter study, using a wide panel of samples (n > 9000, clinical samples and viral lysates) representative of genetic diversity for both antibodies and antigens, early phases of infection, negative, and cross-reacting samples. The clinical sensitivity was 100 % for clinical samples as well as for viral lysates. Data on viral lysates and early detection on seroconversion panels showed a better result with the Access assay. Analytical sensitivity showed a limit of p24 detection determined around 0.2 IU/mL. The overall specificity was 99.91 %, and no interference was found using the potentially cross-reactive samples. In conclusion, the Access HIV Ag/Ab combo assay demonstrated its ability for accurate diagnosis of chronic as well as primary HIV infections on the DxI 9000 Analyzer, despite the high level of genetic diversity of these viruses.
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Affiliation(s)
- V Lemée
- CHU Rouen, Department of Virology, National Reference Center of HIV, F-76000 Rouen, France; Univ Rouen Normandie, Univ de Caen, INSERM, DYNAMICURE UMR 1311, CHU Rouen, Department of Virology, National Reference Center of HIV, F-76000 Rouen, France
| | - S Gréaume
- Etablissement Français du Sang (EFS) Hauts-de-France - Normandie (HFNO), Bois Guillaume, France
| | | | | | - C Coignard
- Eurofins Biomnis, Ivry-sur-Seine, France
| | - S A Jortani
- Kentucky Clinical Trials Laboratory (KCTL), Louisville, KY, USA; University of Louisville School of Medicine, Louisville, KY, USA
| | - B Grillet
- Beckman Coulter Immunotech, Marseille, France
| | - M Badawi
- Beckman Coulter Immunotech, Marseille, France
| | - J-C Plantier
- CHU Rouen, Department of Virology, National Reference Center of HIV, F-76000 Rouen, France; Univ Rouen Normandie, Univ de Caen, INSERM, DYNAMICURE UMR 1311, CHU Rouen, Department of Virology, National Reference Center of HIV, F-76000 Rouen, France.
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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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4
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Kirschnick LB, Calderipe CB, Villa A, Santana Dos Santos E, Migliorati C, Martins MD, Santos-Silva AR. Patient communication protocols for sexually transmitted infections: A systematic review. SPECIAL CARE IN DENTISTRY 2024; 44:990-1001. [PMID: 38375918 DOI: 10.1111/scd.12976] [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: 09/06/2023] [Revised: 11/27/2023] [Accepted: 02/04/2024] [Indexed: 02/21/2024]
Abstract
AIMS We conducted a systematic review of post-test communication protocols and observational studies regarding counseling for a positive sexually transmitted infection (STI) result and also discuss the role of dental specialist (e.g., oral medicine) in this sense. METHODS AND RESULTS The search process followed the parameters of PRISMA 2020 guidelines. MEDLINE/PubMed, Web of Science, Scopus, EMBASE, and LILACS were consulted with a specific search strategy for each one. Additionally, the references of the included studies, grey literature, and experts were consulted. Four protocols and 18 observational studies were included in this systematic review, published between 1997 and 2022 in the Americas and Europe. The communication protocols emphasized the importance of conducting personal and private discussions with patients to address their fears and questions. Among the observational studies, 56% indicated that post-test counseling was either ineffective or absent. Furthermore, 22% of the studies used telephone communication to deliver results to patients. CONCLUSIONS Our study showed that the communication process of a positive STI result affects the patients in several aspects, as treatment adherence and their relationship with the community. Nevertheless, this process of STI post-test communication seems to be flawed, which brings potential negative effects to patients.
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Affiliation(s)
- Laura Borges Kirschnick
- Oral Diagnosis Department, Semiology and Oral Pathology Areas, Piracicaba Dental School, State University of Campinas (UNICAMP), Piracicaba, São Paulo, Brazil
| | - Camila Barcellos Calderipe
- Oral Diagnosis Department, Semiology and Oral Pathology Areas, Piracicaba Dental School, State University of Campinas (UNICAMP), Piracicaba, São Paulo, Brazil
| | - Alessandro Villa
- Oral Medicine, Oral Oncology and Dentistry, Miami Cancer Institute, Baptist Health South Florida, Miami, Florida, USA
- Herbert Wertheim College of Medicine, Florida International University, Miami, Florida, USA
| | - Erison Santana Dos Santos
- Oral Diagnosis Department, Semiology and Oral Pathology Areas, Piracicaba Dental School, State University of Campinas (UNICAMP), Piracicaba, São Paulo, Brazil
| | - Cesar Migliorati
- Department of Oral & Maxillofacial Diagnostic Sciences, University of Florida, Gainesville, Florida, USA
| | - Manoela Domingues Martins
- Oral Diagnosis Department, Semiology and Oral Pathology Areas, Piracicaba Dental School, State University of Campinas (UNICAMP), Piracicaba, São Paulo, Brazil
- Department of Oral Pathology, School of Dentistry, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Alan Roger Santos-Silva
- Oral Diagnosis Department, Semiology and Oral Pathology Areas, Piracicaba Dental School, State University of Campinas (UNICAMP), Piracicaba, São Paulo, Brazil
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Gotora PT, Brown K, Martin DR, van der Sluis R, Cloete R, Williams ME. Impact of subtype C-specific amino acid variants on HIV-1 Tat-TAR interaction: insights from molecular modelling and dynamics. Virol J 2024; 21:144. [PMID: 38918875 PMCID: PMC11202254 DOI: 10.1186/s12985-024-02419-6] [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: 03/19/2024] [Accepted: 06/19/2024] [Indexed: 06/27/2024] Open
Abstract
BACKGROUND HIV-1 produces Tat, a crucial protein for transcription, viral replication, and CNS neurotoxicity. Tat interacts with TAR, enhancing HIV reverse transcription. Subtype C Tat variants (C31S, R57S, Q63E) are associated with reduced transactivation and neurovirulence compared to subtype B. However, their precise impact on Tat-TAR binding is unclear. This study investigates how these substitutions affect Tat-TAR interaction. METHODS We utilized molecular modelling techniques, including MODELLER, to produce precise three-dimensional structures of HIV-1 Tat protein variants. We utilized Tat subtype B as the reference or wild type, and generated Tat variants to mirror those amino acid variants found in Tat subtype C. Subtype C-specific amino acid substitutions were selected based on their role in the neuropathogenesis of HIV-1. Subsequently, we conducted molecular docking of each Tat protein variant to TAR using HDOCK, followed by molecular dynamic simulations. RESULTS Molecular docking results indicated that Tat subtype B (TatWt) showed the highest affinity for the TAR element (-262.07), followed by TatC31S (-261.61), TatQ63E (-256.43), TatC31S/R57S/Q63E (-238.92), and TatR57S (-222.24). However, binding free energy analysis showed higher affinities for single variants TatQ63E (-349.2 ± 10.4 kcal/mol) and TatR57S (-290.0 ± 9.6 kcal/mol) compared to TatWt (-247.9 ± 27.7 kcal/mol), while TatC31S and TatC31S/R57SQ/63E showed lower values. Interactions over the protein trajectory were also higher for TatQ63E and TatR57S compared to TatWt, TatC31S, and TatC31S/R57SQ/63E, suggesting that modifying amino acids within the Arginine/Glutamine-rich region notably affects TAR interaction. Single amino acid mutations TatR57S and TatQ63E had a significant impact, while TatC31S had minimal effect. Introducing single amino acid variants from TatWt to a more representative Tat subtype C (TatC31S/R57SQ/63E) resulted in lower predicted binding affinity, consistent with previous findings. CONCLUSIONS These identified amino acid positions likely contribute significantly to Tat-TAR interaction and the differential pathogenesis and neuropathogenesis observed between subtype B and subtype C. Additional experimental investigations should prioritize exploring the influence of these amino acid signatures on TAR binding to gain a comprehensive understanding of their impact on viral transactivation, potentially identifying them as therapeutic targets.
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Affiliation(s)
- Piwai T Gotora
- Human Metabolomics, North-West University, Potchefstroom, South Africa
| | - Keaghan Brown
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa
| | - Darius R Martin
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa
- Department of Science and Innovation/Mintek Nanotechnology Innovation Centre, Biolabels Node, University of the Western Cape, Bellville, South Africa
| | | | - Ruben Cloete
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa
| | - Monray E Williams
- Human Metabolomics, North-West University, Potchefstroom, South Africa.
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Sonela N, Mann J, Godwe C, Goni OH, Tchakoute M, Nkoue N, de Oliveira T, Brockman MA, Brumme ZL, Ndung'u T, Tongo M. No detectable differences in Nef-mediated downregulation of HLA-I and CD4 molecules among HIV-1 group M lineages circulating in Cameroon, where the pandemic originated. FRONTIERS IN VIROLOGY (LAUSANNE, SWITZERLAND) 2024; 4:fviro.2024.1379217. [PMID: 38883214 PMCID: PMC7616105 DOI: 10.3389/fviro.2024.1379217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
HIV-1 group M (HIV-1M) lineages downregulate HLA-I and CD4 expression via their Nef proteins. We hypothesized that these Nef functions may be partially responsible for the differences in prevalence of viruses from different lineages that co-circulate within an epidemic. Here, we characterized these two Nef activities in HIV-1M isolates from Cameroon, where multiple variants have been circulating since the pandemic's origin. Single HIV-1 Nef clones from 234 HIV-1-ART naïve individuals living in remote villages and two cosmopolitan cities of Cameroon, sampled between 2000 and 2013, were isolated from plasma HIV RNA and analyzed for their capacity to downregulate HLA-I and CD4 molecules. We found that, despite a large degree of within- and inter- lineage variation, the ability of Nef to downregulate HLA-I was similar across these different viruses. Moreover, Nef-mediated CD4 downregulation activity was also well conserved across the different lineages found in Cameroon. In addition, we observed a trend towards higher HLA-I downregulation activity of viruses circulating in the cosmopolitan cities versus the remote villages, whereas the CD4 downregulation activities were similar across the two settings. Furthermore, we noted a significant decline of HLA-I downregulation activity from 2000 to 2013, providing additional evidence supporting the attenuation of the global HIV-1M population over time. Finally, we identified 18 amino acids associated with differential HLA-I downregulation and 13 amino acids associated with differential CD4 downregulation within the dominant CRF02_AG lineage. Our lack of observation of HIV lineage-related differences in Nef-mediated HLA-I and CD4 downregulation function suggests that these activities do not substantively influence the prevalence of different HIV-1M lineages in Cameroon.
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Affiliation(s)
- Nelson Sonela
- Center of Research for Emerging and Re-Emerging Diseases (CREMER), Institute of Medical Research and Study of Medicinal Plants (IMPM), Yaoundé, Cameroon
- Chantal BIYA International Reference Centre for Research on HIV/AIDS prevention and management (CIRCB), Yaoundé, Cameroon
- Department of Medicine, Weill Cornell Medical College, Cornell University, New York, NY, United States
| | - Jaclyn Mann
- HIV Pathogenesis Programme, University of KwaZulu-Natal, Durban, South Africa
| | - Celestin Godwe
- Center of Research for Emerging and Re-Emerging Diseases (CREMER), Institute of Medical Research and Study of Medicinal Plants (IMPM), Yaoundé, Cameroon
- Départment of Biochemistry, University of Douala, Douala, Cameroon
| | - Oumarou H Goni
- Center of Research for Emerging and Re-Emerging Diseases (CREMER), Institute of Medical Research and Study of Medicinal Plants (IMPM), Yaoundé, Cameroon
- Départment of Microbiology, Faculty of Sciences, University of Yaoundé 1, Yaoundé, Cameroon
| | - Mérime Tchakoute
- Programmes de Santé et développement au sein du Groupement de la Filière Bois du Cameroun, Yaoundé, Cameroon
| | - Nathalie Nkoue
- Programmes de Santé et développement au sein du Groupement de la Filière Bois du Cameroun, Yaoundé, Cameroon
| | - Tulio de Oliveira
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Mark A Brockman
- Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Thumbi Ndung'u
- HIV Pathogenesis Programme, University of KwaZulu-Natal, Durban, South Africa
- Max Planck Institute for Infection Biology, Berlin, Germany
- Africa Health Research Institute (AHRI), Durban, South Africa
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, United States
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Marcel Tongo
- Center of Research for Emerging and Re-Emerging Diseases (CREMER), Institute of Medical Research and Study of Medicinal Plants (IMPM), Yaoundé, Cameroon
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7
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Windels EM, Wampande EM, Joloba ML, Boom WH, Goig GA, Cox H, Hella J, Borrell S, Gagneux S, Brites D, Stadler T. HIV co-infection is associated with reduced Mycobacterium tuberculosis transmissibility in sub-Saharan Africa. PLoS Pathog 2024; 20:e1011675. [PMID: 38696531 DOI: 10.1371/journal.ppat.1011675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 05/14/2024] [Accepted: 04/10/2024] [Indexed: 05/04/2024] Open
Abstract
Persons living with HIV are known to be at increased risk of developing tuberculosis (TB) disease upon infection with Mycobacterium tuberculosis (Mtb). However, it has remained unclear how HIV co-infection affects subsequent Mtb transmission from these patients. Here, we customized a Bayesian phylodynamic framework to estimate the effects of HIV co-infection on the Mtb transmission dynamics from sequence data. We applied our model to four Mtb genomic datasets collected in sub-Saharan African countries with a generalized HIV epidemic. Our results confirm that HIV co-infection is a strong risk factor for developing active TB. Additionally, we demonstrate that HIV co-infection is associated with a reduced effective reproductive number for TB. Stratifying the population by CD4+ T-cell count yielded similar results, suggesting that, in this context, CD4+ T-cell count is not a better predictor of Mtb transmissibility than HIV infection status alone. Together, our genome-based analyses complement observational household contact studies, and more firmly establish the negative association between HIV co-infection and Mtb transmissibility.
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Affiliation(s)
- Etthel M Windels
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | | | | - W Henry Boom
- Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, Ohio, United States of America
| | - Galo A Goig
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Helen Cox
- University of Cape Town, Cape Town, South Africa
| | - Jerry Hella
- Ifakara Health Institute, Dar es Salaam, Tanzania
| | - Sonia Borrell
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Daniela Brites
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Tanja Stadler
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
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8
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Apetroaei MM, Velescu BȘ, Nedea MI(I, Dinu-Pîrvu CE, Drăgănescu D, Fâcă AI, Udeanu DI, Arsene AL. The Phenomenon of Antiretroviral Drug Resistance in the Context of Human Immunodeficiency Virus Treatment: Dynamic and Ever Evolving Subject Matter. Biomedicines 2024; 12:915. [PMID: 38672269 PMCID: PMC11048092 DOI: 10.3390/biomedicines12040915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 04/11/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
Human immunodeficiency virus (HIV) is a significant global health issue that affects a substantial number of individuals across the globe, with a total of 39 million individuals living with HIV/AIDS. ART has resulted in a reduction in HIV-related mortality. Nevertheless, the issue of medication resistance is a significant obstacle in the management of HIV/AIDS. The unique genetic composition of HIV enables it to undergo rapid mutations and adapt, leading to the emergence of drug-resistant forms. The development of drug resistance can be attributed to various circumstances, including noncompliance with treatment regimens, insufficient dosage, interactions between drugs, viral mutations, preexposure prophylactics, and transmission from mother to child. It is therefore essential to comprehend the molecular components of HIV and the mechanisms of antiretroviral medications to devise efficacious treatment options for HIV/AIDS.
