1
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Shahid A, MacLennan S, Jones BR, Sudderuddin H, Dang Z, Cobarrubias K, Duncan MC, Kinloch NN, Dapp MJ, Archin NM, Fischl MA, Ofotokun I, Adimora A, Gange S, Aouizerat B, Kuniholm MH, Kassaye S, Mullins JI, Goldstein H, Joy JB, Anastos K, Brumme ZL. The replication-competent HIV reservoir is a genetically restricted, younger subset of the overall pool of HIV proviruses persisting during therapy, which is highly genetically stable over time. J Virol 2024; 98:e0165523. [PMID: 38214547 PMCID: PMC10878278 DOI: 10.1128/jvi.01655-23] [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: 10/24/2023] [Accepted: 12/07/2023] [Indexed: 01/13/2024] Open
Abstract
Within-host HIV populations continually diversify during untreated infection, and this diversity persists within infected cell reservoirs during antiretroviral therapy (ART). Achieving a better understanding of on-ART proviral evolutionary dynamics, and a better appreciation of how the overall persisting pool of (largely genetically defective) proviruses differs from the much smaller replication-competent HIV reservoir, is critical to HIV cure efforts. We reconstructed within-host HIV evolutionary histories in blood from seven participants of the Women's Interagency HIV Study who experienced HIV seroconversion, and used these data to characterize the diversity, lineage origins, and ages of proviral env-gp120 sequences sampled longitudinally up to 12 years on ART. We also studied HIV sequences emerging from the reservoir in two participants. We observed that proviral clonality generally increased over time on ART, with clones frequently persisting long term. While on-ART proviral integration dates generally spanned the duration of untreated infection, HIV emerging in plasma was exclusively younger (i.e., dated to the years immediately pre-ART). The genetic and age distributions of distinct proviral sequences remained stable during ART in all but one participant, in whom there was evidence that younger proviruses had been preferentially eliminated after 12 years on ART. Analysis of the gag region in three participants corroborated our env-gp120-based observations, indicating that our observations are not influenced by the HIV region studied. Our results underscore the remarkable genetic stability of the distinct proviral sequences that persist in blood during ART. Our results also suggest that the replication-competent HIV reservoir is a genetically restricted, younger subset of this overall proviral pool.IMPORTANCECharacterizing the genetically diverse HIV sequences that persist in the reservoir despite antiretroviral therapy (ART) is critical to cure efforts. Our observations confirm that proviruses persisting in blood on ART, which are largely genetically defective, broadly reflect the extent of within-host HIV evolution pre-ART. Moreover, on-ART clonal expansion is not appreciably accompanied by the loss of distinct proviral lineages. In fact, on-ART proviral genetic composition remained stable in all but one participant, in whom, after 12 years on ART, proviruses dating to around near ART initiation had been preferentially eliminated. We also identified recombinant proviruses between parental sequence fragments of different ages. Though rare, such sequences suggest that reservoir cells can be superinfected with HIV from another infection era. Overall, our finding that the replication-competent reservoir in blood is a genetically restricted, younger subset of all persisting proviruses suggests that HIV cure strategies will need to eliminate a reservoir that differs in key respects from the overall proviral pool.
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Affiliation(s)
- Aniqa Shahid
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Signe MacLennan
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Bradley R. Jones
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Bioinformatics Program, University of British Columbia, Vancouver, British Columbia, Canada
| | - Hanwei Sudderuddin
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Zhong Dang
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Kyle Cobarrubias
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Maggie C. Duncan
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Natalie N. Kinloch
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Michael J. Dapp
- Department of Microbiology, University of Washington, School of Medicine, Seattle, Washington, USA
| | - Nancie M. Archin
- UNC HIV Cure Center, Institute of Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Margaret A. Fischl
- Department of Medicine, University of Miami School of Medicine, Miami, Florida, USA
| | - Igho Ofotokun
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Adaora Adimora
- Department of Epidemiology, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Stephen Gange
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | | | - Mark H. Kuniholm
- Department of Epidemiology and Biostatistics, University at Albany, State University of New York, Rensselaer, New York, New York, USA
| | - Seble Kassaye
- Division of Infectious Diseases and Tropical Medicine, Georgetown University, Washington, DC, USA
| | - James I. Mullins
- Department of Microbiology, University of Washington, School of Medicine, Seattle, Washington, USA
- Department of Global Health, University of Washington, School of Medicine, Seattle, Washington, USA
- Department of Medicine, University of Washington, School of Medicine, Seattle, Washington, USA
| | - Harris Goldstein
- Departments of Microbiology and Immunology and Pediatrics, Albert Einstein College of Medicine, Bronx, New York, New York, USA
| | - Jeffrey B. Joy
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Bioinformatics Program, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kathryn Anastos
- Department of Medicine, Albert Einstein College of Medicine, New York, New York, USA
| | - Zabrina L. Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - the MACS/WIHS combined cohort study (MWCSS)OfotokunIghovwerha1ShethAnandi1WingoodGina1BrownTodd2MargolickJoseph2AnastosKathryn3HannaDavid3SharmaAnjali3GustafsonDeborah4WilsonTracey4D’SouzaGypsyamber5GangeStephen5TopperElizabeth5CohenMardge6FrenchAudrey6WolinskySteven7PalellaFrank7StosorValentina7AouizeratBradley8PriceJennifer8TienPhyllis8DetelsRoger9MimiagaMatthew9KassayeSeble10MerensteinDaniel10AlcaideMaria11FischlMargaret11JonesDeborah11MartinsonJeremy12RinaldoCharles12KempfMirjam-Colette13Dionne-OdomJodie13Konkle-ParkerDeborah13BrockJames B.13AdimoraAdaora14Floris-MooreMichelle14Emory University, Atlanta, Georgia, USAJohns Hopkins University, Baltimore, Maryland, USAAlbert Einstein College of Medicine, Bronx, New York, USASuny Downstate Medical Center, Brooklyn, New York, USAJohns Hopkins University, Baltimore, Maryland, USAHektoen Institute for Medical Research, Chicago, Illinois, USANorthwestern University at Chicago, Chicago, Illinois, USAUniversity of California San Francisco, San Francisco, California, USAUniversity of California Los Angeles, Los Angeles, California, USAGeorgetown University, Washington, DC, USAUniversity of Miami School of Medicine, Coral Gables, Florida, USAUniversity of Pittsburgh, Pittsburgh, Pennsylvania, USAUniversity of Alabama Birmingham, Birmingham, Alabama, USAUniversity of North Carolina Chapel Hill, Chapel Hill, North Carolina, USA
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Bioinformatics Program, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Microbiology, University of Washington, School of Medicine, Seattle, Washington, USA
- UNC HIV Cure Center, Institute of Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Medicine, University of Miami School of Medicine, Miami, Florida, USA
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
- Department of Epidemiology, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- College of Dentistry, New York University, New York, New York, USA
- Department of Epidemiology and Biostatistics, University at Albany, State University of New York, Rensselaer, New York, New York, USA
- Division of Infectious Diseases and Tropical Medicine, Georgetown University, Washington, DC, USA
- Department of Global Health, University of Washington, School of Medicine, Seattle, Washington, USA
- Department of Medicine, University of Washington, School of Medicine, Seattle, Washington, USA
- Departments of Microbiology and Immunology and Pediatrics, Albert Einstein College of Medicine, Bronx, New York, New York, USA
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Medicine, Albert Einstein College of Medicine, New York, New York, USA
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2
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Kalirad A, Burch CL, Azevedo RBR. Genetic drift promotes and recombination hinders speciation on holey fitness landscapes. PLoS Genet 2024; 20:e1011126. [PMID: 38252672 PMCID: PMC10833538 DOI: 10.1371/journal.pgen.1011126] [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: 04/03/2023] [Revised: 02/01/2024] [Accepted: 01/06/2024] [Indexed: 01/24/2024] Open
Abstract
Dobzhansky and Muller proposed a general mechanism through which microevolution, the substitution of alleles within populations, can cause the evolution of reproductive isolation between populations and, therefore, macroevolution. As allopatric populations diverge, many combinations of alleles differing between them have not been tested by natural selection and may thus be incompatible. Such genetic incompatibilities often cause low fitness in hybrids between species. Furthermore, the number of incompatibilities grows with the genetic distance between diverging populations. However, what determines the rate and pattern of accumulation of incompatibilities remains unclear. We investigate this question by simulating evolution on holey fitness landscapes on which genetic incompatibilities can be identified unambiguously. We find that genetic incompatibilities accumulate more slowly among genetically robust populations and identify two determinants of the accumulation rate: recombination rate and population size. In large populations with abundant genetic variation, recombination selects for increased genetic robustness and, consequently, incompatibilities accumulate more slowly. In small populations, genetic drift interferes with this process and promotes the accumulation of genetic incompatibilities. Our results suggest a novel mechanism by which genetic drift promotes and recombination hinders speciation.