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Affiliation(s)
- Miruna-Maria Apetroaei
- Faculty of Pharmacy, Carol Davila University of Medicine and Pharmacy, 6 Traian Vuia Street, 020956 Bucharest, Romania; (M.-M.A.); (M.I.N.); (C.E.D.-P.); (D.D.); (A.I.F.); (D.I.U.); (A.L.A.)
| | - Bruno Ștefan Velescu
- Faculty of Pharmacy, Carol Davila University of Medicine and Pharmacy, 6 Traian Vuia Street, 020956 Bucharest, Romania; (M.-M.A.); (M.I.N.); (C.E.D.-P.); (D.D.); (A.I.F.); (D.I.U.); (A.L.A.)
| | - Marina Ionela (Ilie) Nedea
- Faculty of Pharmacy, Carol Davila University of Medicine and Pharmacy, 6 Traian Vuia Street, 020956 Bucharest, Romania; (M.-M.A.); (M.I.N.); (C.E.D.-P.); (D.D.); (A.I.F.); (D.I.U.); (A.L.A.)
| | - Cristina Elena Dinu-Pîrvu
- Faculty of Pharmacy, Carol Davila University of Medicine and Pharmacy, 6 Traian Vuia Street, 020956 Bucharest, Romania; (M.-M.A.); (M.I.N.); (C.E.D.-P.); (D.D.); (A.I.F.); (D.I.U.); (A.L.A.)
| | - Doina Drăgănescu
- Faculty of Pharmacy, Carol Davila University of Medicine and Pharmacy, 6 Traian Vuia Street, 020956 Bucharest, Romania; (M.-M.A.); (M.I.N.); (C.E.D.-P.); (D.D.); (A.I.F.); (D.I.U.); (A.L.A.)
| | - Anca Ionela Fâcă
- Faculty of Pharmacy, Carol Davila University of Medicine and Pharmacy, 6 Traian Vuia Street, 020956 Bucharest, Romania; (M.-M.A.); (M.I.N.); (C.E.D.-P.); (D.D.); (A.I.F.); (D.I.U.); (A.L.A.)
- Marius Nasta Institute of Pneumophthisiology, 90 Viilor Street, 050159 Bucharest, Romania
| | - Denisa Ioana Udeanu
- Faculty of Pharmacy, Carol Davila University of Medicine and Pharmacy, 6 Traian Vuia Street, 020956 Bucharest, Romania; (M.-M.A.); (M.I.N.); (C.E.D.-P.); (D.D.); (A.I.F.); (D.I.U.); (A.L.A.)
- Marius Nasta Institute of Pneumophthisiology, 90 Viilor Street, 050159 Bucharest, Romania
| | - Andreea Letiția Arsene
- Faculty of Pharmacy, Carol Davila University of Medicine and Pharmacy, 6 Traian Vuia Street, 020956 Bucharest, Romania; (M.-M.A.); (M.I.N.); (C.E.D.-P.); (D.D.); (A.I.F.); (D.I.U.); (A.L.A.)
- Marius Nasta Institute of Pneumophthisiology, 90 Viilor Street, 050159 Bucharest, Romania
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9
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Müller NF, Bouckaert RR, Wu CH, Bedford T. MASCOT-Skyline integrates population and migration dynamics to enhance phylogeographic reconstructions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.06.583734. [PMID: 38496513 PMCID: PMC10942421 DOI: 10.1101/2024.03.06.583734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
The spread of infectious diseases is shaped by spatial and temporal aspects, such as host population structure or changes in the transmission rate or number of infected individuals over time. These spatiotemporal dynamics are imprinted in the genome of pathogens and can be recovered from those genomes using phylodynamics methods. However, phylodynamic methods typically quantify either the temporal or spatial transmission dynamics, which leads to unclear biases, as one can potentially not be inferred without the other. Here, we address this challenge by introducing a structured coalescent skyline approach, MASCOT-Skyline that allows us to jointly infer spatial and temporal transmission dynamics of infectious diseases using Markov chain Monte Carlo inference. To do so, we model the effective population size dynamics in different locations using a non-parametric function, allowing us to approximate a range of population size dynamics. We show, using a range of different viral outbreak datasets, potential issues with phylogeographic methods. We then use these viral datasets to motivate simulations of outbreaks that illuminate the nature of biases present in the different phylogeographic methods. We show that spatial and temporal dynamics should be modeled jointly even if one seeks to recover just one of the two. Further, we showcase conditions under which we can expect phylogeographic analyses to be biased, particularly different subsampling approaches, as well as provide recommendations of when we can expect them to perform well. We implemented MASCOT-Skyline as part of the open-source software package MASCOT for the Bayesian phylodynamics platform BEAST2.
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Affiliation(s)
- Nicola F. Müller
- Division of HIV, ID and Global Medicine, University of California San Francisco, San Francisco, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, USA
| | - Remco R. Bouckaert
- Centre for Computational Evolution, The University of Auckland, New Zealand
| | - Chieh-Hsi Wu
- School of Mathematical Sciences, University of Southampton, UK
| | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, USA
- Howard Hughes Medical Institute, Seattle, USA
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10
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Singh S, Sharma P, Pal N, Sarma DK, Tiwari R, Kumar M. Holistic One Health Surveillance Framework: Synergizing Environmental, Animal, and Human Determinants for Enhanced Infectious Disease Management. ACS Infect Dis 2024; 10:808-826. [PMID: 38415654 DOI: 10.1021/acsinfecdis.3c00625] [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] [Indexed: 02/29/2024]
Abstract
Recent pandemics, including the COVID-19 outbreak, have brought up growing concerns about transmission of zoonotic diseases from animals to humans. This highlights the requirement for a novel approach to discern and address the escalating health threats. The One Health paradigm has been developed as a responsive strategy to confront forthcoming outbreaks through early warning, highlighting the interconnectedness of humans, animals, and their environment. The system employs several innovative methods such as the use of advanced technology, global collaboration, and data-driven decision-making to come up with an extraordinary solution for improving worldwide disease responses. This Review deliberates environmental, animal, and human factors that influence disease risk, analyzes the challenges and advantages inherent in using the One Health surveillance system, and demonstrates how these can be empowered by Big Data and Artificial Intelligence. The Holistic One Health Surveillance Framework presented herein holds the potential to revolutionize our capacity to monitor, understand, and mitigate the impact of infectious diseases on global populations.
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Affiliation(s)
- Samradhi Singh
- ICMR - National Institute for Research in Environmental Health, Bhopal Bypass Road, Bhouri, Bhopal-462030, Madhya Pradesh, India
| | - Poonam Sharma
- ICMR - National Institute for Research in Environmental Health, Bhopal Bypass Road, Bhouri, Bhopal-462030, Madhya Pradesh, India
| | - Namrata Pal
- ICMR - National Institute for Research in Environmental Health, Bhopal Bypass Road, Bhouri, Bhopal-462030, Madhya Pradesh, India
| | - Devojit Kumar Sarma
- ICMR - National Institute for Research in Environmental Health, Bhopal Bypass Road, Bhouri, Bhopal-462030, Madhya Pradesh, India
| | - Rajnarayan Tiwari
- ICMR - National Institute for Research in Environmental Health, Bhopal Bypass Road, Bhouri, Bhopal-462030, Madhya Pradesh, India
| | - Manoj Kumar
- ICMR - National Institute for Research in Environmental Health, Bhopal Bypass Road, Bhouri, Bhopal-462030, Madhya Pradesh, India
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11
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Godwe C, Vidal N, Muwonga J, Butel C, Serrano L, Edidi S, Ahuka-Mundeke S, Koro Koro F, Etoa X, Tongo M, Peeters M, Ayouba A. Structural Features and Genetic Diversity in Gag Gene of Rare HIV-1 Subtypes from the Democratic Republic of Congo. AIDS Res Hum Retroviruses 2024; 40:181-187. [PMID: 37335033 DOI: 10.1089/aid.2022.0154] [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] [Indexed: 06/21/2023] Open
Abstract
Type-1 HIV (HIV-1) group M (HIV-1M) genetic diversity is highest in the Congo Basin where the epidemic ignited a century ago. HIV-1M has diversified into multiple subtypes, sub-subtypes, and circulating and unique recombinant forms (CRFs/URFs). An unanswered question is why some rare subtypes never reached epidemic levels despite their age. Several studies identified the role of HIV-1M accessory genes nef and vpu in virus adaptation to human hosts and subsequent spread. Other reports also pointed out the pivotal role of gag in transmissibility, virulence, and replication capacity. In this study we characterized the HIV-1 gag gene of 148 samples collected in different localities of the Democratic Republic of the Congo (DRC) between 1997 and 2013. We used nested polymerase chain reaction (PCR) to amplify the whole gag gene. PCR products were sequenced either by Sanger method or by next generation sequencing on Illumina MiSeq or iSeq100 platforms. Generated sequences were used for subsequent analyses using different bioinformatic tools. Phylogenetic analysis of the generated sequences revealed a high genetic diversity with up to 22 different subtypes, sub-subtypes, CRFs. Up to 15% (22/148) URFs were identified, in addition to rare subtypes such as H, J, and K. At least two amino acid motifs present in the gag gene have been shown to modulate HIV-1 replication, budding, and fitness: the P(T/S)AP and the LYPXnL motifs. Structural analysis revealed the presence of P(T/S)AP in all the 148 sequences with the majority (136/148) bearing the PTAP. Three samples presented a duplication of this motif. The LYPXnL motif was identified in 38 of 148 sequences. There was no clear link between the frequency of these motifs and HIV-1M subtypes. In summary, we confirmed a high genetic diversity of HIV-1M in the DRC. We observed the presence of amino acid motifs important for viral replication and budding even in some rare HIV-1 subtypes. Their impact on viral fitness needs be further evaluated by in vitro studies.
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Affiliation(s)
- Célestin Godwe
- Laboratoire de Virologie-Cremer, Institut de Recherches Médicales et d'Études des Plantes Médicinales (IMPM), Yaoundé, Cameroon
- Department of Biochemistry, Faculty of Sciences, University of Douala, Douala, Cameroon
| | - Nicole Vidal
- TransVIHMI, Université de Montpellier, IRD, INSERM, Montpellier, France
| | - Jérémie Muwonga
- National AIDS Control Program, Kinshasa, Democratic Republic of the Congo
| | - Christelle Butel
- TransVIHMI, Université de Montpellier, IRD, INSERM, Montpellier, France
| | - Laetitia Serrano
- TransVIHMI, Université de Montpellier, IRD, INSERM, Montpellier, France
| | - Samuel Edidi
- National AIDS Control Program, Kinshasa, Democratic Republic of the Congo
| | - Steve Ahuka-Mundeke
- Department of Virology, Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
- Service de Microbiologie, Département de Biologie Médicale, Cliniques Universitaires de Kinshasa, Université de Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Francioli Koro Koro
- Department of Biochemistry, Faculty of Sciences, University of Douala, Douala, Cameroon
| | - Xavier Etoa
- Department of Microbiology, Faculty of Sciences, University of Yaoundé I, Yaoundé, Cameroon
| | - Marcel Tongo
- Laboratoire de Virologie-Cremer, Institut de Recherches Médicales et d'Études des Plantes Médicinales (IMPM), Yaoundé, Cameroon
| | - Martine Peeters
- TransVIHMI, Université de Montpellier, IRD, INSERM, Montpellier, France
| | - Ahidjo Ayouba
- Laboratoire de Virologie-Cremer, Institut de Recherches Médicales et d'Études des Plantes Médicinales (IMPM), Yaoundé, Cameroon
- TransVIHMI, Université de Montpellier, IRD, INSERM, Montpellier, France
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12
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Yang Q, Wang B, Lemey P, Dong L, Mu T, Wiebe RA, Guo F, Trovão NS, Park SW, Lewis N, Tsui JLH, Bajaj S, Cheng Y, Yang L, Haba Y, Li B, Zhang G, Pybus OG, Tian H, Grenfell B. Synchrony of Bird Migration with Global Dispersal of Avian Influenza Reveals Exposed Bird Orders. Nat Commun 2024; 15:1126. [PMID: 38321046 PMCID: PMC10847442 DOI: 10.1038/s41467-024-45462-1] [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: 05/29/2023] [Accepted: 01/23/2024] [Indexed: 02/08/2024] Open
Abstract
Highly pathogenic avian influenza virus (HPAIV) A H5, particularly clade 2.3.4.4, has caused worldwide outbreaks in domestic poultry, occasional spillover to humans, and increasing deaths of diverse species of wild birds since 2014. Wild bird migration is currently acknowledged as an important ecological process contributing to the global dispersal of HPAIV H5. However, this mechanism has not been quantified using bird movement data from different species, and the timing and location of exposure of different species is unclear. We sought to explore these questions through phylodynamic analyses based on empirical data of bird movement tracking and virus genome sequences of clade 2.3.4.4 and 2.3.2.1. First, we demonstrate that seasonal bird migration can explain salient features of the global dispersal of clade 2.3.4.4. Second, we detect synchrony between the seasonality of bird annual cycle phases and virus lineage movements. We reveal the differing exposed bird orders at geographical origins and destinations of HPAIV H5 clade 2.3.4.4 lineage movements, including relatively under-discussed orders. Our study provides a phylodynamic framework that links the bird movement ecology and genomic epidemiology of avian influenza; it highlights the importance of integrating bird behavior and life history in avian influenza studies.
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Affiliation(s)
- Qiqi Yang
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA.
| | - Ben Wang
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, Faculty of Geographical Science, Beijing Normal University, Beijing, China
| | - Phillipe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Lu Dong
- College of Life Sciences, Beijing Normal University, Beijing, China
| | - Tong Mu
- Princeton School of Public and International Affairs, Princeton University, Princeton, NJ, USA
| | - R Alex Wiebe
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Fengyi Guo
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | | | - Sang Woo Park
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Nicola Lewis
- Animal and Plant Health Agency-Weybridge, OIE/FAO International Reference Laboratory for Avian Influenza, Swine Influenza and Newcastle Disease Virus, Department of Virology, Addlestone, UK
- Department of Pathobiology and Population Science, Royal Veterinary College, London, UK
| | | | - Sumali Bajaj
- Department of Biology, University of Oxford, Oxford, UK
| | - Yachang Cheng
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Luojun Yang
- Institute for Disease Modeling, Bill and Melinda Gates Foundation, Seattle, WA, USA
| | - Yuki Haba
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Bingying Li
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, Faculty of Geographical Science, Beijing Normal University, Beijing, China
| | - Guogang Zhang
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, National Bird Banding Center of China, Beijing, China
| | - Oliver G Pybus
- Department of Pathobiology and Population Science, Royal Veterinary College, London, UK
- Department of Biology, University of Oxford, Oxford, UK
| | - Huaiyu Tian
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, Faculty of Geographical Science, Beijing Normal University, Beijing, China.
| | - Bryan Grenfell
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA.
- Princeton School of Public and International Affairs, Princeton University, Princeton, NJ, USA.
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13
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Hall M, Golubchik T, Bonsall D, Abeler-Dörner L, Limbada M, Kosloff B, Schaap A, de Cesare M, MacIntyre-Cockett G, Otecko N, Probert W, Ratmann O, Bulas Cruz A, Piwowar-Manning E, Burns DN, Cohen MS, Donnell DJ, Eshleman SH, Simwinga M, Fidler S, Hayes R, Ayles H, Fraser C. Demographics of sources of HIV-1 transmission in Zambia: a molecular epidemiology analysis in the HPTN 071 PopART study. THE LANCET. MICROBE 2024; 5:e62-e71. [PMID: 38081203 PMCID: PMC10789608 DOI: 10.1016/s2666-5247(23)00220-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 07/07/2023] [Accepted: 07/14/2023] [Indexed: 01/19/2024]
Abstract
BACKGROUND In the last decade, universally available antiretroviral therapy (ART) has led to greatly improved health and survival of people living with HIV in sub-Saharan Africa, but new infections continue to appear. The design of effective prevention strategies requires the demographic characterisation of individuals acting as sources of infection, which is the aim of this study. METHODS Between 2014 and 2018, the HPTN 071 PopART study was conducted to quantify the public health benefits of ART. Viral samples from 7124 study participants in Zambia were deep-sequenced as part of HPTN 071-02 PopART Phylogenetics, an ancillary study. We used these sequences to identify likely transmission pairs. After demographic weighting of the recipients in these pairs to match the overall HIV-positive population, we analysed the demographic characteristics of the sources to better understand transmission in the general population. FINDINGS We identified a total of 300 likely transmission pairs. 178 (59·4%) were male to female, with 130 (95% CI 110-150; 43·3%) from males aged 25-40 years. Overall, men transmitted 2·09-fold (2·06-2·29) more infections per capita than women, a ratio peaking at 5·87 (2·78-15·8) in the 35-39 years source age group. 40 (26-57; 13·2%) transmissions linked individuals from different communities in the trial. Of 288 sources with recorded information on drug resistance mutations, 52 (38-69; 18·1%) carried viruses resistant to first-line ART. INTERPRETATION HIV-1 transmission in the HPTN 071 study communities comes from a wide range of age and sex groups, and there is no outsized contribution to new infections from importation or drug resistance mutations. Men aged 25-39 years, underserved by current treatment and prevention services, should be prioritised for HIV testing and ART. FUNDING National Institute of Allergy and Infectious Diseases, US President's Emergency Plan for AIDS Relief, International Initiative for Impact Evaluation, Bill & Melinda Gates Foundation, National Institute on Drug Abuse, and National Institute of Mental Health.
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Affiliation(s)
- Matthew Hall
- Pandemic Sciences Institute and Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Tanya Golubchik
- Pandemic Sciences Institute and Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Sydney Infectious Diseases Institute, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - David Bonsall
- Pandemic Sciences Institute and Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Lucie Abeler-Dörner
- Pandemic Sciences Institute and Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Barry Kosloff
- Zambart, University of Zambia, Lusaka, Zambia; Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, UK
| | - Ab Schaap
- Zambart, University of Zambia, Lusaka, Zambia
| | - Mariateresa de Cesare
- Pandemic Sciences Institute and Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - George MacIntyre-Cockett
- Pandemic Sciences Institute and Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Newton Otecko
- Pandemic Sciences Institute and Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - William Probert
- Pandemic Sciences Institute and Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Oliver Ratmann
- Department of Mathematics, Imperial College London, London, UK
| | - Ana Bulas Cruz
- Pandemic Sciences Institute and Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - David N Burns
- Division of AIDS, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Myron S Cohen
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Susan H Eshleman
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Sarah Fidler
- Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Richard Hayes
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | - Helen Ayles
- Zambart, University of Zambia, Lusaka, Zambia; Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, UK
| | - Christophe Fraser
- Pandemic Sciences Institute and Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
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14
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Kishimoto N, Misumi S. From Glycolysis to Viral Defense: The Multifaceted Impact of Glycolytic Enzymes on Human Immunodeficiency Virus Type 1 Replication. Biol Pharm Bull 2024; 47:905-911. [PMID: 38692867 DOI: 10.1248/bpb.b23-00605] [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] [Indexed: 05/03/2024]
Abstract
Viruses require host cells to replicate and proliferate, which indicates that viruses hijack the cellular machinery. Human immunodeficiency virus type 1 (HIV-1) primarily infects CD4-positive T cells, and efficiently uses cellular proteins to replicate. Cells already have proteins that inhibit the replication of the foreign HIV-1, but their function is suppressed by viral proteins. Intriguingly, HIV-1 infection also changes the cellular metabolism to aerobic glycolysis. This phenomenon has been interpreted as a cellular response to maintain homeostasis during viral infection, yet HIV-1 efficiently replicates even in this environment. In this review, we discuss the regulatory role of glycolytic enzymes in viral replication and the impact of aerobic glycolysis on viral infection by introducing various host proteins involved in viral replication. Furthermore, we would like to propose a "glyceraldehyde-3-phosphate dehydrogenase-induced shock (G-shock) and kill strategy" that maximizes the antiviral effect of the glycolytic enzyme glyceraldehyde 3-phosphate dehydrogenase (GAPDH) to eliminate latently HIV-1-infected cells.
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Affiliation(s)
- Naoki Kishimoto
- Department of Environmental and Molecular Health Sciences, Faculty of Medical and Pharmaceutical Sciences, Kumamoto University
| | - Shogo Misumi
- Department of Environmental and Molecular Health Sciences, Faculty of Medical and Pharmaceutical Sciences, Kumamoto University
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15
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Gonzalez A, Nikparvar B, Matson MJ, Seifert SN, Ross HD, Munster V, Bharti N. Human movement and transmission dynamics early in Ebola outbreaks. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.12.18.23300175. [PMID: 38196653 PMCID: PMC10775320 DOI: 10.1101/2023.12.18.23300175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
Human movement drives the transmission and spread of communicable pathogens. It is especially influential for emerging pathogens when population immunity is low and spillover events are rare. We digitized serial printed maps to measure transportation networks (roads and rivers) in Central and West Africa as proxies for population mobility to assess relationships between movement and Ebola transmission. We find that the lengths of roads and rivers in close proximity to spillover sites at or near the time of spillover events are significantly correlated with the number of EVD cases, particularly in the first 100 days of each outbreak. Early management and containment efforts along transportation networks may be beneficial in mitigation during the early days of transmission and spatial spread for Ebola outbreaks.
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Affiliation(s)
- Alexandria Gonzalez
- Biology Department and Center for Infectious Disease Dynamics, Penn State University, University Park, PA, 16802, USA
| | - Behnam Nikparvar
- Biology Department and Center for Infectious Disease Dynamics, Penn State University, University Park, PA, 16802, USA
| | - M. Jeremiah Matson
- University of Utah Health, Department of Internal Medicine, Salt Lake City, UT 84132, USA
| | - Stephanie N. Seifert
- Paul G. Allen School for Global Health, Washington State University, Pullman, WA, 99164 USA
| | - Heather D. Ross
- Donald W. Hamer Center for Maps and Geospatial Information, Penn State University Libraries, Penn State University, University Park, PA, 16802, USA
| | - Vincent Munster
- Division of Intramural Research, Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, Montana, 59840 USA
| | - Nita Bharti
- Biology Department and Center for Infectious Disease Dynamics, Penn State University, University Park, PA, 16802, USA
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16
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Tang CY, Li T, Haynes TA, McElroy JA, Ritter D, Hammer RD, Sampson C, Webby R, Hang J, Wan XF. Rural populations facilitated early SARS-CoV-2 evolution and transmission in Missouri, USA. NPJ VIRUSES 2023; 1:7. [PMID: 38186942 PMCID: PMC10769004 DOI: 10.1038/s44298-023-00005-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 10/20/2023] [Indexed: 01/09/2024]
Abstract
In the United States, rural populations comprise 60 million individuals and suffered from high COVID-19 disease burdens. Despite this, surveillance efforts are biased toward urban centers. Consequently, how rurally circulating SARS-CoV-2 viruses contribute toward emerging variants remains poorly understood. In this study, we aim to investigate the role of rural communities in the evolution and transmission of SARS-CoV-2 during the early pandemic. We collected 544 urban and 435 rural COVID-19-positive respiratory specimens from an overall vaccine-naïve population in Southwest Missouri between July and December 2020. Genomic analyses revealed 53 SARS-CoV-2 Pango lineages in our study samples, with 14 of these lineages identified only in rural samples. Phylodynamic analyses showed that frequent bi-directional diffusions occurred between rural and urban communities in Southwest Missouri, and that four out of seven Missouri rural-origin lineages spread globally. Further analyses revealed that the nucleocapsid protein (N):R203K/G204R paired substitutions, which were detected disproportionately across multiple Pango lineages, were more associated with urban than rural sequences. Positive selection was detected at N:204 among rural samples but was not evident in urban samples, suggesting that viruses may encounter distinct selection pressures in rural versus urban communities. This study demonstrates that rural communities may be a crucial source of SARS-CoV-2 evolution and transmission, highlighting the need to expand surveillance and resources to rural populations for COVID-19 mitigation.
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Affiliation(s)
- Cynthia Y. Tang
- Center for Influenza and Emerging Infectious Diseases, University of Missouri, Columbia, MO, USA
- Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, USA
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA
- These authors contributed equally: Cynthia Y. Tang, Tao Li
| | - Tao Li
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- These authors contributed equally: Cynthia Y. Tang, Tao Li
| | - Tricia A. Haynes
- Center for Influenza and Emerging Infectious Diseases, University of Missouri, Columbia, MO, USA
- Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, USA
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Jane A. McElroy
- Family and Community Medicine, University of Missouriś, Columbia, MO, USA
| | - Detlef Ritter
- Anatomic Pathology & Clinical Pathology, University of Missouri, Columbia, MO, USA
| | - Richard D. Hammer
- Anatomic Pathology & Clinical Pathology, University of Missouri, Columbia, MO, USA
| | | | - Richard Webby
- Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Jun Hang
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Xiu-Feng Wan
- Center for Influenza and Emerging Infectious Diseases, University of Missouri, Columbia, MO, USA
- Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, USA
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA
- Department of Electrical Engineering & Computer Science, College of Engineering, University of Missouri, Columbia, MO, USA
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17
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Li X, Trovão NS, Wertheim JO, Baele G, de Bernardi Schneider A. Optimizing ancestral trait reconstruction of large HIV Subtype C datasets through multiple-trait subsampling. Virus Evol 2023; 9:vead069. [PMID: 38046219 PMCID: PMC10691791 DOI: 10.1093/ve/vead069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 10/29/2023] [Accepted: 11/20/2023] [Indexed: 12/05/2023] Open
Abstract
Large datasets along with sampling bias represent a challenge for phylodynamic reconstructions, particularly when the study data are obtained from various heterogeneous sources and/or through convenience sampling. In this study, we evaluate the presence of unbalanced sampled distribution by collection date, location, and risk group of human immunodeficiency virus Type 1 Subtype C using a comprehensive subsampling strategy and assess their impact on the reconstruction of the viral spatial and risk group dynamics using phylogenetic comparative methods. Our study shows that a most suitable dataset for ancestral trait reconstruction can be obtained through subsampling by all available traits, particularly using multigene datasets. We also demonstrate that sampling bias is inflated when considerable information for a given trait is unavailable or of poor quality, as we observed for the trait risk group. In conclusion, we suggest that, even if traits are not well recorded, including them deliberately optimizes the representativeness of the original dataset rather than completely excluding them. Therefore, we advise the inclusion of as many traits as possible with the aid of subsampling approaches in order to optimize the dataset for phylodynamic analysis while reducing the computational burden. This will benefit research communities investigating the evolutionary and spatio-temporal patterns of infectious diseases.
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Affiliation(s)
| | - Nídia S Trovão
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, 31 Center Dr, Bethesda, MA 20892, USA
| | - Joel O Wertheim
- Department of Medicine, University of California, La Jolla, San Diego, CA 92093, USA
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven BE-3000, Belgium
| | - Adriano de Bernardi Schneider
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
- Ningbo No.2 Hospital, Ningbo 315010, China
- Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo 315000, China
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Togna Pabo WLR, Fokam J, Njume D, Takou D, Santoro MM, Nyasa RB, Chenwi C, Mpouel ML, Beloumou G, Jagni ESN, Nka AD, Ka’e AC, Teto G, Dambaya B, Djupsa S, Gouissi Anguechia DH, Evariste M, Kamta C, Bala L, Lambo V, Halle-Ekane EG, Colizzi V, Perno CF, Ndjolo A, Ndip Ndip R. HIV-1 subtype diversity and immuno-virological outcomes among adolescents failing antiretroviral therapy in Cameroon: A cohort study. PLoS One 2023; 18:e0293326. [PMID: 37878637 PMCID: PMC10599502 DOI: 10.1371/journal.pone.0293326] [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: 11/30/2022] [Accepted: 10/10/2023] [Indexed: 10/27/2023] Open
Abstract
OBJECTIVE We sought to evaluate the variability of HIV-1 and its effect on immuno-virological response among adolescents living with perinatally acquired HIV (APHI). METHODS A cohort study was conducted from 2018-2020 among 311 APHI receiving antiretroviral therapy (ART) in Cameroon. Sequencing of protease and reverse transcriptase regions was performed for participants experiencing virological failure, VF, (Plasma viral load, PVL ≥ 1000 RNA copies/ml). HIV-1 subtypes were inferred by phylogeny; immuno-virological responses were monitored at 3-time points (T1-T3). Cox regression modeling was used to estimate adjusted hazard ratios (aHRs) of progression to: CD4 < 250, and PVL > 5log10, adjusted for acquired drug resistance, gender, ART line, adherence, and duration on treatment; p < 0.05 was considered statistically significant. RESULTS Of the 141 participants in VF enrolled, the male-female ratio was 1:1; mean age was 15 (±3) years; and median [IQR] duration on ART was 51 [46-60] months. In all phases, 17 viral clades were found with a predominant CRF02_AG (58.2%, 59.4%, and 58.3%). From T1-T3 respectively, there was an increasing CD4 count (213 [154-313], 366 [309-469], and 438 [364-569] cells/mm3) and decline log10 PVL (5.23, 4.43, and 4.43), similar across subtypes. Among participants with CRF02_AG infection, duration of treatment was significantly associated with both rates of progression to CD4 < 250, and PVL > 5log10, aHR = 0.02 (0.001-0.52), and aHR = 0.05 (0.01-0.47) respectively. Moreover, four potential new HIV-1 recombinants were identified (CRF02_AG/02D, CRF02_AG/02A1F2, D/CRF02_AG, and AF2/CRF02_AG), indicating a wide viral diversity. CONCLUSION Among APHI in settings like Cameroon, there is a wide genetic diversity of HIV-1, driven by CRF02_AG and with potential novel clades due to ongoing recombination events. Duration of treatment significantly reduces the risk of disease progression.