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Affiliation(s)
- Ata Kalirad
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
- Department for Integrative Evolutionary Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Christina L. Burch
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Ricardo B. R. Azevedo
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
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3
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Shahid A, MacLennan S, Jones BR, Sudderuddin H, Dang Z, Cobamibias K, Duncan MC, Kinloch NN, Dapp MJ, Archin NM, Fischl MA, Ofotokun I, Adimora A, Gange S, Aouizerat B, Kuniholm MH, Kassaye S, Mullins JI, Goldstein H, Joy JB, Anastos K, Brumme ZL. The replication-competent HIV reservoir is a genetically restricted, younger subset of the overall pool of HIV proviruses persisting during therapy, which is highly genetically stable over time. RESEARCH SQUARE 2023:rs.3.rs-3259040. [PMID: 37645749 PMCID: PMC10462229 DOI: 10.21203/rs.3.rs-3259040/v1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Within-host HIV populations continually diversify during untreated infection, and members of these diverse forms persist within infected cell reservoirs, even during antiretroviral therapy (ART). Characterizing the diverse viral sequences that persist during ART is critical to HIV cure efforts, but our knowledge of on-ART proviral evolutionary dynamics remains incomplete, as does our understanding of the differences between the overall pool of persisting proviral DNA (which is largely genetically defective) and the subset of intact HIV sequences capable of reactivating. Here, we reconstructed within-host HIV evolutionary histories in blood from seven participants of the Women's Interagency HIV Study (WIHS) who experienced HIV seroconversion. We measured diversity, lineage origins and ages of proviral sequences (env-gp120) sampled up to four times, up to 12 years on ART. We used the same techniques to study HIV sequences emerging from the reservoir in two participants. Proviral clonality generally increased over time on ART, with clones frequently persisting across multiple time points. The integration dates of proviruses persisting on ART generally spanned the duration of untreated infection (though were often skewed towards years immediately pre-ART), while in contrast, reservoir-origin viremia emerging in plasma was exclusively "younger" (i.e., dated to the years immediately pre-ART). The genetic and age distributions of distinct proviral sequences remained highly stable during ART in all but one participant in whom, after 12 years, there was evidence that "younger" proviruses had been preferentially eliminated. Analysis of within-host recombinant proviral sequences also suggested that HIV reservoirs can be superinfected with virus reactivated from an older era, yielding infectious viral progeny with mosaic genomes of sequences with different ages. Overall, results underscore the remarkable genetic stability of distinct proviral sequences that persist on ART, yet suggest that replication-competent HIV reservoir represents a genetically-restricted and overall "younger" subset of the overall persisting proviral pool in blood.
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Affiliation(s)
- Aniqa Shahid
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Signe MacLennan
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Bradley R Jones
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Hanwei Sudderuddin
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Zhong Dang
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Kyle Cobamibias
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Maggie C Duncan
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Natalie N Kinloch
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Michael J Dapp
- Department of Microbiology, University of Washington, School of Medicine, Seattle, WA, USA
| | - Nande M Archin
- UNC HIV Cure Center, Institute of Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, NC, USA
| | - Margaret A Fischl
- Department of Medicine, University of Miami School of Medicine, Miami, FL, USA
| | - Igho Ofotokun
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Adaora Adimora
- Departments of Medicine and Epidemiology, University of North Carolina School of Medicine, UNC Gillings School of Global Public Health, Chapel Hill, NC, USA
| | - Stephen Gange
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | | | - Mark H Kuniholm
- Department of Epidemiology and Biostatistics, University at Albany, State University of New York, Rensselaer, New York, NY, USA
| | - Seble Kassaye
- Division of Infectious Diseases and Tropical Medicine, Georgetown University, Washington, DC, USA
| | - James I Mullins
- Department of Microbiology, University of Washington, School of Medicine, Seattle, WA, USA
| | - Harris Goldstein
- Departments of Microbiology and Immunology and Pediatrics, Albert Einstein College of Medicine, Bronx, New York, NY, USA
| | - Jeffrey B Joy
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Kathryn Anastos
- Department of Medicine, Albert Einstein College of Medicine, New York, NY, USA
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
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4
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Xu S, Mu X, Xu X, Bi C, Ji J, Kan Y, Yao L, Bi Y, Xie Q. Genetic Heterogeneity and Mutated PreS Analysis of Duck Hepatitis B Virus Recently Isolated from Ducks and Geese in China. Animals (Basel) 2023; 13:ani13081282. [PMID: 37106845 PMCID: PMC10135025 DOI: 10.3390/ani13081282] [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: 02/23/2023] [Revised: 04/05/2023] [Accepted: 04/07/2023] [Indexed: 04/29/2023] Open
Abstract
In this study, we detected 12 duck and 11 goose flocks that were positive for duck hepatitis B virus (DHBV) using polymerase chain reaction and isolated 23 strains between 2020 and 2022 in China. The complete genomes of goose strains E200801 and E210501 shared the highest identity (99.9%), whereas those of strains Y220217 and E210526 shared the lowest identity (91.39%). The phylogenetic tree constructed based on the genome sequences of these strains and reference strains was classified into three major clusters: the Chinese branch DHBV-I, the Chinese branch DHBV-II, and the Western branch DHBV-III. Furthermore, the duck-origin strain Y200122 was clustered into a separate branch and was predicted to be a recombinant strain derived from DHBV-M32990 (belonging to the Chinese branch DHBV-I) and Y220201 (belonging to the Chinese branch DHBV-II). Additionally, preS protein analysis of the 23 DHBV strains revealed extensive mutation sites, almost half of which were of duck origin. All goose-origin DHBV contained the mutation site G133E, which is related to increased viral pathogenicity. These data are expected to promote further research on the epidemiology and evolution of DHBV. Continuing DHBV surveillance in poultry will enhance the understanding of the evolution of HBV.
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Affiliation(s)
- Shuqi Xu
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Nanyang Normal University, Nanyang 473061, China
- Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Nanyang Normal University, Nanyang 473061, China
| | - Xinhao Mu
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Nanyang Normal University, Nanyang 473061, China
- Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Nanyang Normal University, Nanyang 473061, China
| | - Xin Xu
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Nanyang Normal University, Nanyang 473061, China
- Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Nanyang Normal University, Nanyang 473061, China
| | - Congying Bi
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Nanyang Normal University, Nanyang 473061, China
- Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Nanyang Normal University, Nanyang 473061, China
| | - Jun Ji
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Nanyang Normal University, Nanyang 473061, China
- Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Nanyang Normal University, Nanyang 473061, China
| | - Yunchao Kan
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Nanyang Normal University, Nanyang 473061, China
- Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Nanyang Normal University, Nanyang 473061, China
| | - Lunguang Yao
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Nanyang Normal University, Nanyang 473061, China
- Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Nanyang Normal University, Nanyang 473061, China
| | - Yingzuo Bi
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Qingmei Xie
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
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5
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Khan A, Pillay M, Chimukangara B, Gounder L, Manyana S, Francois KL, Chipango K. Identification of HIV-1 subtype CRF18_cpx in a patient with multidrug resistance in KwaZulu-Natal, South Africa: An epidemiological worry? JOURNAL OF CLINICAL VIROLOGY PLUS 2023. [DOI: 10.1016/j.jcvp.2023.100143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
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6
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Del Amparo R, González-Vázquez LD, Rodríguez-Moure L, Bastolla U, Arenas M. Consequences of Genetic Recombination on Protein Folding Stability. J Mol Evol 2023; 91:33-45. [PMID: 36463317 PMCID: PMC9849154 DOI: 10.1007/s00239-022-10080-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 11/25/2022] [Indexed: 12/05/2022]
Abstract
Genetic recombination is a common evolutionary mechanism that produces molecular diversity. However, its consequences on protein folding stability have not attracted the same attention as in the case of point mutations. Here, we studied the effects of homologous recombination on the computationally predicted protein folding stability for several protein families, finding less detrimental effects than we previously expected. Although recombination can affect multiple protein sites, we found that the fraction of recombined proteins that are eliminated by negative selection because of insufficient stability is not significantly larger than the corresponding fraction of proteins produced by mutation events. Indeed, although recombination disrupts epistatic interactions, the mean stability of recombinant proteins is not lower than that of their parents. On the other hand, the difference of stability between recombined proteins is amplified with respect to the parents, promoting phenotypic diversity. As a result, at least one third of recombined proteins present stability between those of their parents, and a substantial fraction have higher or lower stability than those of both parents. As expected, we found that parents with similar sequences tend to produce recombined proteins with stability close to that of the parents. Finally, the simulation of protein evolution along the ancestral recombination graph with empirical substitution models commonly used in phylogenetics, which ignore constraints on protein folding stability, showed that recombination favors the decrease of folding stability, supporting the convenience of adopting structurally constrained models when possible for inferences of protein evolutionary histories with recombination.
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Affiliation(s)
- Roberto Del Amparo
- CINBIO, Universidade de Vigo, 36310 Vigo, Spain ,Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, 36310 Vigo, Spain
| | - Luis Daniel González-Vázquez
- CINBIO, Universidade de Vigo, 36310 Vigo, Spain ,Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, 36310 Vigo, Spain
| | - Laura Rodríguez-Moure
- CINBIO, Universidade de Vigo, 36310 Vigo, Spain ,Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, 36310 Vigo, Spain
| | - Ugo Bastolla
- Centre for Molecular Biology Severo Ochoa (CSIC-UAM), 28049 Madrid, Spain
| | - Miguel Arenas
- CINBIO, Universidade de Vigo, 36310 Vigo, Spain ,Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, 36310 Vigo, Spain ,Galicia Sur Health Research Institute (IIS Galicia Sur), 36310 Vigo, Spain
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7
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Umviligihozo G, Muok E, Nyirimihigo Gisa E, Xu R, Dilernia D, Herard K, Song H, Qin Q, Bizimana J, Farmer P, Hare J, Gilmour J, Allen S, Karita E, Hunter E, Yue L. Increased Frequency of Inter-Subtype HIV-1 Recombinants Identified by Near Full-Length Virus Sequencing in Rwandan Acute Transmission Cohorts. Front Microbiol 2021; 12:734929. [PMID: 34690973 PMCID: PMC8529237 DOI: 10.3389/fmicb.2021.734929] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 09/07/2021] [Indexed: 12/01/2022] Open
Abstract
Most studies of HIV-1 transmission have focused on subtypes B and C. In this study, we determined the genomic sequences of the transmitted founder (TF) viruses from acutely infected individuals enrolled between 2005 and 2011 into IAVI protocol C in Rwanda and have compared these isolates to viruses from more recent (2016–2019) acute/early infections in three at risk populations – MSM, high risk women (HRW), and discordant couples (DC). For the Protocol C samples, we utilized near full-length single genome (NFLG) amplification to generate 288 HIV-1 amplicons from 26 acutely infected seroconverters (SC), while for the 21 recent seroconverter samples (13 from HRW, two from DC, and six from MSM), we PCR amplified overlapping half-genomes. Using PacBio SMRT technology combined with the MDPseq workflow, we performed multiplex sequencing to obtain high accuracy sequences for each amplicon. Phylogenetic analyses indicated that the majority of recent transmitted viruses from DC and HRW clustered within those of the earlier Protocol C cohort. However, five of six sequences from the MSM cohort branched together and were greater than 97% identical. Recombination analyses revealed a high frequency (6/26; 23%) of unique inter-subtype recombination in Protocol C with 19% AC and 4% CD recombinant viruses, which contrasted with only 6.5% of recombinants defined by sequencing of the pol gene previously. The frequency of recombinants was significantly higher (12/21; 57%) in the more recent isolates, although, the five related viruses from the MSM cohort had identical recombination break points. While major drug resistance mutations were absent from Protocol C viruses, 4/21 of recent isolates exhibited transmitted nevirapine resistance. These results demonstrate the ongoing evolution and increased prevalence of recombinant and drug resistant transmitted viruses in Rwanda and highlight the importance of defining NFLG sequences to fully understand the nature of TF viruses and in particular the prevalence of unique recombinant forms (URFs) in transmission cohorts.
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Affiliation(s)
| | - Erick Muok
- Centre for Family Health Research, Kigali, Rwanda
| | | | - Rui Xu
- Emory Vaccine Center at Yerkes National Primate Research Center, Atlanta, GA, United States
| | - Dario Dilernia
- Emory Vaccine Center at Yerkes National Primate Research Center, Atlanta, GA, United States
| | - Kimberley Herard
- Emory Vaccine Center at Yerkes National Primate Research Center, Atlanta, GA, United States
| | - Heeyah Song
- Emory Vaccine Center at Yerkes National Primate Research Center, Atlanta, GA, United States
| | - Qianhong Qin
- Emory Vaccine Center at Yerkes National Primate Research Center, Atlanta, GA, United States
| | | | - Paul Farmer
- Emory Vaccine Center at Yerkes National Primate Research Center, Atlanta, GA, United States
| | | | - Jill Gilmour
- Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Susan Allen
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, United States
| | | | - Eric Hunter
- Emory Vaccine Center at Yerkes National Primate Research Center, Atlanta, GA, United States.,Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, United States
| | - Ling Yue
- Emory Vaccine Center at Yerkes National Primate Research Center, Atlanta, GA, United States
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8
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Parker Miller E, Finkelstein MT, Erdman MC, Seth PC, Fera D. A Structural Update of Neutralizing Epitopes on the HIV Envelope, a Moving Target. Viruses 2021; 13:v13091774. [PMID: 34578355 PMCID: PMC8472920 DOI: 10.3390/v13091774] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 08/29/2021] [Accepted: 09/02/2021] [Indexed: 11/16/2022] Open
Abstract
Antibodies that can neutralize diverse HIV-1 strains develop in ~10–20% of HIV-1 infected individuals, and their elicitation is a goal of vaccine design. Such antibodies can also serve as therapeutics for those who have already been infected with the virus. Structural characterizations of broadly reactive antibodies in complex with the HIV-1 spike indicate that there are a limited number of sites of vulnerability on the spike. Analysis of their structures can help reveal commonalities that would be useful in vaccine design and provide insights on combinations of antibodies that can be used to minimize the incidence of viral resistance mutations. In this review, we give an update on recent structures determined of the spike in complex with broadly neutralizing antibodies in the context of all epitopes on the HIV-1 spike identified to date.