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Affiliation(s)
- Willy Le roi Togna Pabo
- Chantal BIYA International Reference Centre for Research on HIV/AIDS prevention and management, Yaoundé, Cameroon
- Faculty of Medicine and Biomedical Sciences, Yaoundé, Cameroon
- Faculty of Science, University of Buea, Buea, Cameroon
| | - Joseph Fokam
- Chantal BIYA International Reference Centre for Research on HIV/AIDS prevention and management, Yaoundé, Cameroon
- Faculty of Medicine and Biomedical Sciences, Yaoundé, Cameroon
- Faculty of Health Sciences, University of Buea, Buea, Cameroon
- National HIV Drug Resistance Group, Ministry of Public Health, Yaoundé, Cameroon
| | - Debimeh Njume
- Chantal BIYA International Reference Centre for Research on HIV/AIDS prevention and management, Yaoundé, Cameroon
- Faculty of Medicine and Biomedical Sciences, Yaoundé, Cameroon
- Faculty of Health Sciences, University of Buea, Buea, Cameroon
| | - Désiré Takou
- Chantal BIYA International Reference Centre for Research on HIV/AIDS prevention and management, Yaoundé, Cameroon
| | | | | | - Collins Chenwi
- Chantal BIYA International Reference Centre for Research on HIV/AIDS prevention and management, Yaoundé, Cameroon
- Faculty of Medicine and Biomedical Sciences, Yaoundé, Cameroon
| | - Marie Laure Mpouel
- Chantal BIYA International Reference Centre for Research on HIV/AIDS prevention and management, Yaoundé, Cameroon
- Faculty of Medicine and Biomedical Sciences, Yaoundé, Cameroon
| | - Grace Beloumou
- Chantal BIYA International Reference Centre for Research on HIV/AIDS prevention and management, Yaoundé, Cameroon
| | - Ezechiel Semengue Ngoufack Jagni
- Chantal BIYA International Reference Centre for Research on HIV/AIDS prevention and management, Yaoundé, Cameroon
- University of Rome Tor Vergata, Rome, Italy
- Evangelic University of Cameroon, Bandjoun, Cameroon
| | - Alex Durand Nka
- Chantal BIYA International Reference Centre for Research on HIV/AIDS prevention and management, Yaoundé, Cameroon
- University of Rome Tor Vergata, Rome, Italy
- Evangelic University of Cameroon, Bandjoun, Cameroon
| | - Aude Christelle Ka’e
- Chantal BIYA International Reference Centre for Research on HIV/AIDS prevention and management, Yaoundé, Cameroon
- University of Rome Tor Vergata, Rome, Italy
| | - Georges Teto
- Chantal BIYA International Reference Centre for Research on HIV/AIDS prevention and management, Yaoundé, Cameroon
| | - Beatrice Dambaya
- Chantal BIYA International Reference Centre for Research on HIV/AIDS prevention and management, Yaoundé, Cameroon
| | - Sandrine Djupsa
- Chantal BIYA International Reference Centre for Research on HIV/AIDS prevention and management, Yaoundé, Cameroon
| | - Davy Hyacinthe Gouissi Anguechia
- Chantal BIYA International Reference Centre for Research on HIV/AIDS prevention and management, Yaoundé, Cameroon
- Faculty of Medicine and Biomedical Sciences, Yaoundé, Cameroon
| | - Molimbou Evariste
- Chantal BIYA International Reference Centre for Research on HIV/AIDS prevention and management, Yaoundé, Cameroon
| | | | - Lionel Bala
- Mbalmayo District Hospital, Mbalmayo, Cameroon
| | | | | | - Vittorio Colizzi
- Chantal BIYA International Reference Centre for Research on HIV/AIDS prevention and management, Yaoundé, Cameroon
- University of Rome Tor Vergata, Rome, Italy
- Evangelic University of Cameroon, Bandjoun, Cameroon
| | - Carlo Federico Perno
- Chantal BIYA International Reference Centre for Research on HIV/AIDS prevention and management, Yaoundé, Cameroon
- University of Rome Tor Vergata, Rome, Italy
- Bambino Gesu Pediatric Hospital, Rome, Italy
| | - Alexis Ndjolo
- Chantal BIYA International Reference Centre for Research on HIV/AIDS prevention and management, Yaoundé, Cameroon
- Faculty of Medicine and Biomedical Sciences, Yaoundé, Cameroon
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Guzmán-Solís AA, Navarro MA, Ávila-Arcos MC, Blanco-Melo D. A Glimpse into the Past: What Ancient Viral Genomes Reveal About Human History. Annu Rev Virol 2023; 10:49-75. [PMID: 37268008 DOI: 10.1146/annurev-virology-111821-123859] [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] [Indexed: 06/04/2023]
Abstract
Humans have battled viruses for millennia. However, directly linking the symptomatology of disease outbreaks to specific viral pathogens was not possible until the twentieth century. With the advent of the genomic era and the development of advanced protocols for isolation, sequencing, and analysis of ancient nucleic acids from diverse human remains, the identification and characterization of ancient viruses became feasible. Recent studies have provided invaluable information about past epidemics and made it possible to examine assumptions and inferences on the origin and evolution of certain viral families. In parallel, the study of ancient viruses also uncovered their importance in the evolution of the human lineage and their key roles in shaping major events in human history. In this review, we describe the strategies used for the study of ancient viruses, along with their limitations, and provide a detailed account of what past viral infections have revealed about human history.
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Affiliation(s)
- Axel A Guzmán-Solís
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Miguel Alejandro Navarro
- Licenciatura en Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
- International Laboratory for Human Genome Research, Universidad Nacional Autónoma de México, Querétaro, México;
| | - María C Ávila-Arcos
- International Laboratory for Human Genome Research, Universidad Nacional Autónoma de México, Querétaro, México;
| | - Daniel Blanco-Melo
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA;
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20
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Song J, Okano JT, Ponce J, Busang L, Seipone K, Valdano E, Blower S. The role of migration networks in the development of Botswana's generalized HIV epidemic. eLife 2023; 12:e85435. [PMID: 37665629 PMCID: PMC10476964 DOI: 10.7554/elife.85435] [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: 12/08/2022] [Accepted: 08/02/2023] [Indexed: 09/05/2023] Open
Abstract
The majority of people with HIV live in sub-Saharan Africa, where epidemics are generalized. For these epidemics to develop, populations need to be mobile. However, the role of population-level mobility in the development of generalized HIV epidemics has not been studied. Here we do so by studying historical migration data from Botswana, which has one of the most severe generalized HIV epidemics worldwide; HIV prevalence was 21% in 2021. The country reported its first AIDS case in 1985 when it began to rapidly urbanize. We hypothesize that, during the development of Botswana's epidemic, the population was extremely mobile and the country was highly connected by substantial migratory flows. We test this mobility hypothesis by conducting a network analysis using a historical time series (1981-2011) of micro-census data from Botswana. Our results support our hypothesis. We found complex migration networks with very high rates of rural-to-urban, and urban-to-rural, migration: 10% of the population moved annually. Mining towns (where AIDS cases were first reported, and risk behavior was high) were important in-flow and out-flow migration hubs, suggesting that they functioned as 'core groups' for HIV transmission and dissemination. Migration networks could have dispersed HIV throughout Botswana and generated the current hyperendemic epidemic.
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Affiliation(s)
- Janet Song
- Center for Biomedical Modeling, Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los AngelesLos AngelesUnited States
| | - Justin T Okano
- Center for Biomedical Modeling, Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los AngelesLos AngelesUnited States
| | - Joan Ponce
- Center for Biomedical Modeling, Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los AngelesLos AngelesUnited States
| | - Lesego Busang
- The African Comprehensive HIV/AIDS Partnerships (ACHAP)GaboroneBotswana
| | - Khumo Seipone
- The African Comprehensive HIV/AIDS Partnerships (ACHAP)GaboroneBotswana
| | - Eugenio Valdano
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé PubliqueParisFrance
| | - Sally Blower
- Center for Biomedical Modeling, Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los AngelesLos AngelesUnited States
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21
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Rothstein AP, Jesser KJ, Feistel DJ, Konstantinidis KT, Trueba G, Levy K. Population genomics of diarrheagenic Escherichia coli uncovers high connectivity between urban and rural communities in Ecuador. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 113:105476. [PMID: 37392822 PMCID: PMC10599324 DOI: 10.1016/j.meegid.2023.105476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 05/11/2023] [Accepted: 06/28/2023] [Indexed: 07/03/2023]
Abstract
Human movement may be an important driver of transmission dynamics for enteric pathogens but has largely been underappreciated except for international 'travelers' diarrhea or cholera. Phylodynamic methods, which combine genomic and epidemiological data, are used to examine rates and dynamics of disease matching underlying evolutionary history and biogeographic distributions, but these methods often are not applied to enteric bacterial pathogens. We used phylodynamics to explore the phylogeographic and evolutionary patterns of diarrheagenic E. coli in northern Ecuador to investigate the role of human travel in the geographic distribution of strains across the country. Using whole genome sequences of diarrheagenic E. coli isolates, we built a core genome phylogeny, reconstructed discrete ancestral states across urban and rural sites, and estimated migration rates between E. coli populations. We found minimal structuring based on site locations, urban vs. rural locality, pathotype, or clinical status. Ancestral states of phylogenomic nodes and tips were inferred to have 51% urban ancestry and 49% rural ancestry. Lack of structuring by location or pathotype E. coli isolates imply highly connected communities and extensive sharing of genomic characteristics across isolates. Using an approximate structured coalescent model, we estimated rates of migration among circulating isolates were 6.7 times larger for urban towards rural populations compared to rural towards urban populations. This suggests increased inferred migration rates of diarrheagenic E. coli from urban populations towards rural populations. Our results indicate that investments in water and sanitation prevention in urban areas could limit the spread of enteric bacterial pathogens among rural populations.
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Affiliation(s)
- Andrew P. Rothstein
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, USA
| | - Kelsey J. Jesser
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, USA
| | - Dorian J. Feistel
- School of a Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Konstantinos T. Konstantinidis
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
- School of a Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Gabriel Trueba
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Pichincha, Ecuador
| | - Karen Levy
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, USA
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22
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Goodman ML, Seidel SE, Springer A, Elliott A, Markham C, Serag H, Keiser P, Raimer B, Raimer-Goodman L, Gatwiri C, Munene K, Gitari S. Enabling structural resilience of street-involved children and youth in Kenya: reintegration outcomes and the Flourishing Community model. Front Psychol 2023; 14:1175593. [PMID: 37680240 PMCID: PMC10482225 DOI: 10.3389/fpsyg.2023.1175593] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 07/31/2023] [Indexed: 09/09/2023] Open
Abstract
Introduction Millions of children and youth live on city streets across the globe, vulnerable to substance use, abuse, material and structural neglect. Structural resilience, the re-establishment of access to structural goods within a society such as housing, education, and healthcare following some interruption, provides an orientation for research and interventional efforts with street-involved children and youth (SICY). Further, a structural resilience framework supports organizing interactions between levels and sectors of a socio-ecology. Methods Following the expressed interests of Kenyan SICY, and consistent with emerging policy interests at national and global levels, we assess reintegration trajectories of Kenyan SICY (n = 227) participating in a new program intervention and model. The intervention combines two coordinated, parallel programs - one focused on the rescue, rehabilitation, reintegration and resocialization of SICY, and the other focused on empowering families and communities to provide better care for children and youth who are reintegrating from life on the streets to the broader community. Data were collected and analyzed from multiple stages across SICY involvement with the intervention. Results We found 79% of SICY participants reintegrated with the broader community, and 50% reintegrated with families of origin and returned to school. Twenty-five percent of participants reintegrated to a boarding school, polytechnical school, or began a business. Probability of reintegrating successfully was significantly improved among participants whose families participated in the family- and community-oriented program, who were younger, with less street-exposure, expressed more personal interests, and desired to reintegrate with family. Discussion To our knowledge, these are the first quantitative data published of successful reintegration of SICY to the broader, non-institutionalized community in any low- or middle-income country. Future research should (1) identify factors across socio-ecological levels and sectors contributing to health and developmental outcomes of reintegrated children and youth, (2) mechanisms to support SICY for whom the interventional strategy did not work, (3) methods to prevent street-migration by children and youth, and (4) system development to coordinate follow-up and relevant investment by institutions, organizations and community leaders to continue reintegration work.
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Affiliation(s)
- Michael L. Goodman
- Department of Internal Medicine, The University of Texas Medical Branch, Galveston, TX, United States
- Sodzo International, Houston, TX, United States
| | | | - Andrew Springer
- The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Aleisha Elliott
- Texas AHEC East, The University of Texas Medical Branch, Galveston, TX, United States
| | - Christine Markham
- The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Hani Serag
- Department of Internal Medicine, The University of Texas Medical Branch, Galveston, TX, United States
| | - Philip Keiser
- School of Public and Population Health, The University of Texas Medical Branch, Galveston, TX, United States
| | - Ben Raimer
- Office of the President, The University of Texas Medical Branch, Galveston, TX, United States
| | - Lauren Raimer-Goodman
- Community-based Clinics, The University of Texas Medical Branch, Galveston, TX, United States
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23
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Ladner JT, Sahl JW. Towards a post-pandemic future for global pathogen genome sequencing. PLoS Biol 2023; 21:e3002225. [PMID: 37527248 PMCID: PMC10393143 DOI: 10.1371/journal.pbio.3002225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2023] Open
Abstract
Pathogen genome sequencing has become a routine part of our response to active outbreaks of infectious disease and should be an important part of our preparations for future epidemics. In this Essay, we discuss the innovations that have enabled routine pathogen genome sequencing, as well as how genome sequences can be used to understand and control the spread of infectious disease. We also explore the impact of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic on the field of pathogen genomics and outline the challenges we must address to further improve the utility of pathogen genome sequencing in the future.
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Affiliation(s)
- Jason T Ladner
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Jason W Sahl
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
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24
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de Almeida Rego FF, de Moraes L, Giovanetti M, Silva JAG, Torres FG, de Oliveira Silva M, da Purificação Pereira da Silva M, Van Weyenbergh J, Santos LA, Khouri R. Genomic Detection of the Emerging, Highly Pathogenic HIV-1 Subtype D in Bahia, Northeast Brazil. Viruses 2023; 15:1650. [PMID: 37631993 PMCID: PMC10458544 DOI: 10.3390/v15081650] [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: 05/31/2023] [Revised: 06/30/2023] [Accepted: 07/06/2023] [Indexed: 08/27/2023] Open
Abstract
(1) Background: The HIV subtype D is generally associated with a faster decline in CD4+ T cell counts, a higher viral load, and a faster progression to AIDS. However, it is still poorly characterized in Brazil. In this study, we used genomics and epidemiological data to investigate the transmission dynamics of HIV subtype D in the state of Bahia, Northeast Brazil. (2) Methods: To achieve this goal, we obtained four novel HIV-1 subtype D partial pol genome sequences using the Sanger method. To understand the emergence of this novel subtype in the state of Bahia, we used phylodynamic analysis on a dataset comprising 3704 pol genome sequences downloaded from the Los Alamos database. (3) Results: Our analysis revealed three branching patterns, indicating multiple introductions of the HIV-1 subtype D in Brazil from the late 1980s to the late 2000s and a single introduction event in the state of Bahia. Our data further suggest that these introductions most likely originated from European, Eastern African, Western African, and Southern African countries. (4) Conclusion: Understanding the distribution of HIV-1 viral strains and their temporal dynamics is crucial for monitoring the real-time evolution of circulating subtypes and recombinant forms, as well as for designing novel diagnostic and vaccination strategies. We advocate for a shift to active surveillance, to ensure adequate preparedness for future epidemics mediated by emerging viral strains.
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Affiliation(s)
- Filipe Ferreira de Almeida Rego
- Escola Bahiana de Medicina e Saúde Pública, Avenida Dom João VI, 275, Brotas, Salvador 40290-000, Bahia, Brazil; (F.F.d.A.R.); (L.A.S.)
| | - Laise de Moraes
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Rua Waldemar Falcão, 121, Candeal, Salvador 40296-710, Bahia, Brazil; (L.d.M.); (J.A.G.S.); (F.G.T.)
- Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Praça Ramos de Queirós, s/n, Largo do Terreiro de Jesus, Salvador 40026-010, Bahia, Brazil
| | - Marta Giovanetti
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Avenida Augusto de Lima, 1715, Barro Preto, Belo Horizonte 30190-002, Minas Gerais, Brazil;
- Sciences and Technologies for Sustainable Development and One Health, University of Campus Bio-Medico, 21-00128 Rome, Italy
| | - José Adriano Góes Silva
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Rua Waldemar Falcão, 121, Candeal, Salvador 40296-710, Bahia, Brazil; (L.d.M.); (J.A.G.S.); (F.G.T.)
- Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Praça Ramos de Queirós, s/n, Largo do Terreiro de Jesus, Salvador 40026-010, Bahia, Brazil
- Centro Estadual Especializado em Diagnóstico, Assistência e Pesquisa, Secretaria de Saúde do Estado da Bahia, Salvador 40110-050, Bahia, Brazil; (M.d.O.S.); (M.d.P.P.d.S.)
| | - Felipe Guimarães Torres
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Rua Waldemar Falcão, 121, Candeal, Salvador 40296-710, Bahia, Brazil; (L.d.M.); (J.A.G.S.); (F.G.T.)
| | - Marcio de Oliveira Silva
- Centro Estadual Especializado em Diagnóstico, Assistência e Pesquisa, Secretaria de Saúde do Estado da Bahia, Salvador 40110-050, Bahia, Brazil; (M.d.O.S.); (M.d.P.P.d.S.)
| | - Maria da Purificação Pereira da Silva
- Centro Estadual Especializado em Diagnóstico, Assistência e Pesquisa, Secretaria de Saúde do Estado da Bahia, Salvador 40110-050, Bahia, Brazil; (M.d.O.S.); (M.d.P.P.d.S.)
| | - Johan Van Weyenbergh
- Rega Institute for Medical Research, Department of Immunology, Microbiology and Transplantation, KU Leuven, Herestraat 49-Box 1030, 3000 Leuven, Belgium;
| | - Luciane Amorim Santos
- Escola Bahiana de Medicina e Saúde Pública, Avenida Dom João VI, 275, Brotas, Salvador 40290-000, Bahia, Brazil; (F.F.d.A.R.); (L.A.S.)