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Cilento ME, Kirby KA, Sarafianos SG. Avoiding Drug Resistance in HIV Reverse Transcriptase. Chem Rev 2021; 121:3271-3296. [PMID: 33507067 DOI: 10.1021/acs.chemrev.0c00967] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
HIV reverse transcriptase (RT) is an enzyme that plays a major role in the replication cycle of HIV and has been a key target of anti-HIV drug development efforts. Because of the high genetic diversity of the virus, mutations in RT can impart resistance to various RT inhibitors. As the prevalence of drug resistance mutations is on the rise, it is necessary to design strategies that will lead to drugs less susceptible to resistance. Here we provide an in-depth review of HIV reverse transcriptase, current RT inhibitors, novel RT inhibitors, and mechanisms of drug resistance. We also present novel strategies that can be useful to overcome RT's ability to escape therapies through drug resistance. While resistance may not be completely avoidable, designing drugs based on the strategies and principles discussed in this review could decrease the prevalence of drug resistance.
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Affiliation(s)
- Maria E Cilento
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia 30322, United States.,Children's Healthcare of Atlanta, Atlanta, Georgia 30307, United States
| | - Karen A Kirby
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia 30322, United States.,Children's Healthcare of Atlanta, Atlanta, Georgia 30307, United States
| | - Stefan G Sarafianos
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia 30322, United States.,Children's Healthcare of Atlanta, Atlanta, Georgia 30307, United States
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10
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Giovanetti M, Ciccozzi M, Parolin C, Borsetti A. Molecular Epidemiology of HIV-1 in African Countries: A Comprehensive Overview. Pathogens 2020; 9:pathogens9121072. [PMID: 33371264 PMCID: PMC7766877 DOI: 10.3390/pathogens9121072] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 12/16/2020] [Accepted: 12/18/2020] [Indexed: 01/07/2023] Open
Abstract
The human immunodeficiency virus type 1 (HIV-1) originated in non-human primates in West-central Africa and continues to be a major global public health issue, having claimed almost 33 million lives so far. In Africa, it is estimated that more than 20 million people are living with HIV/Acquired Immunodeficiency Syndrome (AIDS) and that more than 730,000 new HIV-1 infections still occur each year, likely due to low access to testing. The high genetic variability of HIV-1, due to a fast replication cycle and high mutation rate, may cause the generation of many viral variants in a single infected patient during a single day. Therefore, the active monitoring and characterization of the HIV-1 subtypes and recombinant forms circulating through African countries poses a significant challenge to more specific diagnoses, treatments, care, and intervention strategies. In this review, a concise characterization of all the subtypes and recombinant forms circulating in Africa is presented to highlight the magnitude of the HIV-1 threat among the African countries and to understand virus genetic diversity and dispersion dynamics better.
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Affiliation(s)
- Marta Giovanetti
- Reference Laboratory of Flavivirus, Oswaldo Cruz Institute, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, Brazil;
- Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, 00128 Rome, Italy;
| | - Massimo Ciccozzi
- Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, 00128 Rome, Italy;
| | - Cristina Parolin
- Department of Molecular, Medicine University of Padova, 35121 Padova, Italy;
| | - Alessandra Borsetti
- National HIV/AIDS Research Center, Istituto Superiore di Sanità, 00162 Rome, Italy
- Correspondence: ; Tel.: +39-06-49903082
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11
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Hemelaar J, Elangovan R, Yun J, Dickson-Tetteh L, Kirtley S, Gouws-Williams E, Ghys PD. Global and regional epidemiology of HIV-1 recombinants in 1990-2015: a systematic review and global survey. Lancet HIV 2020; 7:e772-e781. [PMID: 33128904 DOI: 10.1016/s2352-3018(20)30252-6] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/26/2020] [Accepted: 08/27/2020] [Indexed: 01/06/2023]
Abstract
BACKGROUND Global HIV-1 genetic diversity and evolution form a major challenge to treatment and prevention efforts. An increasing number of distinct HIV-1 recombinants have been identified worldwide, but their contribution to the global epidemic is unknown. We aimed to estimate the global and regional distribution of HIV-1 recombinant forms during 1990-2015. METHODS We assembled a global HIV-1 molecular epidemiology database through a systematic literature review and a global survey. We searched the PubMed, Embase (Ovid), CINAHL (Ebscohost), and Global Health (Ovid) databases for HIV-1 subtyping studies published from Jan 1, 1990, to Dec 31, 2015. Unpublished original HIV-1 subtyping data were collected through a survey among experts in the field who were members of the WHO-UNAIDS Network for HIV Isolation and Characterisation. We included prevalence studies with HIV-1 subtyping data collected during 1990-2015. Countries were grouped into 14 regions and analyses were done for four time periods (1990-99, 2000-04, 2005-09, and 2010-15). The distribution of circulating recombinant forms (CRFs) and unique recombinant forms (URFs) in individual countries was weighted according to the UNAIDS estimates of the number of people living with HIV in each country to generate regional and global estimates of numbers and proportions of HIV-1 recombinants in each time period. The systematic review is registered with PROSPERO, CRD42017067164. FINDINGS Our global data collection yielded an HIV-1 molecular epidemiology database of 383 519 samples from 116 countries in 1990-2015. We found that the proportion of recombinants increased over time, both globally and in most regions, reaching 22·8% (7 978 517 of 34 921 639) of global HIV-1 infections in 2010-15. Both the proportion and the number of distinct CRFs detected increased over time to 16·7% and 57 CRFs in 2010-15. The global and regional distribution of HIV-1 recombinants was diverse and evolved over time, and we found large regional variation in the numbers (0-44 CRFs), types (58 distinct CRFs), and proportions (0-80·5%) of HIV-1 recombinants. Globally, CRF02_AG was the most prevalent recombinant, accounting for 33·9% (2 701 364 of 7 978 517) of all recombinant infections in 2010-15. URFs accounted for 26·7% (2 131 450 of 7 978 517), CRF01_AE for 23·0% (1 838 433), and other CRFs for 16·4% (1 307 270) of all recombinant infections in 2010-15. Although other CRFs accounted for small proportions of infections globally (<1% each), they were prominent in regional epidemics, including in east and southeast Asia, west and central Africa, Middle East and north Africa, and eastern Europe and central Asia. In addition, in 2010-15, central Africa (21·3% [243 041 of 1 143 531]), west Africa (15·5% [838 476 of 5 419 010]), east Africa (12·6% [591 140 of 4 704 986]), and Latin America (9·6% [153 069 of 1 586 605]) had high proportions of URFs. INTERPRETATION HIV-1 recombinants are increasingly prominent in global and regional HIV epidemics, which has important implications for the development of an HIV vaccine and the design of diagnostic, resistance, and viral load assays. Continued and improved surveillance of the global molecular epidemiology of HIV is crucial. FUNDING None.
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Affiliation(s)
- Joris Hemelaar
- Nuffield Department of Population Health, University of Oxford, Oxford, UK; Nuffield Department of Women's & Reproductive Health, Women's Centre, John Radcliffe Hospital, University of Oxford, Oxford, UK.
| | - Ramyiadarsini Elangovan
- Nuffield Department of Women's & Reproductive Health, Women's Centre, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Jason Yun
- Nuffield Department of Women's & Reproductive Health, Women's Centre, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Leslie Dickson-Tetteh
- Nuffield Department of Women's & Reproductive Health, Women's Centre, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Shona Kirtley
- Centre for Statistics in Medicine, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Botnar Research Centre, Oxford, UK
| | | | - Peter D Ghys
- Strategic Information Department, UNAIDS, Geneva, Switzerland
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12
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Grant HE, Hodcroft EB, Ssemwanga D, Kitayimbwa JM, Yebra G, Esquivel Gomez LR, Frampton D, Gall A, Kellam P, de Oliveira T, Bbosa N, Nsubuga RN, Kibengo F, Kwan TH, Lycett S, Kao R, Robertson DL, Ratmann O, Fraser C, Pillay D, Kaleebu P, Leigh Brown AJ. Pervasive and non-random recombination in near full-length HIV genomes from Uganda. Virus Evol 2020; 6:veaa004. [PMID: 32395255 PMCID: PMC7204518 DOI: 10.1093/ve/veaa004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Recombination is an important feature of HIV evolution, occurring both within and between the major branches of diversity (subtypes). The Ugandan epidemic is primarily composed of two subtypes, A1 and D, that have been co-circulating for 50 years, frequently recombining in dually infected patients. Here, we investigate the frequency of recombinants in this population and the location of breakpoints along the genome. As part of the PANGEA-HIV consortium, 1,472 consensus genome sequences over 5 kb have been obtained from 1,857 samples collected by the MRC/UVRI & LSHTM Research unit in Uganda, 465 (31.6 per cent) of which were near full-length sequences (>8 kb). Using the subtyping tool SCUEAL, we find that of the near full-length dataset, 233 (50.1 per cent) genomes contained only one subtype, 30.8 per cent A1 (n = 143), 17.6 per cent D (n = 82), and 1.7 per cent C (n = 8), while 49.9 per cent (n = 232) contained more than one subtype (including A1/D (n = 164), A1/C (n = 13), C/D (n = 9); A1/C/D (n = 13), and 33 complex types). K-means clustering of the recombinant A1/D genomes revealed a section of envelope (C2gp120-TMgp41) is often inherited intact, whilst a generalized linear model was used to demonstrate significantly fewer breakpoints in the gag-pol and envelope C2-TM regions compared with accessory gene regions. Despite similar recombination patterns in many recombinants, no clearly supported circulating recombinant form (CRF) was found, there was limited evidence of the transmission of breakpoints, and the vast majority (153/164; 93 per cent) of the A1/D recombinants appear to be unique recombinant forms. Thus, recombination is pervasive with clear biases in breakpoint location, but CRFs are not a significant feature, characteristic of a complex, and diverse epidemic.
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Affiliation(s)
- Heather E Grant
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Emma B Hodcroft
- Biozentrum, University of Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Deogratius Ssemwanga
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
- Uganda Virus Research Institute, Entebbe, Uganda
| | | | - Gonzalo Yebra
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | | | - Dan Frampton
- Division of Infection and Immunity, University College London, London, UK
| | - Astrid Gall
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - Paul Kellam
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - Tulio de Oliveira
- Nelson R. Mandela School of Medicine, Africa Health Research Institute, Durban, South Africa
| | - Nicholas Bbosa
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
| | - Rebecca N Nsubuga
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
| | - Freddie Kibengo
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
| | - Tsz Ho Kwan
- Stanley Ho Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Samantha Lycett
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Rowland Kao
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | | | - Oliver Ratmann
- Department of Mathematics, Imperial College London, London, UK
| | - Christophe Fraser
- Nuffield Department of Medicine, Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Deenan Pillay
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
- Nelson R. Mandela School of Medicine, Africa Health Research Institute, Durban, South Africa
| | - Pontiano Kaleebu
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
- Uganda Virus Research Institute, Entebbe, Uganda
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13
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Yuan H, Liu Z, Wu X, Wu M, Fang Q, Tully DC, Zhang T. Evolutionary characteristics and genetic transmission patterns of predominant HIV-1 subtypes among men who have sex with men in China. Int J Infect Dis 2019; 90:125-131. [PMID: 31682961 DOI: 10.1016/j.ijid.2019.10.035] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 10/24/2019] [Accepted: 10/27/2019] [Indexed: 01/01/2023] Open
Abstract
OBJECTIVES Men who have sex with men (MSM) represent one of the major risk groups for HIV-1 infection in China, and the predominant subtypes among this population has changed over the last two decades. The objective of this study was to determine the evolutionary characteristics and transmission patterns of the dominant HIV-1 strains in the Chinese MSM population. METHODS A total of 4980 published HIV-1 pol gene sequences from MSM in China were retrieved and comprehensive evolutionary and transmission analyses were then conducted. Bayesian coalescent-based methods and selection pressure analyses were used to reconstruct the time-scale and demographic history and to estimate other evolutionary parameters. Transmission patterns were characterized using network analyses. RESULTS There were 2546 (51.12%) CRF01_AE, 1263 (25.36%) CRF07_BC, and 623 (12.51%) subtype B, accounting for 88.99% of the total sequences. From 2000 to 2016, the prevalence of CRF01_AE was stable, comprising nearly half of all sequences over time (58.33-45.38%, p=0.071). CRF07_BC increased slightly from 13.3% to 22.49% (p<0.001), while subtype B decreased dramatically from 41.67% to 9.04% (p<0.001). Demographic reconstruction showed that the greatest expansion of the HIV epidemic occurred between 1999 and 2005. CRF01_AE had a higher estimated evolutionary rate (2.97×10-3 substitutions/site/year) and exhibited more sites under positive selection (25/351 codons) compared to the other subtypes. Network analyses showed that CRF07_BC (68.29%, 84/123) had a higher proportion of cross-region networks than CRF01_AE (49.1%, 174/354) and subtype B (36.46%, 35/96) (p<0.001). CONCLUSIONS The predominant subtypes of HIV-1 in Chinese MSM have different evolutionary characteristics and transmission patterns, which poses a significant challenge to HIV treatment and disease prevention.
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Affiliation(s)
- Huangbo Yuan
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China; Key Laboratory of Public Health Safety (Fudan University), Ministry of Education, Shanghai, China
| | - Zhenqiu Liu
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China; Key Laboratory of Public Health Safety (Fudan University), Ministry of Education, Shanghai, China; State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Xuefu Wu
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China; Key Laboratory of Public Health Safety (Fudan University), Ministry of Education, Shanghai, China
| | - Mingshan Wu
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China; Key Laboratory of Public Health Safety (Fudan University), Ministry of Education, Shanghai, China
| | - Qiwen Fang
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China; Key Laboratory of Public Health Safety (Fudan University), Ministry of Education, Shanghai, China
| | - Damien C Tully
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Tiejun Zhang
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China; Key Laboratory of Public Health Safety (Fudan University), Ministry of Education, Shanghai, China.