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Rua Waldemar Falcão, 121, Candeal, Salvador 40296-710, Bahia, Brazil; (L.d.M.); (J.A.G.S.); (F.G.T.)
- Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Praça Ramos de Queirós, s/n, Largo do Terreiro de Jesus, Salvador 40026-010, Bahia, Brazil
| | - Ricardo Khouri
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Rua Waldemar Falcão, 121, Candeal, Salvador 40296-710, Bahia, Brazil; (L.d.M.); (J.A.G.S.); (F.G.T.)
- Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Praça Ramos de Queirós, s/n, Largo do Terreiro de Jesus, Salvador 40026-010, Bahia, Brazil
- Rega Institute for Medical Research, Department of Immunology, Microbiology and Transplantation, KU Leuven, Herestraat 49-Box 1030, 3000 Leuven, Belgium;
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Marie V, Gordon ML. The (Re-)Emergence and Spread of Viral Zoonotic Disease: A Perfect Storm of Human Ingenuity and Stupidity. Viruses 2023; 15:1638. [PMID: 37631981 PMCID: PMC10458268 DOI: 10.3390/v15081638] [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: 06/23/2023] [Revised: 07/22/2023] [Accepted: 07/25/2023] [Indexed: 08/27/2023] Open
Abstract
Diseases that are transmitted from vertebrate animals to humans are referred to as zoonotic diseases. Although microbial agents such as bacteria and parasites are linked to zoonotic events, viruses account for a high percentage of zoonotic diseases that have emerged. Worryingly, the 21st century has seen a drastic increase in the emergence and re-emergence of viral zoonotic disease. Even though humans and animals have coexisted for millennia, anthropogenic factors have severely increased interactions between the two populations, thereby increasing the risk of disease spill-over. While drivers such as climate shifts, land exploitation and wildlife trade can directly affect the (re-)emergence of viral zoonotic disease, globalisation, geopolitics and social perceptions can directly facilitate the spread of these (re-)emerging diseases. This opinion paper discusses the "intelligent" nature of viruses and their exploitation of the anthropogenic factors driving the (re-)emergence and spread of viral zoonotic disease in a modernised and connected world.
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Affiliation(s)
- Veronna Marie
- Microbiology Laboratory, Department of Analytical Services, Rand Water, Vereeniging 1939, South Africa
| | - Michelle L. Gordon
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4001, South Africa;
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Hamede R, Fountain‐Jones NM, Arce F, Jones M, Storfer A, Hohenlohe PA, McCallum H, Roche B, Ujvari B, Thomas F. The tumour is in the detail: Local phylogenetic, population and epidemiological dynamics of a transmissible cancer in Tasmanian devils. Evol Appl 2023; 16:1316-1327. [PMID: 37492149 PMCID: PMC10363845 DOI: 10.1111/eva.13569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 06/01/2023] [Accepted: 06/01/2023] [Indexed: 07/27/2023] Open
Abstract
Infectious diseases are a major threat for biodiversity conservation and can exert strong influence on wildlife population dynamics. Understanding the mechanisms driving infection rates and epidemic outcomes requires empirical data on the evolutionary trajectory of pathogens and host selective processes. Phylodynamics is a robust framework to understand the interaction of pathogen evolutionary processes with epidemiological dynamics, providing a powerful tool to evaluate disease control strategies. Tasmanian devils have been threatened by a fatal transmissible cancer, devil facial tumour disease (DFTD), for more than two decades. Here we employ a phylodynamic approach using tumour mitochondrial genomes to assess the role of tumour genetic diversity in epidemiological and population dynamics in a devil population subject to 12 years of intensive monitoring, since the beginning of the epidemic outbreak. DFTD molecular clock estimates of disease introduction mirrored observed estimates in the field, and DFTD genetic diversity was positively correlated with estimates of devil population size. However, prevalence and force of infection were the lowest when devil population size and tumour genetic diversity was the highest. This could be due to either differential virulence or transmissibility in tumour lineages or the development of host defence strategies against infection. Our results support the view that evolutionary processes and epidemiological trade-offs can drive host-pathogen coexistence, even when disease-induced mortality is extremely high. We highlight the importance of integrating pathogen and population evolutionary interactions to better understand long-term epidemic dynamics and evaluating disease control strategies.
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Affiliation(s)
- Rodrigo Hamede
- School of Natural SciencesUniversity of TasmaniaHobartTasmaniaAustralia
- CANECEV, Centre de Recherches Ecologiques et Evolutives sur le CancerMontpellierFrance
| | | | - Fernando Arce
- School of Natural SciencesUniversity of TasmaniaHobartTasmaniaAustralia
| | - Menna Jones
- School of Natural SciencesUniversity of TasmaniaHobartTasmaniaAustralia
| | - Andrew Storfer
- School of Biological SciencesWashington State UniversityPullmanWashingtonUSA
| | - Paul A. Hohenlohe
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary StudiesUniversity of IdahoMoscowIdahoUSA
| | - Hamish McCallum
- Centre for Planetary Health and Food SecurityGriffith University, Nathan CampusNathanQueenslandAustralia
| | - Benjamin Roche
- CREEC, MIVEGEC (CREES)University of Montpellier, CNRS, IRDMontpelierFrance
| | - Beata Ujvari
- CANECEV, Centre de Recherches Ecologiques et Evolutives sur le CancerMontpellierFrance
- Centre for Integrative Ecology, School of Life and Environmental SciencesDeakin UniversityWaurn PondsVictoriaAustralia
| | - Frédéric Thomas
- CANECEV, Centre de Recherches Ecologiques et Evolutives sur le CancerMontpellierFrance
- CREEC, MIVEGEC (CREES)University of Montpellier, CNRS, IRDMontpelierFrance
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27
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Abboud C, Parent E, Bonnefon O, Soubeyrand S. Forecasting Pathogen Dynamics with Bayesian Model-Averaging: Application to Xylella fastidiosa. Bull Math Biol 2023; 85:67. [PMID: 37300801 PMCID: PMC10257384 DOI: 10.1007/s11538-023-01169-w] [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: 08/26/2022] [Accepted: 05/15/2023] [Indexed: 06/12/2023]
Abstract
Forecasting invasive-pathogen dynamics is paramount to anticipate eradication and containment strategies. Such predictions can be obtained using a model grounded on partial differential equations (PDE; often exploited to model invasions) and fitted to surveillance data. This framework allows the construction of phenomenological but concise models relying on mechanistic hypotheses and real observations. However, it may lead to models with overly rigid behavior and possible data-model mismatches. Hence, to avoid drawing a forecast grounded on a single PDE-based model that would be prone to errors, we propose to apply Bayesian model averaging (BMA), which allows us to account for both parameter and model uncertainties. Thus, we propose a set of different competing PDE-based models for representing the pathogen dynamics, we use an adaptive multiple importance sampling algorithm (AMIS) to estimate parameters of each competing model from surveillance data in a mechanistic-statistical framework, we evaluate the posterior probabilities of models by comparing different approaches proposed in the literature, and we apply BMA to draw posterior distributions of parameters and a posterior forecast of the pathogen dynamics. This approach is applied to predict the extent of Xylella fastidiosa in South Corsica, France, a phytopathogenic bacterium detected in situ in Europe less than 10 years ago (Italy 2013, France 2015). Separating data into training and validation sets, we show that the BMA forecast outperforms competing forecast approaches.
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Affiliation(s)
- Candy Abboud
- College of Engineering and Technology, American University of the Middle East, Egaila, Kuwait.
- INRAE, BioSP, 84914, Avignon, France.
| | - Eric Parent
- AgroParisTech, INRAE, UMR 518 Math. Info. Appli., Paris, France
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28
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Yu X. Genofunc: genome annotation and identification of genome features for automated pipelining analysis of virus whole genome sequences. BMC Bioinformatics 2023; 24:218. [PMID: 37254048 DOI: 10.1186/s12859-023-05356-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 05/25/2023] [Indexed: 06/01/2023] Open
Abstract
BACKGROUND Viral genomics and epidemiology have been increasingly important tools for analysing the spread of key pathogens affecting daily lives of individuals worldwide. With the rapidly expanding scale of pathogen genome sequencing efforts for epidemics and outbreaks efficient workflows in extracting genomic information are becoming increasingly important for answering key research questions. RESULTS Here we present Genofunc, a toolkit offering a range of command line orientated functions for processing of raw virus genome sequences into aligned and annotated data ready for analysis. The tool contains functions such as genome annotation, feature extraction etc. for processing of large genomic datasets both manual or as part of pipeline such as Snakemake or Nextflow ready for down-stream phylogenetic analysis. Originally designed for a large-scale HIV sequencing project, Genofunc has been benchmarked against annotated sequence gene coordinates from the Los Alamos HIV database as validation with downstream phylogenetic analysis result comparable to past literature as case study. CONCLUSION Genofunc is implemented fully in Python and licensed under the MIT license. Source code and documentation is available at: https://github.com/xiaoyu518/genofunc .
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Affiliation(s)
- Xiaoyu Yu
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3FL, Scotland, UK.
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29
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Masenga SK, Mweene BC, Luwaya E, Muchaili L, Chona M, Kirabo A. HIV-Host Cell Interactions. Cells 2023; 12:1351. [PMID: 37408185 DOI: 10.3390/cells12101351] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/04/2023] [Accepted: 05/05/2023] [Indexed: 07/07/2023] Open
Abstract
The development of antiretroviral drugs (ARVs) was a great milestone in the management of HIV infection. ARVs suppress viral activity in the host cell, thus minimizing injury to the cells and prolonging life. However, an effective treatment has remained elusive for four decades due to the successful immune evasion mechanisms of the virus. A thorough understanding of the molecular interaction of HIV with the host cell is essential in the development of both preventive and curative therapies for HIV infection. This review highlights several inherent mechanisms of HIV that promote its survival and propagation, such as the targeting of CD4+ lymphocytes, the downregulation of MHC class I and II, antigenic variation and an envelope complex that minimizes antibody access, and how they collaboratively render the immune system unable to mount an effective response.
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Affiliation(s)
- Sepiso K Masenga
- HAND Research Group, School of Medicine and Health Sciences, Mulungushi University, Livingstone Campus, Livingstone 10101, Zambia
- Vanderbilt University Medical Center, Department of Medicine, Division of Clinical Pharmacology, Room 536 Robinson Research Building, Nashville, TN 37232-6602, USA
| | - Bislom C Mweene
- HAND Research Group, School of Medicine and Health Sciences, Mulungushi University, Livingstone Campus, Livingstone 10101, Zambia
| | - Emmanuel Luwaya
- HAND Research Group, School of Medicine and Health Sciences, Mulungushi University, Livingstone Campus, Livingstone 10101, Zambia
| | - Lweendo Muchaili
- HAND Research Group, School of Medicine and Health Sciences, Mulungushi University, Livingstone Campus, Livingstone 10101, Zambia
| | - Makondo Chona
- HAND Research Group, School of Medicine and Health Sciences, Mulungushi University, Livingstone Campus, Livingstone 10101, Zambia
| | - Annet Kirabo
- Vanderbilt University Medical Center, Department of Medicine, Division of Clinical Pharmacology, Room 536 Robinson Research Building, Nashville, TN 37232-6602, USA
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30
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Vu NL, Nguyen TP, Nguyen BT, Dinh V, Ho LST. When can we reconstruct the ancestral state? Beyond Brownian motion. J Math Biol 2023; 86:88. [PMID: 37142869 DOI: 10.1007/s00285-023-01922-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 02/18/2023] [Accepted: 04/17/2023] [Indexed: 05/06/2023]
Abstract
Reconstructing the ancestral state of a group of species helps answer many important questions in evolutionary biology. Therefore, it is crucial to understand when we can estimate the ancestral state accurately. Previous works provide a necessary and sufficient condition, called the big bang condition, for the existence of an accurate reconstruction method under discrete trait evolution models and the Brownian motion model. In this paper, we extend this result to a wide range of continuous trait evolution models. In particular, we consider a general setting where continuous traits evolve along the tree according to stochastic processes that satisfy some regularity conditions. We verify these conditions for popular continuous trait evolution models including Ornstein-Uhlenbeck, reflected Brownian Motion, bounded Brownian Motion, and Cox-Ingersoll-Ross.
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Affiliation(s)
- Nhat L Vu
- Department of Mathematics and Statistics, Dalhousie University, Halifax, NS, Canada
| | - Thanh P Nguyen
- AISIA Research Lab, Ho Chi Minh City, Vietnam
- Department of Computer Science, University of Science, Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
| | - Binh T Nguyen
- AISIA Research Lab, Ho Chi Minh City, Vietnam
- Department of Computer Science, University of Science, Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
| | - Vu Dinh
- Department of Mathematical Sciences, University of Delaware, Newark, DE, USA
| | - Lam Si Tung Ho
- Department of Mathematics and Statistics, Dalhousie University, Halifax, NS, Canada.
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31
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Varanda J, Santos JM. It Was Not the Perfect Storm: The Social History of the HIV-2 Virus in Guinea-Bissau. Trop Med Infect Dis 2023; 8:tropicalmed8050261. [PMID: 37235309 DOI: 10.3390/tropicalmed8050261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/24/2023] [Accepted: 04/25/2023] [Indexed: 05/28/2023] Open
Abstract
The perfect storm model that was elaborated for the HIV-1M pandemic has also been used to explain the emergence of HIV-2, a second human immunodeficiency virus-acquired immunodeficiency syndrome (HIV-AIDS) that became an epidemic in Guinea-Bissau, West Africa. The use of this model creates epidemiological generalizations, ecological oversimplifications and historical misunderstandings as its assumptions-an urban center with explosive population growth, a high level of commercial sex and a surge in STDs, a network of mechanical transport and country-wide, en masse mobile campaigns-are absent from the historical record. This model fails to explain how the HIV-2 epidemic actually came about. This is the first study to conduct an exhaustive examination of sociohistorical contextual developments and align them with environmental, virological and epidemiological data. The interdisciplinary dialogue indicates that the emergence of the HIV-2 epidemic piggybacked on local sociopolitical transformations. The war's indirect effects on ecological relations, mobility and sociability were acute in rural areas and are a key to the HIV-2 epidemic. This setting had the natural host of the virus, the population numbers, the mobility trends and the use of technology on a scale needed to foster viral adaptation and amplification. The present analysis suggests new reflections on the processes of zoonotic spillovers and disease emergence.