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A Zoonotic Adenoviral Human Pathogen Emerged through Genomic Recombination among Human and Nonhuman Simian Hosts. J Virol 2019; 93:JVI.00564-19. [PMID: 31243128 DOI: 10.1128/jvi.00564-19] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 06/18/2019] [Indexed: 12/14/2022] Open
Abstract
Genomics analysis of a historically intriguing and predicted emergent human adenovirus (HAdV) pathogen, which caused pneumonia and death, provides insight into a novel molecular evolution pathway involving "ping-pong" zoonosis and anthroponosis. The genome of this promiscuous pathogen is embedded with evidence of unprecedented multiple, multidirectional, stable, and reciprocal cross-species infections of hosts from three species (human, chimpanzee, and bonobo). This recombinant genome, typed as HAdV-B76, is identical to two recently reported simian AdV (SAdV) genomes isolated from chimpanzees and bonobos. Additionally, the presence of a critical adenoviral replication element found in HAdV genomes, in addition to genes that are highly similar to counterparts in other HAdVs, reinforces its potential as a human pathogen. Reservoirs in nonhuman hosts may explain periods of apparent absence and then reemergence of human adenoviral pathogens, as well as present pathways for the genesis of those thought to be newly emergent. The nature of the HAdV-D76 genome has implications for the use of SAdVs as gene delivery vectors in human gene therapy and vaccines, selected to avoid preexisting and potentially fatal host immune responses to HAdV.IMPORTANCE An emergent adenoviral human pathogen, HAdV-B76, associated with a fatality in 1965, shows a remarkable degree of genome identity with two recently isolated simian adenoviruses that contain cross-species genome recombination events from three hosts: human, chimpanzee, and bonobo. Zoonosis (nonhuman-to-human transmission) and anthroponosis (human to nonhuman transmission) may play significant roles in the emergence of human adenoviral pathogens.
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15
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Ge Z, Liu D, Lv B, Liang Y, Li K, Feng Y, Sun J, Ou W, Ma P, Shao Y. Genomic Characterization of a Novel HIV-1 CRF01_AE/07_BC Recombinant Virus from a Married Man Who Has Sex with Men in Tianjin, China. AIDS Res Hum Retroviruses 2019; 35:780-784. [PMID: 31187637 DOI: 10.1089/aid.2019.0093] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We report in this study a novel HIV-1 second-generation recombinant form (TJIH0172) composed of CRF01_AE and CRF07_BC isolated from a married HIV-positive male subject infected through homosexual behavior in Tianjin, China. The phylogenetic analysis of the near full-length genome of TJIH0172 reveals that one region of CRF07_BC inserted into the CRF01_AE backbone with two recombinant breakpoints observed in the vpu and env gene regions, respectively. The CRF01_AE regions (the regions I and III) of the recombinant are greatly clustered with the CRF01_AE subcluster 4 lineage, which is mainly circulating among men who have sex with men (MSM) in northern China. The CRF07_BC region (II) is clustered with two sequences (JX960600 and KF250366), which were discovered in the MSM population in Liaoning Province and Beijing city in northern China, respectively. The emergence of the novel recombinant strain from a married man who has sex with men in Tianjin, China, highlights the increasing complexity of the HIV-1 epidemic between MSM and their female partners and further molecular epidemiological investigation should be taken to track married MSM and their female partners to prevent HIV transmit from HIV high-risk populations to general populations.
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Affiliation(s)
- Zhangwen Ge
- School of Medicine, Nankai University, Tianjin, China
| | - Dan Liu
- Nankai University Second People's Hospital, School of Medicine, Nankai University, Tianjin, China
| | - Bowen Lv
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yanling Liang
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Guangxi Key Laboratory of AIDS Prevention and Treatment and Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
| | - Kang Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Guangxi Key Laboratory of AIDS Prevention and Treatment and Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
| | - Yi Feng
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jia Sun
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Weidong Ou
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Guangxi Key Laboratory of AIDS Prevention and Treatment and Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
| | - Ping Ma
- School of Medicine, Nankai University, Tianjin, China
- Nankai University Second People's Hospital, School of Medicine, Nankai University, Tianjin, China
| | - Yiming Shao
- School of Medicine, Nankai University, Tianjin, China
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
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Lai A, Simonetti FR, Brindicci G, Bergna A, Di Giambenedetto S, Sterrantino G, Mussini C, Menzo S, Bagnarelli P, Zazzi M, Angarano G, Galli M, Monno L, Balotta C. Local Epidemics Gone Viral: Evolution and Diffusion of the Italian HIV-1 Recombinant Form CRF60_BC. Front Microbiol 2019; 10:769. [PMID: 31031735 PMCID: PMC6474184 DOI: 10.3389/fmicb.2019.00769] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 03/26/2019] [Indexed: 12/15/2022] Open
Abstract
The molecular epidemiology of HIV-1 in Italy is becoming increasingly complex, mainly due to the spread of non-B subtypes and the emergence of new recombinant forms. We previously characterized the outbreak of the first Italian circulating recombinant form (CRF60_BC), occurring among young MSM living in Apulia between the years 2009 and 2011. Here we show a 5-year follow-up surveillance to trace the evolution of CRF60_BC and to investigate its further spread in Italy. We collected additional sequences and clinical data from patients harboring CRF60_BC, enrolled at the Infectious Diseases Clinic of the University of Bari. In addition to the 24 previously identified sequences, we retrieved 27 CRF60_BC sequences from patients residing in Apulia, whose epidemiological and clinical features did not differ from those of the initial outbreak, i.e., the Italian origin, young age at HIV diagnosis (median: 24 years; range: 18–37), MSM risk factor (23/25, 92%) and recent infection (from 2008 to 2017). Sequence analysis revealed a growing overall nucleotide diversity, with few nucleotide changes that were fixed over time. Twenty-seven additional sequences were detected across Italy, spanning multiple distant regions. Using a BLAST search, we also identified a CRF60_BC sequence isolated in United Kingdom in 2013. Three patients harbored a unique second generation recombinant form in which CRF60_BC was one of the parental strains. Our data show that CRF60_BC gained epidemic importance, spreading among young MSM in multiple Italian regions and increasing its population size in few years, as the number of sequences identified so far has triplicated since our first report. The observed further divergence of CRF60_BC is likely due to evolutionary bottlenecks and host adaptation during transmission chains. Of note, we detected three second-generation recombinants, further supporting a widespread circulation of CRF60_BC and the increasing complexity of the HIV-1 epidemic in Italy.
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Affiliation(s)
- Alessia Lai
- Department of Biomedical and Clinical Sciences L. Sacco, University of Milan, Milan, Italy
| | | | - Gaetano Brindicci
- Clinic of Infectious Diseases, University of Bari Aldo Moro, Bari, Italy
| | - Annalisa Bergna
- Department of Biomedical and Clinical Sciences L. Sacco, University of Milan, Milan, Italy
| | | | - Gaetana Sterrantino
- Division of Tropical and Infectious Diseases, Careggi Hospital, Florence, Italy
| | - Cristina Mussini
- Clinic of Infectious Diseases, University of Modena and Reggio Emilia, Modena, Italy
| | - Stefano Menzo
- Unit of Virology, Azienda Ospedaliero-Universitaria 'Ospedali Riuniti', Torrette, Italy
| | - Patrizia Bagnarelli
- Unit of Virology, Azienda Ospedaliero-Universitaria 'Ospedali Riuniti', Torrette, Italy
| | - Maurizio Zazzi
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | | | - Massimo Galli
- Department of Biomedical and Clinical Sciences L. Sacco, University of Milan, Milan, Italy
| | - Laura Monno
- Clinic of Infectious Diseases, University of Bari Aldo Moro, Bari, Italy
| | - Claudia Balotta
- Department of Biomedical and Clinical Sciences L. Sacco, University of Milan, Milan, Italy
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17
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Huang Q, Ou W, Feng Y, Li F, Li K, Sun J, Ge Z, Xing H, Liang H, Shao Y. Near Full-Length Genomic Characterization of HIV-1 CRF01_AE/B Recombinant Strains Identified in Hebei, China. AIDS Res Hum Retroviruses 2019; 35:196-204. [PMID: 30117324 DOI: 10.1089/aid.2018.0130] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
This study reports a novel HIV-1 recombinant form of CRF01_AE/B that was isolated from a 22-year-old male individual (HE150308) residing in Hebei province, China. The near full-length genome (NFLG) phylogenetic tree showed that the strain was clustered with CRF01_AE reference sequences and placed at the peripheral position within the branch of CRF01_AE strains. The bootscaning and similarity plot analysis revealed that the NFLG of this novel recombinant was composed of eight interlaced segments, including four CRF01_AE and four subtype B segments separated by seven breakpoints observed in the gag, pol, and nef regions of HIV-1 genome. Phylogenetic analysis demonstrated that the CRF01_AE subregions were from the previously identified CRF01_AE cluster 5, and the B subregions were correlated with the B strains originated from Europe and America. They were all the lineages widely prevalent in men who have sex with men (MSM) population in China. In recent years, a large number of recombinants between CRF01_AE and B strains are constantly emerging in the MSM population in China. This continual and recurrent recombination between CRF01_AE and B in high-risk group people deserves more attention and further monitoring.
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Affiliation(s)
- Qiao Huang
- Guangxi Key Laboratory of AIDS Prevention and Treatment and Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, School of Public Health, Guangxi Medical University, Nanning, China
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Weidong Ou
- Guangxi Key Laboratory of AIDS Prevention and Treatment and Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, School of Public Health, Guangxi Medical University, Nanning, China
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yi Feng
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Fan Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Kang Li
- Guangxi Key Laboratory of AIDS Prevention and Treatment and Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, School of Public Health, Guangxi Medical University, Nanning, China
| | - Jia Sun
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Zhangwen Ge
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Hui Xing
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Hao Liang
- Guangxi Key Laboratory of AIDS Prevention and Treatment and Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, School of Public Health, Guangxi Medical University, Nanning, China
| | - Yiming Shao
- Guangxi Key Laboratory of AIDS Prevention and Treatment and Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, School of Public Health, Guangxi Medical University, Nanning, China
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
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18
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Ma P, Ge Z, Feng Y, Ou W, Sun J, Li K, Xing H, Shao Y. Near Full-Length Genome Sequence of a Novel HIV-1 Second-Generation Recombinant Form (CRF01_AE/CRF07_BC) Detected Among Men Who Have Sex with Men in Tianjin, China. AIDS Res Hum Retroviruses 2019; 35:205-212. [PMID: 30229668 DOI: 10.1089/aid.2018.0177] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In recent years, men who have sex with men (MSM) have been the most affected population with fastest growing human immunodeficiency virus (HIV) prevalence in China. In our study, a novel CRF01_AE/07_BC HIV-1 recombinant form (TJIH0069), with four unique breakpoints in the pol, vpr, and nef gene regions, was identified among MSM in Tianjin City in north China. The CRF01_AE regions (regions I, III, and V) of the recombinant are all clustered together with a previously described sequence (HQ215555), which was exclusively circulating among MSM in Shijiazhuang city of Hebei Province in north China. The CRF07_BC regions (II and IV) are clustered with BJ070032 and JX960600, which were discovered from MSM population in north China. The continuous emergence of a similar pattern of recombinant strain between the two MSM-adapted existing circulating recombinant forms (CRFs) highlights the importance to monitor potential new CRFs for early and precise control and prevention.
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Affiliation(s)
- Ping Ma
- Nankai University Second People's Hospital, School of Medicine, Nankai University, Tianjin, China
| | - Zhangwen Ge
- School of Medicine, Nankai University, Tianjin, China
| | - Yi Feng
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Weidong Ou
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jia Sun
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Kang Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Hui Xing
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yiming Shao
- School of Medicine, Nankai University, Tianjin, China
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
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19
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The N-Terminus of the HIV-1 p6 Gag Protein Regulates Susceptibility to Degradation by IDE. Viruses 2018; 10:v10120710. [PMID: 30545091 PMCID: PMC6316412 DOI: 10.3390/v10120710] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 12/07/2018] [Accepted: 12/09/2018] [Indexed: 12/14/2022] Open
Abstract
As part of the Pr55Gag polyprotein, p6 fulfills an essential role in the late steps of the replication cycle. However, almost nothing is known about the functions of the mature HIV-1 p6 protein. Recently, we showed that p6 is a bona fide substrate of the insulin-degrading enzyme (IDE), a ubiquitously expressed zinc metalloprotease. This phenomenon appears to be specific for HIV-1, since p6 homologs of HIV-2, SIV and EIAV were IDE-insensitive. Furthermore, abrogation of the IDE-mediated degradation of p6 reduces the replication capacity of HIV-1 in an Env-dependent manner. However, it remained unclear to which extent the IDE mediated degradation is phylogenetically conserved among HIV-1. Here, we describe two HIV-1 isolates with IDE resistant p6 proteins. Sequence comparison allowed deducing one single amino acid regulating IDE sensitivity of p6. Exchanging the N-terminal leucine residue of p6 derived from the IDE sensitive isolate HIV-1NL4-3 with proline enhances its stability, while replacing Pro-1 of p6 from the IDE insensitive isolate SG3 with leucine restores susceptibility towards IDE. Phylogenetic analyses of this natural polymorphism revealed that the N-terminal leucine is characteristic for p6 derived from HIV-1 group M except for subtype A, which predominantly expresses p6 with an N-terminal proline. Consequently, p6 peptides derived from subtype A are not degraded by IDE. Thus, IDE mediated degradation of p6 is specific for HIV-1 group M isolates and not occasionally distributed among HIV-1.
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20
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Relationship between intact HIV-1 proviruses in circulating CD4 + T cells and rebound viruses emerging during treatment interruption. Proc Natl Acad Sci U S A 2018; 115:E11341-E11348. [PMID: 30420517 PMCID: PMC6275529 DOI: 10.1073/pnas.1813512115] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Combination antiretroviral therapy controls but does not cure HIV-1 infection because a small fraction of cells harbor latent viruses that can produce rebound viremia when therapy is interrupted. The circulating latent virus reservoir has been documented by a variety of methods, most prominently by viral outgrowth assays (VOAs) in which CD4+ T cells are activated to produce virus in vitro, or more recently by amplifying proviral near full-length (NFL) sequences from DNA. Analysis of samples obtained in clinical studies in which individuals underwent analytical treatment interruption (ATI), showed little if any overlap between circulating latent viruses obtained from outgrowth cultures and rebound viruses from plasma. To determine whether intact proviruses amplified from DNA are more closely related to rebound viruses than those obtained from VOAs, we assayed 12 individuals who underwent ATI after infusion of a combination of two monoclonal anti-HIV-1 antibodies. A total of 435 intact proviruses obtained by NFL sequencing were compared with 650 latent viruses from VOAs and 246 plasma rebound viruses. Although, intact NFL and outgrowth culture sequences showed similar levels of stability and diversity with 39% overlap, the size of the reservoir estimated from NFL sequencing was larger than and did not correlate with VOAs. Finally, intact proviruses documented by NFL sequencing showed no sequence overlap with rebound viruses; however, they appear to contribute to recombinant viruses found in plasma during rebound.