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Affiliation(s)
- Jorge Varanda
- Centre for Research in Anthropology (CRIA-UC), Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal
- Global Health and Tropical Medicine, Institute of Hygiene and Tropical Medicine-NOVA-Lisbon (GHTM-UNL), Rua da Junqueira, 100, 1349-008 Lisboa, Portugal
| | - José Maurício Santos
- Centre for Geographical Studies, Institute of Geography and Spatial Planning, Universidade de Lisboa, 1600-276 Lisboa, Portugal
- Associated Laboratory TERRA, 1349-017 Lisboa, Portugal
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32
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Song J, Okano JT, Ponce J, Busang L, Seipone K, Valdano E, Blower S. Population mobility and the development of Botswana's generalized HIV epidemic: a network analysis. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.02.01.23285339. [PMID: 36778345 PMCID: PMC9915826 DOI: 10.1101/2023.02.01.23285339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The majority of people with HIV live in sub-Saharan Africa, where HIV epidemics are generalized. For these epidemics to develop, populations need to be mobile. However, population-level mobility has not yet been studied in the context of the development of generalized HIV epidemics. Here we do so by studying historical migration data from Botswana which has one of the most severe generalized HIV epidemics worldwide; in 2021, HIV prevalence was 21%. The country reported its first AIDS case in 1985 when it began to rapidly urbanize. We hypothesize that, during the development of Botswana's epidemic, the population was highly mobile and there were substantial urban-to-rural and rural-to-urban migratory flows. We test this hypothesis by conducting a network analysis using a historical time series (1981 to 2011) of micro-census data from Botswana. We found 10% of the population moved their residency annually, complex migration networks connected urban with rural areas, and there were very high rates of rural-to-urban migration. Notably, we also found mining towns were both important in-flow and out-flow migration hubs; consequently, there was a very high turnover of residents in towns. Our results support our hypothesis, and together, provide one explanation for the development of Botswana's generalized epidemic.
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Affiliation(s)
- Janet Song
- Center for Biomedical Modeling, Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
| | - Justin T. Okano
- Center for Biomedical Modeling, Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
| | - Joan Ponce
- Center for Biomedical Modeling, Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
| | - Lesego Busang
- The African Comprehensive HIV/AIDS Partnerships (ACHAP), Gaborone, Botswana
| | - Khumo Seipone
- The African Comprehensive HIV/AIDS Partnerships (ACHAP), Gaborone, Botswana
| | - Eugenio Valdano
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique, IPLESP, F75012, Paris, France
| | - Sally Blower
- Center for Biomedical Modeling, Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
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33
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Chau BA, Chen V, Cochrane AW, Parent LJ, Mouland AJ. Liquid-liquid phase separation of nucleocapsid proteins during SARS-CoV-2 and HIV-1 replication. Cell Rep 2023; 42:111968. [PMID: 36640305 PMCID: PMC9790868 DOI: 10.1016/j.celrep.2022.111968] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 10/27/2022] [Accepted: 12/20/2022] [Indexed: 12/28/2022] Open
Abstract
The leap of retroviruses and coronaviruses from animal hosts to humans has led to two ongoing pandemics and tens of millions of deaths worldwide. Retrovirus and coronavirus nucleocapsid proteins have been studied extensively as potential drug targets due to their central roles in virus replication, among which is their capacity to bind their respective genomic RNAs for packaging into nascent virions. This review focuses on fundamental studies of these nucleocapsid proteins and how their intrinsic abilities to condense through liquid-liquid phase separation (LLPS) contribute to viral replication. Therapeutic targeting of these condensates and methodological advances are also described to address future questions on how phase separation contributes to viral replication.
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Affiliation(s)
- Bao-An Chau
- HIV-1 RNA Trafficking Lab, Lady Davis Institute at the Jewish General Hospital, Montreal, QC H3T 1E2, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada
| | - Venessa Chen
- HIV-1 RNA Trafficking Lab, Lady Davis Institute at the Jewish General Hospital, Montreal, QC H3T 1E2, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada
| | - Alan W Cochrane
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Leslie J Parent
- Division of Infectious Diseases and Epidemiology, Departments of Medicine and Microbiology and Immunology, Penn State College of Medicine, Hershey, PA 17033, USA
| | - Andrew J Mouland
- HIV-1 RNA Trafficking Lab, Lady Davis Institute at the Jewish General Hospital, Montreal, QC H3T 1E2, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada; Department of Medicine, McGill University, Montreal, QC H4A 3J1, Canada.
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34
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Carrozza ML, Niewiadomska AM, Mazzei M, Abi-Said MR, Hué S, Hughes J, Gatseva A, Gifford RJ. Emergence and pandemic spread of small ruminant lentiviruses. Virus Evol 2023; 9:vead005. [PMID: 36793939 PMCID: PMC9924038 DOI: 10.1093/ve/vead005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 01/02/2023] [Accepted: 01/17/2023] [Indexed: 01/19/2023] Open
Abstract
Small ruminant lentiviruses (SRLVs) cause chronic, persistent infections in populations of domestic sheep (Ovis aries) and goats (Capra hircus) worldwide. The vast majority of SRLV infections involve two genotypes (A and B) that spread in association with the emergence of global livestock trade. However, SRLVs have likely been present in Eurasian ruminant populations since at least the early Neolithic period. Here, we use phylogenetic and phylogeographic approaches to reconstruct the origin of pandemic SRLV strains and infer their historical pattern of global spread. We constructed an open computational resource ('Lentivirus-GLUE') via which an up-to-date database of published SRLV sequences, multiple sequence alignments (MSAs), and sequence-associated metadata can be maintained. We used data collated in Lentivirus-GLUE to perform a comprehensive phylogenetic investigation of global SRLV diversity. Phylogenies reconstructed from genome-length alignments reveal that the deep divisions in the SRLV phylogeny are consistent with an ancient split into Eastern (A-like) and Western (B-like) lineages as agricultural systems disseminated out of domestication centres during the Neolithic period. These findings are also consistent with historical and phylogeographic evidence linking the early 20th century emergence of SRLV-A to the international export of Central Asian Karakul sheep. Investigating the global diversity of SRLVs can help reveal how anthropogenic factors have impacted the ecology and evolution of livestock diseases. The open resources generated in our study can expedite these studies and can also serve more broadly to facilitate the use of genomic data in SRLV diagnostics and research.
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Affiliation(s)
| | - Anna-Maria Niewiadomska
- Virus Pathogen Resource, J. Craig Venter Institute, 9605 Medical Center Drive, Suite 150, Rockville, MD 20850, USA
| | | | - Mounir R Abi-Said
- Faculty of Sciences II, Lebanese University, Campus Pierre Gemayel Fanar, Jdeidet 90656, Lebanon
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35
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Appah A, Beelen CJ, Kirkby D, Dong W, Shahid A, Foley B, Mensah M, Ganu V, Puplampu P, Amoah LE, Nii-Trebi NI, Brumme CJ, Brumme ZL. Molecular Epidemiology of HIV-1 in Ghana: Subtype Distribution, Drug Resistance and Coreceptor Usage. Viruses 2022; 15:128. [PMID: 36680168 PMCID: PMC9865111 DOI: 10.3390/v15010128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 12/27/2022] [Accepted: 12/29/2022] [Indexed: 01/03/2023] Open
Abstract
The greatest HIV-1 genetic diversity is found in West/Central Africa due to the pandemic’s origins in this region, but this diversity remains understudied. We characterized HIV-1 subtype diversity (from both sub-genomic and full-genome viral sequences), drug resistance and coreceptor usage in 103 predominantly (90%) antiretroviral-naive individuals living with HIV-1 in Ghana. Full-genome HIV-1 subtyping confirmed the circulating recombinant form CRF02_AG as the dominant (53.9%) subtype in the region, with the complex recombinant 06_cpx (4%) present as well. Unique recombinants, most of which were mosaics containing CRF02_AG and/or 06_cpx, made up 37% of sequences, while “pure” subtypes were rare (<6%). Pretreatment resistance to at least one drug class was observed in 17% of the cohort, with NNRTI resistance being the most common (12%) and INSTI resistance being relatively rare (2%). CXCR4-using HIV-1 sequences were identified in 23% of participants. Overall, our findings advance our understanding of HIV-1 molecular epidemiology in Ghana. Extensive HIV-1 genetic diversity in the region appears to be fueling the ongoing creation of novel recombinants, the majority CRF02_AG-containing, in the region. The relatively high prevalence of pretreatment NNRTI resistance but low prevalence of INSTI resistance supports the use of INSTI-based first-line regimens in Ghana.
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Affiliation(s)
- Anna Appah
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada
| | - Charlotte J. Beelen
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada
| | - Don Kirkby
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada
| | - Winnie Dong
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada
| | - Aniqa Shahid
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada
| | - Brian Foley
- Los Alamos National Laboratory, P.O. Box 1663, Los Alamos, NM 87545, USA
| | - Miriam Mensah
- Fevers Unit, Department of Medicine, Korle Bu Teaching Hospital, Accra P.O. Box KB 77, Ghana
| | - Vincent Ganu
- Department of Internal Medicine, Korle Bu Teaching Hospital, Accra P.O. Box KB 77, Ghana
| | - Peter Puplampu
- Department of Internal Medicine, Korle Bu Teaching Hospital, Accra P.O. Box KB 77, Ghana
| | - Linda E. Amoah
- Noguchi Memorial Institute for Medical Research, University of Ghana, Accra P.O. Box LG 581, Ghana
| | - Nicholas I. Nii-Trebi
- Department of Medical Laboratory Sciences, School of Biomedical and Allied Health Sciences, University of Ghana, Accra P.O. Box LG 25, Ghana
| | - Chanson J. Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada
- Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Zabrina L. Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada
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36
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Kozakiewicz CP, Burridge CP, Lee JS, Kraberger SJ, Fountain-Jones NM, Fisher RN, Lyren LM, Jennings MK, Riley SPD, Serieys LEK, Craft ME, Funk WC, Crooks KR, VandeWoude S, Carver S. Habitat connectivity and host relatedness influence virus spread across an urbanising landscape in a fragmentation-sensitive carnivore. Virus Evol 2022; 9:veac122. [PMID: 36694819 PMCID: PMC9865512 DOI: 10.1093/ve/veac122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/22/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022] Open
Abstract
Spatially heterogeneous landscape factors such as urbanisation can have substantial effects on the severity and spread of wildlife diseases. However, research linking patterns of pathogen transmission to landscape features remains rare. Using a combination of phylogeographic and machine learning approaches, we tested the influence of landscape and host factors on feline immunodeficiency virus (FIVLru) genetic variation and spread among bobcats (Lynx rufus) sampled from coastal southern California. We found evidence for increased rates of FIVLru lineage spread through areas of higher vegetation density. Furthermore, single-nucleotide polymorphism (SNP) variation among FIVLru sequences was associated with host genetic distances and geographic location, with FIVLru genetic discontinuities precisely correlating with known urban barriers to host dispersal. An effect of forest land cover on FIVLru SNP variation was likely attributable to host population structure and differences in forest land cover between different populations. Taken together, these results suggest that the spread of FIVLru is constrained by large-scale urban barriers to host movement. Although urbanisation at fine spatial scales did not appear to directly influence virus transmission or spread, we found evidence that viruses transmit and spread more quickly through areas containing higher proportions of natural habitat. These multiple lines of evidence demonstrate how urbanisation can change patterns of contact-dependent pathogen transmission and provide insights into how continued urban development may influence the incidence and management of wildlife disease.
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Affiliation(s)
| | | | - Justin S Lee
- Genomic Sequencing Laboratory, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | | | | | - Robert N Fisher
- Western Ecological Research Center, U.S. Geological Survey, San Diego, CA 92101, USA
| | - Lisa M Lyren
- Western Ecological Research Center, U.S. Geological Survey, San Diego, CA 92101, USA
| | - Megan K Jennings
- Biology Department, San Diego State University, San Diego, CA 92182, USA
| | - Seth P D Riley
- National Park Service, Santa Monica Mountains National Recreation Area, Thousand Oaks, CA 91360, USA
| | | | - Meggan E Craft
- Department of Ecology, Evolution and Behavior, University of Minnesota, St Paul, MN 55108, USA
| | - W Chris Funk
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA,Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO 80523, USA
| | - Kevin R Crooks
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO 80523, USA,Department of Fish, Wildlife, and Conservation Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Sue VandeWoude
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523, USA
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37
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Martin F, Marcelino JM, Palladino C, Bártolo I, Tracana S, Moranguinho I, Gonçalves P, Mateus R, Calado R, Borrego P, Leitner T, Clemente S, Taveira N. Long-Term and Low-Level Envelope C2V3 Stimulation by Highly Diverse Virus Isolates Leads to Frequent Development of Broad and Elite Antibody Neutralization in HIV-1-Infected Individuals. Microbiol Spectr 2022; 10:e0163422. [PMID: 36445130 PMCID: PMC9769935 DOI: 10.1128/spectrum.01634-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 10/29/2022] [Indexed: 12/03/2022] Open
Abstract
A minority of HIV-1-infected patients produce broadly neutralizing antibodies (bNAbs). Identification of viral and host correlates of bNAb production may help develop vaccines. We aimed to characterize the neutralizing response and viral and host-associated factors in Angola, which has one of the oldest, most dynamic, and most diverse HIV-1 epidemics in the world. Three hundred twenty-two HIV-1-infected adults from Angola were included in this retrospective study. Phylogenetic analysis of C2V3C3 env gene sequences was used for virus subtyping. Env-binding antibody reactivity was tested against polypeptides comprising the C2, V3, and C3 regions. Neutralizing-antibody responses were determined against a reference panel of tier 2 Env pseudoviruses in TZM-bl cells; neutralizing epitope specificities were predicted using ClustVis. All subtypes were found, along with untypeable strains and recombinant forms. Notably, 56% of the patients developed cross neutralizing, broadly neutralizing, or elite neutralizing responses. Broad and elite neutralization was associated with longer infection time, subtype C, lower CD4+ T cell counts, higher age, and higher titer of C2V3C3-specific antibodies relative to failure to develop bNAbs. Neutralizing antibodies targeted the V3-glycan supersite in most patients. V3 and C3 regions were significantly less variable in elite neutralizers than in weak neutralizers and nonneutralizers, suggesting an active role of V3C3-directed bNAbs in controlling HIV-1 replication and diversification. In conclusion, prolonged and low-level envelope V3C3 stimulation by highly diverse and ancestral HIV-1 isolates promotes the frequent elicitation of bNAbs. These results provide important clues for the development of an effective HIV-1 vaccine. IMPORTANCE Studies on neutralization by antibodies and their determinants in HIV-1-infected individuals have mostly been conducted in relatively recent epidemics caused by subtype B and C viruses. Results have suggested that elicitation of broadly neutralizing antibodies (bNAbs) is uncommon. The mechanisms underlying the elicitation of bNAbs are still largely unknown. We performed the first characterization of the plasma neutralizing response in a cohort of HIV-1-infected patients from Angola. Angola is characterized by an old and dynamic epidemic caused by highly diverse HIV-1 variants. Remarkably, more than half of the patients produced bNAbs, mostly targeting the V3-glycan supersite in HIV-1. This was associated with higher age, longer infection time, lower CD4+ T cell counts, subtype C infection, or higher titer of C2V3C3-specific antibodies relative to patients that did not develop bNAbs. These results may help develop the next generation of vaccine candidates for HIV-1.
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Affiliation(s)
- Francisco Martin
- Research Institute for Medicine, Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - José Maria Marcelino
- Research Institute for Medicine, Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
- Centro de Investigação Interdisciplinar Egas Moniz, Instituto Universitário Egas Moniz, Caparica, Portugal
| | - Claudia Palladino
- Research Institute for Medicine, Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Inês Bártolo
- Research Institute for Medicine, Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Susana Tracana
- Research Institute for Medicine, Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Inês Moranguinho
- Research Institute for Medicine, Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Paloma Gonçalves
- Research Institute for Medicine, Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Rita Mateus
- Research Institute for Medicine, Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Rita Calado
- Research Institute for Medicine, Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Pedro Borrego
- Research Institute for Medicine, Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Thomas Leitner
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | | | - Nuno Taveira
- Research Institute for Medicine, Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
- Centro de Investigação Interdisciplinar Egas Moniz, Instituto Universitário Egas Moniz, Caparica, Portugal
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Chao E, Chato C, Vender R, Olabode AS, Ferreira RC, Poon AFY. Molecular source attribution. PLoS Comput Biol 2022; 18:e1010649. [PMID: 36395093 PMCID: PMC9671344 DOI: 10.1371/journal.pcbi.1010649] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Elisa Chao
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
| | - Connor Chato
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
| | - Reid Vender
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
- School of Medicine, Queen’s University, Kingston, Ontario, Canada
| | - Abayomi S. Olabode
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
| | - Roux-Cil Ferreira
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
| | - Art F. Y. Poon
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
- * E-mail:
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39
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Sethuraman A. Teaching computational genomics and bioinformatics on a high performance computing cluster-a primer. Biol Methods Protoc 2022; 7:bpac032. [PMID: 36561335 PMCID: PMC9767868 DOI: 10.1093/biomethods/bpac032] [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] [Received: 07/19/2022] [Revised: 10/14/2022] [Accepted: 10/17/2022] [Indexed: 11/16/2022] Open
Abstract
The burgeoning field of genomics as applied to personalized medicine, epidemiology, conservation, agriculture, forensics, drug development, and other fields comes with large computational and bioinformatics costs, which are often inaccessible to student trainees in classroom settings at universities. However, with increased availability of resources such as NSF XSEDE, Google Cloud, Amazon AWS, and other high-performance computing (HPC) clouds and clusters for educational purposes, a growing community of academicians are working on teaching the utility of HPC resources in genomics and big data analyses. Here, I describe the successful implementation of a semester-long (16 week) upper division undergraduate/graduate level course in Computational Genomics and Bioinformatics taught at San Diego State University in Spring 2022. Students were trained in the theory, algorithms and hands-on applications of genomic data quality control, assembly, annotation, multiple sequence alignment, variant calling, phylogenomic analyses, population genomics, genome-wide association studies, and differential gene expression analyses using RNAseq data on their own dedicated 6-CPU NSF XSEDE Jetstream virtual machines. All lesson plans, activities, examinations, tutorials, code, lectures, and notes are publicly available at https://github.com/arunsethuraman/biomi609spring2022.
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Affiliation(s)
- Arun Sethuraman
- Correspondence address. Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182, USA. E-mail:
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40
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Zuliani-Alvarez L, Govasli ML, Rasaiyaah J, Monit C, Perry SO, Sumner RP, McAlpine-Scott S, Dickson C, Rifat Faysal KM, Hilditch L, Miles RJ, Bibollet-Ruche F, Hahn BH, Boecking T, Pinotsis N, James LC, Jacques DA, Towers GJ. Evasion of cGAS and TRIM5 defines pandemic HIV. Nat Microbiol 2022; 7:1762-1776. [PMID: 36289397 PMCID: PMC9613477 DOI: 10.1038/s41564-022-01247-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 09/08/2022] [Indexed: 11/29/2022]
Abstract
Of the 13 known independent zoonoses of simian immunodeficiency viruses to humans, only one, leading to human immunodeficiency virus (HIV) type 1(M) has become pandemic, causing over 80 million human infections. To understand the specific features associated with pandemic human-to-human HIV spread, we compared replication of HIV-1(M) with non-pandemic HIV-(O) and HIV-2 strains in myeloid cell models. We found that non-pandemic HIV lineages replicate less well than HIV-1(M) owing to activation of cGAS and TRIM5-mediated antiviral responses. We applied phylogenetic and X-ray crystallography structural analyses to identify differences between pandemic and non-pandemic HIV capsids. We found that genetic reversal of two specific amino acid adaptations in HIV-1(M) enables activation of TRIM5, cGAS and innate immune responses. We propose a model in which the parental lineage of pandemic HIV-1(M) evolved a capsid that prevents cGAS and TRIM5 triggering, thereby allowing silent replication in myeloid cells. We hypothesize that this capsid adaptation promotes human-to-human spread through avoidance of innate immune response activation.
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Affiliation(s)
- Lorena Zuliani-Alvarez
- Division of Infection and Immunity, UCL, London, UK
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
| | | | | | - Chris Monit
- Division of Infection and Immunity, UCL, London, UK
- Carnall Farrar, London, UK
| | - Stephen O Perry
- Division of Infection and Immunity, UCL, London, UK
- Quell Therapeutics Ltd, Translation & Innovation Hub, London, UK
| | | | | | - Claire Dickson
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - K M Rifat Faysal
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - Laura Hilditch
- Division of Infection and Immunity, UCL, London, UK
- Nucleus Global, London, UK
| | | | - Frederic Bibollet-Ruche
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Beatrice H Hahn
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Till Boecking
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - Nikos Pinotsis
- Institute of Structural and Molecular Biology, Birkbeck College, London, UK
| | - Leo C James
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - David A Jacques
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences, UNSW Sydney, Sydney, New South Wales, Australia.
| | - Greg J Towers
- Division of Infection and Immunity, UCL, London, UK.
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41
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Zarudnaya MI, Potyahaylo AL, Kolomiets IM, Gorb LG. Genome sequence analysis suggests coevolution of the DIS, SD, and Psi hairpins in HIV-1 genomes. Virus Res 2022; 321:198910. [PMID: 36070810 DOI: 10.1016/j.virusres.2022.198910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 08/28/2022] [Accepted: 08/31/2022] [Indexed: 12/24/2022]
Abstract
HIV-1 RNA dimerization is a critical step in viral life cycle. It is a prerequisite for genome packaging and plays an important role in reverse transcription and recombination. Dimerization is promoted by the DIS (dimerization initiation site) hairpin located in the 5' leader of HIV-1 genome. Despite the high genetic diversity in HIV-1 group M, only five apical loops (AAGCGCGCA, AAGUGCGCA, AAGUGCACA, AGGUGCACA and AGUGCAC) are commonly found in DIS hairpins. We refer to the parent DISes with these apical loops as DISLai, DISTrans, DISF, DISMal, and DISC, respectively. Based on identity or similarity of DIS hairpins to parent DISes, we distributed HIV-1 M genomes into five dimerization groups. Comparison of the primary and secondary structures of DIS, SD and Psi hairpins in about 3000 HIV-1 M genomes showed that the mutation frequencies at particular nucleotide positions of these hairpins differ among the dimerization groups, and DISF may be an origin of other parent DISes. We found that DIS, SD and Psi hairpins have hundreds of variants, only some of them occurring rather frequently. The lower part of DIS hairpin with G x AGG internal loop is highly conserved in both HIV-1 and SIV genomes. We supposed that the G-quadruplex, located 56 nts downstream of the Gag start codon, may participate in switching of HIV-1 leader RNA from BMH (branched multiple hairpins) to LDI (long distance interaction) conformation.
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Affiliation(s)
- Margarita I Zarudnaya
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Akademika Zabolotnoho Str, Kyiv 03143, Ukraine
| | - Andriy L Potyahaylo
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Akademika Zabolotnoho Str, Kyiv 03143, Ukraine
| | - Iryna M Kolomiets
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Akademika Zabolotnoho Str, Kyiv 03143, Ukraine
| | - Leonid G Gorb
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Akademika Zabolotnoho Str, Kyiv 03143, Ukraine.
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42
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Tang D, Wang Y, Dong X, Yuan Y, Kang F, Tian W, Wang K, Li H, Qi S. Scramblases and virus infection. Bioessays 2022; 44:e2100261. [DOI: 10.1002/bies.202100261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 09/26/2022] [Accepted: 09/27/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Dan Tang
- Department of Urology Institute of Urology (Laboratory of Reconstructive Urology) State Key Laboratory of Oral Disease West China Hospital of Stomatology West China Hospital Sichuan University Chengdu Sichuan China
| | - Yichang Wang
- Department of Urology Institute of Urology (Laboratory of Reconstructive Urology) State Key Laboratory of Oral Disease West China Hospital of Stomatology West China Hospital Sichuan University Chengdu Sichuan China
| | - Xiuju Dong
- Department of Urology Institute of Urology (Laboratory of Reconstructive Urology) State Key Laboratory of Oral Disease West China Hospital of Stomatology West China Hospital Sichuan University Chengdu Sichuan China
| | - Yiqiong Yuan
- Department of Urology Institute of Urology (Laboratory of Reconstructive Urology) State Key Laboratory of Oral Disease West China Hospital of Stomatology West China Hospital Sichuan University Chengdu Sichuan China
| | - Fanchen Kang
- Department of Urology Institute of Urology (Laboratory of Reconstructive Urology) State Key Laboratory of Oral Disease West China Hospital of Stomatology West China Hospital Sichuan University Chengdu Sichuan China
| | - Weidong Tian
- Department of Urology Institute of Urology (Laboratory of Reconstructive Urology) State Key Laboratory of Oral Disease West China Hospital of Stomatology West China Hospital Sichuan University Chengdu Sichuan China
| | - Kunjie Wang
- Department of Urology Institute of Urology (Laboratory of Reconstructive Urology) State Key Laboratory of Oral Disease West China Hospital of Stomatology West China Hospital Sichuan University Chengdu Sichuan China
| | - Hong Li
- Department of Urology Institute of Urology (Laboratory of Reconstructive Urology) State Key Laboratory of Oral Disease West China Hospital of Stomatology West China Hospital Sichuan University Chengdu Sichuan China
| | - Shiqian Qi
- Department of Urology Institute of Urology (Laboratory of Reconstructive Urology) State Key Laboratory of Oral Disease West China Hospital of Stomatology West China Hospital Sichuan University Chengdu Sichuan China
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43
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Stockdale JE, Liu P, Colijn C. The potential of genomics for infectious disease forecasting. Nat Microbiol 2022; 7:1736-1743. [PMID: 36266338 DOI: 10.1038/s41564-022-01233-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 08/18/2022] [Indexed: 11/09/2022]
Abstract
Genomic technologies have led to tremendous gains in understanding how pathogens function, evolve and interact. Pathogen diversity is now measurable at high precision and resolution, in part because over the past decade, sequencing technologies have increased in speed and capacity, at decreased cost. Alongside this, the use of models that can forecast emergence and size of infectious disease outbreaks has risen, highlighted by the coronavirus disease 2019 pandemic but also due to modelling advances that allow for rapid estimates in emerging outbreaks to inform monitoring, coordination and resource deployment. However, genomics studies have remained largely retrospective. While they contain high-resolution views of pathogen diversification and evolution in the context of selection, they are often not aligned with designing interventions. This is a missed opportunity because pathogen diversification is at the core of the most pressing infectious public health challenges, and interventions need to take the mechanisms of virulence and understanding of pathogen diversification into account. In this Perspective, we assess these converging fields, discuss current challenges facing both surveillance specialists and modellers who want to harness genomic data, and propose next steps for integrating longitudinally sampled genomic data with statistical learning and interpretable modelling to make reliable predictions into the future.
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Affiliation(s)
- Jessica E Stockdale
- Department of Mathematics, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Pengyu Liu
- Department of Mathematics, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Caroline Colijn
- Department of Mathematics, Simon Fraser University, Burnaby, British Columbia, Canada.
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44
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Yu X, Cheng G. Contribution of phylogenetics to understanding the evolution and epidemiology of dengue virus. Animal Model Exp Med 2022; 5:410-417. [PMID: 36245335 PMCID: PMC9610151 DOI: 10.1002/ame2.12283] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 10/05/2022] [Indexed: 11/18/2022] Open
Abstract
Dengue virus (DENV) is one of the most important arboviral pathogens in the tropics and subtropics, and nearly one‐third of the world's population is at risk of infection. The transmission of DENV involves a sylvatic cycle between nonhuman primates (NHP) and Aedes genus mosquitoes, and an endemic cycle between human hosts and predominantly Aedes aegypti. DENV belongs to the genus Flavivirus of the family Flaviviridae and consists of four antigenically distinct serotypes (DENV‐1‐4). Phylogenetic analyses of DENV have revealed its origin, epidemiology, and the drivers that determine its molecular evolution in nature. This review discusses how phylogenetic research has improved our understanding of DENV evolution and how it affects viral ecology and improved our ability to analyze and predict future DENV emergence.
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Affiliation(s)
- Xi Yu
- Tsinghua-Peking Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, China.,Institute of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen, China.,Institute of Pathogenic Organisms, Shenzhen Center for Disease Control and Prevention, Shenzhen, China.,School of Life Sciences, Tsinghua University, Beijing, China
| | - Gong Cheng
- Tsinghua-Peking Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, China.,Institute of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen, China.,Institute of Pathogenic Organisms, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
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45
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Ellwanger JH, Fearnside PM, Ziliotto M, Valverde-Villegas JM, Veiga ABGDA, Vieira GF, Bach E, Cardoso JC, Müller NFD, Lopes G, Caesar L, Kulmann-Leal B, Kaminski VL, Silveira ES, Spilki FR, Weber MN, Almeida SEDEM, Hora VPDA, Chies JAB. Synthesizing the connections between environmental disturbances and zoonotic spillover. AN ACAD BRAS CIENC 2022; 94:e20211530. [PMID: 36169531 DOI: 10.1590/0001-3765202220211530] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 03/03/2022] [Indexed: 11/22/2022] Open
Abstract
Zoonotic spillover is a phenomenon characterized by the transfer of pathogens between different animal species. Most human emerging infectious diseases originate from non-human animals, and human-related environmental disturbances are the driving forces of the emergence of new human pathogens. Synthesizing the sequence of basic events involved in the emergence of new human pathogens is important for guiding the understanding, identification, and description of key aspects of human activities that can be changed to prevent new outbreaks, epidemics, and pandemics. This review synthesizes the connections between environmental disturbances and increased risk of spillover events based on the One Health perspective. Anthropogenic disturbances in the environment (e.g., deforestation, habitat fragmentation, biodiversity loss, wildlife exploitation) lead to changes in ecological niches, reduction of the dilution effect, increased contact between humans and other animals, changes in the incidence and load of pathogens in animal populations, and alterations in the abiotic factors of landscapes. These phenomena can increase the risk of spillover events and, potentially, facilitate new infectious disease outbreaks. Using Brazil as a study model, this review brings a discussion concerning anthropogenic activities in the Amazon region and their potential impacts on spillover risk and spread of emerging diseases in this region.
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Affiliation(s)
- Joel Henrique Ellwanger
- Universidade Federal do Rio Grande do Sul/UFRGS, Laboratório de Imunobiologia e Imunogenética, Departmento de Genética, Campus do Vale, Avenida Bento Gonçalves, 9500, Agronomia, 91501-970 Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Genética e Biologia Molecular/PPGBM, Universidade Federal do Rio Grande do Sul/UFRGS, Departmento de Genética, Campus do Vale, Avenida Bento Gonçalves, 9500, Agronomia, 91501-970 Porto Alegre, RS, Brazil
| | - Philip Martin Fearnside
- Instituto Nacional de Pesquisas da Amazônia/INPA, Avenida André Araújo, 2936, Aleixo, 69067-375 Manaus, AM, Brazil
| | - Marina Ziliotto
- Universidade Federal do Rio Grande do Sul/UFRGS, Laboratório de Imunobiologia e Imunogenética, Departmento de Genética, Campus do Vale, Avenida Bento Gonçalves, 9500, Agronomia, 91501-970 Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Genética e Biologia Molecular/PPGBM, Universidade Federal do Rio Grande do Sul/UFRGS, Departmento de Genética, Campus do Vale, Avenida Bento Gonçalves, 9500, Agronomia, 91501-970 Porto Alegre, RS, Brazil
| | - Jacqueline María Valverde-Villegas
- Institut de Génétique Moléculaire de Montpellier/IGMM, Centre National de la Recherche Scientifique/CNRS, Laboratoire coopératif IGMM/ABIVAX, 1919, route de Mende, 34090 Montpellier, Montpellier, France
| | - Ana Beatriz G DA Veiga
- Universidade Federal de Ciências da Saúde de Porto Alegre/UFCSPA, Departamento de Ciências Básicas de Saúde, Rua Sarmento Leite, 245, Centro Histórico, 90050-170 Porto Alegre, RS, Brazil
| | - Gustavo F Vieira
- Programa de Pós-Graduação em Genética e Biologia Molecular/PPGBM, Universidade Federal do Rio Grande do Sul/UFRGS, Departmento de Genética, Campus do Vale, Avenida Bento Gonçalves, 9500, Agronomia, 91501-970 Porto Alegre, RS, Brazil.,Universidade Federal do Rio Grande do Sul/UFRGS, Laboratório de Imunoinformática, Núcleo de Bioinformática do Laboratório de Imunogenética/NBLI, Departmento de Genética, Campus do Vale, Avenida Bento Gonçalves, 9500, Agronomia, 91501-970 Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Saúde e Desenvolvimento Humano, Universidade La Salle, Laboratório de Saúde Humana in silico, Avenida Victor Barreto, 2288, Centro, 92010-000 Canoas, RS, Brazil
| | - Evelise Bach
- Universidade Federal do Rio Grande do Sul/UFRGS, Laboratório de Imunobiologia e Imunogenética, Departmento de Genética, Campus do Vale, Avenida Bento Gonçalves, 9500, Agronomia, 91501-970 Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Genética e Biologia Molecular/PPGBM, Universidade Federal do Rio Grande do Sul/UFRGS, Departmento de Genética, Campus do Vale, Avenida Bento Gonçalves, 9500, Agronomia, 91501-970 Porto Alegre, RS, Brazil
| | - Jáder C Cardoso
- Centro Estadual de Vigilância em Saúde/CEVS, Divisão de Vigilância Ambiental em Saúde, Secretaria da Saúde do Estado do Rio Grande do Sul, Avenida Ipiranga, 5400, Jardim Botânico, 90610-000 Porto Alegre, RS, Brazil
| | - Nícolas Felipe D Müller
- Centro Estadual de Vigilância em Saúde/CEVS, Divisão de Vigilância Ambiental em Saúde, Secretaria da Saúde do Estado do Rio Grande do Sul, Avenida Ipiranga, 5400, Jardim Botânico, 90610-000 Porto Alegre, RS, Brazil
| | - Gabriel Lopes
- Fundação Oswaldo Cruz/FIOCRUZ, Casa de Oswaldo Cruz, Avenida Brasil, 4365, Manguinhos, 21040-900 Rio de Janeiro, RJ, Brazil
| | - Lílian Caesar
- Programa de Pós-Graduação em Genética e Biologia Molecular/PPGBM, Universidade Federal do Rio Grande do Sul/UFRGS, Departmento de Genética, Campus do Vale, Avenida Bento Gonçalves, 9500, Agronomia, 91501-970 Porto Alegre, RS, Brazil.,Indiana University/IU, Department of Biology, 915 East 3rd Street, Bloomington, IN 47405, USA
| | - Bruna Kulmann-Leal
- Universidade Federal do Rio Grande do Sul/UFRGS, Laboratório de Imunobiologia e Imunogenética, Departmento de Genética, Campus do Vale, Avenida Bento Gonçalves, 9500, Agronomia, 91501-970 Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Genética e Biologia Molecular/PPGBM, Universidade Federal do Rio Grande do Sul/UFRGS, Departmento de Genética, Campus do Vale, Avenida Bento Gonçalves, 9500, Agronomia, 91501-970 Porto Alegre, RS, Brazil
| | - Valéria L Kaminski
- Programa de Pós-Graduação em Biotecnologia, Universidade Federal de São Paulo/UNIFESP, Instituto de Ciência e Tecnologia/ICT, Laboratório de Imunologia Aplicada, Rua Talim, 330, Vila Nair, 12231-280 São José dos Campos, SP, Brazil
| | - Etiele S Silveira
- Programa de Pós-Graduação em Genética e Biologia Molecular/PPGBM, Universidade Federal do Rio Grande do Sul/UFRGS, Departmento de Genética, Campus do Vale, Avenida Bento Gonçalves, 9500, Agronomia, 91501-970 Porto Alegre, RS, Brazil.,Universidade Federal do Rio Grande do Sul/UFRGS, Laboratório de Imunoinformática, Núcleo de Bioinformática do Laboratório de Imunogenética/NBLI, Departmento de Genética, Campus do Vale, Avenida Bento Gonçalves, 9500, Agronomia, 91501-970 Porto Alegre, RS, Brazil
| | - Fernando R Spilki
- Universidade Feevale, Laboratório de Saúde Única, Instituto de Ciências da Saúde/ICS, Rodovia ERS-239, 2755, Vila Nova, 93525-075 Novo Hamburgo, RS, Brazil
| | - Matheus N Weber
- Universidade Feevale, Laboratório de Saúde Única, Instituto de Ciências da Saúde/ICS, Rodovia ERS-239, 2755, Vila Nova, 93525-075 Novo Hamburgo, RS, Brazil
| | - Sabrina E DE Matos Almeida
- Universidade Feevale, Laboratório de Saúde Única, Instituto de Ciências da Saúde/ICS, Rodovia ERS-239, 2755, Vila Nova, 93525-075 Novo Hamburgo, RS, Brazil
| | - Vanusa P DA Hora
- Programa de Pós-Graduação em Ciências da Saúde, Universidade Federal do Rio Grande/FURG, Faculdade de Medicina, Rua Visconde de Paranaguá, 102, Centro, 96203-900, Rio Grande, RS, Brazil
| | - José Artur B Chies
- Universidade Federal do Rio Grande do Sul/UFRGS, Laboratório de Imunobiologia e Imunogenética, Departmento de Genética, Campus do Vale, Avenida Bento Gonçalves, 9500, Agronomia, 91501-970 Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Genética e Biologia Molecular/PPGBM, Universidade Federal do Rio Grande do Sul/UFRGS, Departmento de Genética, Campus do Vale, Avenida Bento Gonçalves, 9500, Agronomia, 91501-970 Porto Alegre, RS, Brazil
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Yu Z, Zhang TT, Wang X, Chang Q, Huang H, Zhang H, Song D, Yu M, Yang J, Liu Y, Li C, Cui Z, Ma J. Sexual behaviour changes and HIV infection among men who have sex with men: evidence from an open cohort in China. BMJ Open 2022; 12:e055046. [PMID: 36171031 PMCID: PMC9528664 DOI: 10.1136/bmjopen-2021-055046] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND The HIV epidemic in key populations such as men who have sex with men (MSM) is a public health issue of worldwide concern. China has seen an increase in newly diagnosed HIV infections through male-male sexual contact in the past decade. In a long-term cohort, how the complex behaviour pattern of MSM changed and the association with the HIV risk are unclear at present. METHODS This study was conducted from October 2011 to December 2019 in Tianjin. MSM were recruited by snowball sampling through online and offline ways. Demographic and sexual behavioural data were collected for analysis. Three indicators (condom use in last anal sex, frequency of condom use during anal sex and the number of sexual partners) were used to define the behaviour change. Participants with zero, one, and two or three risk indicators were categorised into behaviour types of 'protective', 'moderate', and 'fragile', respectively. Change in behaviour type between baseline and each visit was considered. Time-varying Cox models were performed to evaluate HIV infection risk. RESULTS Of 2029 MSM included in the study, 127 were new HIV diagnoses. The overall incidence rate was 3.36 per 100 person-years. The percentage of 'protective' and 'moderate' behaviour types had a conspicuous growth trend as the follow-up. Furthermore, the HIV incidence rate in each visit among different behaviour transition types showed a general downward trend as the number of total follow-up times increased. Individuals who remained in 'fragile' (adjusted HR (aHR): 25.86, 95% CI: 6.92 to 96.57) or changed from 'protective' to 'moderate' (aHR: 4.79, 95% CI: 1.18 to 19.47), 'protective' to 'fragile' (aHR: 23.03, 95% CI: 6.02 to 88.13), and 'moderate' to 'fragile' (aHR: 25.48, 95% CI: 6.79 to 95.40) between baseline and the last follow-up had a higher HIV risk. Gained risk indicators were associated with the increase of HIV risk (gained one indicator, aHR: 2.67, 95% CI: 1.68 to 4.24; gained two or three indicators, aHR: 4.99, 95% CI: 3.00 to 8.31) while losing just one risk indicator could halve the risk (aHR: 0.43, 95% CI: 0.21 to 0.90). CONCLUSIONS Among MSM in Tianjin, it is necessary to get timely behaviour change for those with high-incidence behaviour patterns while sustaining for those with low-incidence patterns. TRIAL REGISTRATION NUMBER Chinese Clinical Trials Registry (ChiCTR2000039500).
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Affiliation(s)
- Zeyang Yu
- School of Public Health, Tianjin Medical University, No. 22 Qixiangtai Road, Heping District, Tianjin, China
| | - Tian-Tian Zhang
- School of Public Health, Tianjin Medical University, No. 22 Qixiangtai Road, Heping District, Tianjin, China
| | - Xiaomeng Wang
- School of Public Health, Tianjin Medical University, No. 22 Qixiangtai Road, Heping District, Tianjin, China
| | - Qinxue Chang
- School of Public Health, Tianjin Medical University, No. 22 Qixiangtai Road, Heping District, Tianjin, China
| | - Huijie Huang
- School of Public Health, Tianjin Medical University, No. 22 Qixiangtai Road, Heping District, Tianjin, China
| | - Honglu Zhang
- School of Public Health, Tianjin Medical University, No. 22 Qixiangtai Road, Heping District, Tianjin, China
| | - Desheng Song
- School of Public Health, Tianjin Medical University, No. 22 Qixiangtai Road, Heping District, Tianjin, China
| | - Maohe Yu
- STD & AIDS Control and Prevention Section, Tianjin Centers for Disease Control and Prevention, No. 6 Huayue Road, Hedong District, Tianjin, China
| | - Jie Yang
- Tianjin Shenlan Community-Based Organization, No. 43, Shuimu Tiancheng Tuanjie Ring Road, Hongqiao District, Tianjin, China
| | - Yuanyuan Liu
- School of Public Health, Tianjin Medical University, No. 22 Qixiangtai Road, Heping District, Tianjin, China
| | - Changping Li
- School of Public Health, Tianjin Medical University, No. 22 Qixiangtai Road, Heping District, Tianjin, China
| | - Zhuang Cui
- School of Public Health, Tianjin Medical University, No. 22 Qixiangtai Road, Heping District, Tianjin, China
| | - Jun Ma
- School of Public Health, Tianjin Medical University, No. 22 Qixiangtai Road, Heping District, Tianjin, China
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Ho LST, Dinh V. When can we reconstruct the ancestral state? A unified theory. Theor Popul Biol 2022; 148:22-27. [PMID: 36167107 DOI: 10.1016/j.tpb.2022.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 09/09/2022] [Accepted: 09/19/2022] [Indexed: 10/14/2022]
Abstract
Ancestral state reconstruction is one of the most important tasks in evolutionary biology. Conditions under which we can reliably reconstruct the ancestral state have been studied for both discrete and continuous traits. However, the connection between these results is unclear, and it seems that each model needs different conditions. In this work, we provide a unifying theory on the consistency of ancestral state reconstruction for various types of trait evolution models. Notably, we show that for a sequence of nested trees with bounded heights, the necessary and sufficient conditions for the existence of a consistent ancestral state reconstruction method under discrete models, the Brownian motion model, and the threshold model are equivalent. When tree heights are unbounded, we provide a simple counter-example to show that this equivalence is no longer valid.
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Affiliation(s)
- Lam Si Tung Ho
- Department of Mathematics and Statistics, Dalhousie University, Halifax, Nova Scotia, Canada.
| | - Vu Dinh
- Department of Mathematical Sciences, University of Delaware, USA.
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The Emergence, Diversification, and Transmission of Subgroup J Avian Leukosis Virus Reveals that the Live Chicken Trade Plays a Critical Role in the Adaption and Endemicity of Viruses to the Yellow-Chickens. J Virol 2022; 96:e0071722. [PMID: 35950858 PMCID: PMC9472763 DOI: 10.1128/jvi.00717-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The geographical spread and inter-host transmission of the subgroup J avian leukosis virus (ALV-J) may be the most important issues for epidemiology. An integrated analysis, including phylogenetic trees, homology modeling, evolutionary dynamics, selection analysis and viral transmission, based on the gp85 gene sequences of the 665 worldwide ALV-J isolates during 1988-2020, was performed. A new Clade 3 has been emerging and was evolved from the dominating Clade 1.3 of the Chinese Yellow-chicken, and the loss of a α-helix or β-sheet of the gp85 protein monomer was found by the homology modeling. The rapid evolution found in Clades 1.3 and 3 may be closely associated with the adaption and endemicity of viruses to the Yellow-chickens. The early U.S. strains from Clade 1.1 acted as an important source for the global spread of ALV-J and the earliest introduction into China was closely associated with the imported chicken breeders in the 1990s. The dominant outward migrations of Clades 1.1 and 1.2, respectively, from the Chinese northern White-chickens and layers to the Chinese southern Yellow-chickens, and the dominating migration of Clade 1.3 from the Chinese southern Yellow-chickens to other regions and hosts, indicated that the long-distance movement of these viruses between regions in China was associated with the live chicken trade. Furthermore, Yellow-chickens have been facing the risk of infections of the emerging Clades 2 and 3. Our findings provide new insights for the epidemiology and help to understand the critical factors involved in ALV-J dissemination. IMPORTANCE Although the general epidemiology of ALV-J is well studied, the ongoing evolutionary and transmission dynamics of the virus remain poorly investigated. The phylogenetic differences and relationship of the clades and subclades were characterized, and the epidemics and factors driving the geographical spread and inter-host transmission of different ALV-J clades were explored for the first time. The results indicated that the earliest ALV-J (Clade 1.1) from the United States, acted as the source for global spreads, and Clades 1.2, 1.3 and 3 were all subsequently evolved. Also the epidemiological investigation showed that the early imported breeders and the inter-region movements of live chickens facilitated the ALV-J dispersal throughout China and highlighted the needs to implement more effective containment measures.
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Postscript: A pandemic read on African health and environmental histories. Health Place 2022; 77:102846. [PMID: 35750572 PMCID: PMC9217063 DOI: 10.1016/j.healthplace.2022.102846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 06/08/2022] [Indexed: 02/08/2023]
Abstract
This postscript reflects on this special issue's contributions for readers preoccupied with the COVID-19 pandemic. First, these articles on African environment and health underscore that past process of and interventions into land use and human health have cumulative effects on disease emergence and re-emergence. Relatedly, although multiple epidemics have affected the African continent and other parts of the world over the past century, global health institutions and actors have sidelined or forgotten these epidemics. These analyses draw our attention to the historical production and mobilization of specific concepts which frame what questions are asked, how they are answered, and the material solutions provided or withheld. And finally, these pieces highlight the ethical stakes of agricultural, conservation, and health interventions, reminding us that the African continent's histories are fraught with inequities from colonial and postcolonial extractive relations and racist assumptions that have undermined livelihoods, food security and health. As African states, institutions, and global health critics politick for vaccine equity and deplore the inequitable access to COVID-19 vaccines in African countries compared to the rest of the world, these articles remind us that these long-standing inequities should catalyze fundamental change.
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Tee KK, Thomson MM, Hemelaar J. Editorial: HIV-1 genetic diversity, volume II. Front Microbiol 2022; 13:1007037. [PMID: 36071960 PMCID: PMC9443081 DOI: 10.3389/fmicb.2022.1007037] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 08/05/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Kok Keng Tee
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
- *Correspondence: Kok Keng Tee
| | - Michael M. Thomson
- HIV Biology and Variability Unit, Centro Nacional de Microbiolog, Instituto de Salud Carlos III, Madrid, Spain
- Michael M. Thomson
| | - Joris Hemelaar
- Infectious Disease Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
- Joris Hemelaar
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