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21
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Malunguza NJ, Hove-Musekwa SD, Dube S, Mukandavire Z. Dynamical properties and thresholds of an HIV model with super-infection. MATHEMATICAL MEDICINE AND BIOLOGY-A JOURNAL OF THE IMA 2018; 34:493-522. [PMID: 27672183 DOI: 10.1093/imammb/dqw014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 08/15/2016] [Indexed: 11/13/2022]
Abstract
Super-infection by multiple HIV-1 subtypes, previously thought restricted to high risk groups, has now been reported in the general heterosexual populations at relatively the same incidence rate as in high risk groups. We present a simple deterministic HIV model with super-infection by two HIV-1 subtypes. Mathematical characteristics including the basic reproductive number $(\mathcal{R}_0)$, invasion threshold $(\mathcal{R}_{21},\mathcal{R}_{12})$ and conditions for asymptotic stability are derived. In the absence of super-infection the model exhibits competitive exclusion, and all equilibria are globally attracting if they exist except for the disease free which is a saddle for $\mathcal{R}_0>1.$ The results show that the subtype with the dominant reproductive number exceeding unity dominates the weaker subtype forcing it to extinction regardless of the size of the reproductive number. On the other end, super-infection may promote subtype co-existence whenever the minimum of the subtype specific reproductive numbers $(\mathcal{R}_1,\mathcal{R}_2)$ and the invasion reproductive numbers $(\mathcal{R}_{12},\mathcal{R}_{21})$ exceed unity. Our results demonstrate that if the partial reproductive numbers $(\mathcal{R}_1~\mbox{and}~\mathcal{R}_2 )$ and the invasion reproductive number for the weaker subtype $(\mathcal{R}_{21})$ satisfy $\mathcal{R}_2<1,~\mathcal{R}_1>1~\mbox{and}~\mathcal{R}_{21}>1,$ then primary infection by subtype $1$ may stay the extinction of subtype $2$ despite its relatively low reproductive fitness. For certain parameter ranges, hysteresis (including backward bifurcation) occurs with possible differences in the asymptotic level of disease prevalence. Super-infection may thus facilitate the continued re-generation of reproductively noncompetent subtypes whose subtype specific reproductive numbers will be less than unity while at the same time allowing for the mutual coexistence and persistence of multiple strains. Persistence and co-existence of multiple strains has detrimental effect on vaccine design and development and administration of ART where one or more of the strains are drug resistant.
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Affiliation(s)
- N J Malunguza
- Department of Applied Mathematics, National University of Science and Technology, Bulawayo, Zimbabwe
| | - S D Hove-Musekwa
- Department of Applied Mathematics, National University of Science and Technology, Bulawayo, Zimbabwe
| | - S Dube
- Department of Applied Biology, National University of Science and Technology, Bulawayo, Zimbabwe
| | - Z Mukandavire
- Social and Mathematical Epidemiology Group, London School of Hygiene and Tropical Medicine, London, UK
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22
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Mendoza P, Gruell H, Nogueira L, Pai JA, Butler AL, Millard K, Lehmann C, Suárez I, Oliveira TY, Lorenzi JCC, Cohen YZ, Wyen C, Kümmerle T, Karagounis T, Lu CL, Handl L, Unson-O'Brien C, Patel R, Ruping C, Schlotz M, Witmer-Pack M, Shimeliovich I, Kremer G, Thomas E, Seaton KE, Horowitz J, West AP, Bjorkman PJ, Tomaras GD, Gulick RM, Pfeifer N, Fätkenheuer G, Seaman MS, Klein F, Caskey M, Nussenzweig MC. Combination therapy with anti-HIV-1 antibodies maintains viral suppression. Nature 2018; 561:479-484. [PMID: 30258136 PMCID: PMC6166473 DOI: 10.1038/s41586-018-0531-2] [Citation(s) in RCA: 342] [Impact Index Per Article: 57.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 07/30/2018] [Indexed: 11/26/2022]
Abstract
HIV-1-infected individuals require lifelong antiretroviral therapy (ART) because treatment interruption leads to rapid rebound viremia. Here we report on a phase 1b clinical trial in which a combination of 3BNC117 and 10-1074, two potent monoclonal anti-HIV-1 broadly neutralizing antibodies that target independent sites on the HIV-1 envelope spike, was administered during analytical treatment interruption. Participants received three infusions of 30 mg/kg of each antibody at 0, 3 and 6 weeks. Infusions of the two antibodies were generally well tolerated. The nine enrolled individuals with antibody-sensitive latent viral reservoirs maintained suppression for 15 to > 30 weeks (median = 21 weeks), and none developed viruses resistant to both antibodies. We conclude that the combination of anti-HIV-1 monoclonal antibodies 3BNC117 and 10-1074 can maintain long-term suppression in the absence of ART in individuals with antibody-sensitive viral reservoirs.
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Affiliation(s)
- Pilar Mendoza
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Henning Gruell
- Laboratory of Experimental Immunology, Institute of Virology, University Hospital Cologne, Cologne, Germany.,Department I of Internal Medicine, University Hospital Cologne, Cologne, Germany.,German Center for Infection Research, partner site Bonn-Cologne, Cologne, Germany
| | - Lilian Nogueira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Joy A Pai
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Allison L Butler
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Katrina Millard
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Clara Lehmann
- Department I of Internal Medicine, University Hospital Cologne, Cologne, Germany.,German Center for Infection Research, partner site Bonn-Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Isabelle Suárez
- Department I of Internal Medicine, University Hospital Cologne, Cologne, Germany.,German Center for Infection Research, partner site Bonn-Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Thiago Y Oliveira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Julio C C Lorenzi
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Yehuda Z Cohen
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Christoph Wyen
- Department I of Internal Medicine, University Hospital Cologne, Cologne, Germany.,Praxis am Ebertplatz, Cologne, Germany
| | - Tim Kümmerle
- Department I of Internal Medicine, University Hospital Cologne, Cologne, Germany.,Praxis am Ebertplatz, Cologne, Germany
| | - Theodora Karagounis
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Ching-Lan Lu
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Lisa Handl
- Methods in Medical Informatics, Department of Computer Science, University of Tübingen, Tübingen, Germany
| | | | - Roshni Patel
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Carola Ruping
- Laboratory of Experimental Immunology, Institute of Virology, University Hospital Cologne, Cologne, Germany
| | - Maike Schlotz
- Laboratory of Experimental Immunology, Institute of Virology, University Hospital Cologne, Cologne, Germany
| | - Maggi Witmer-Pack
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Irina Shimeliovich
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Gisela Kremer
- Department I of Internal Medicine, University Hospital Cologne, Cologne, Germany
| | - Eleonore Thomas
- Department I of Internal Medicine, University Hospital Cologne, Cologne, Germany
| | - Kelly E Seaton
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
| | - Jill Horowitz
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Anthony P West
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Georgia D Tomaras
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA.,Department of Surgery, Duke University, Durham, NC, USA.,Department of Immunology, Duke University, Durham, NC, USA.,Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
| | - Roy M Gulick
- Division of Infectious Diseases, Weill Cornell Medicine, New York, NY, USA
| | - Nico Pfeifer
- Methods in Medical Informatics, Department of Computer Science, University of Tübingen, Tübingen, Germany.,Medical Faculty, University of Tübingen, Tübingen, Germany.,German Center for Infection Research, partner site Tübingen, Tübingen, Germany.,Max Planck Institute for Informatics, Saarbrücken, Germany
| | - Gerd Fätkenheuer
- Department I of Internal Medicine, University Hospital Cologne, Cologne, Germany.,German Center for Infection Research, partner site Bonn-Cologne, Cologne, Germany
| | - Michael S Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Florian Klein
- Laboratory of Experimental Immunology, Institute of Virology, University Hospital Cologne, Cologne, Germany. .,German Center for Infection Research, partner site Bonn-Cologne, Cologne, Germany. .,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.
| | - Marina Caskey
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA.
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA. .,Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA.
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23
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Cohen YZ, Lorenzi JCC, Krassnig L, Barton JP, Burke L, Pai J, Lu CL, Mendoza P, Oliveira TY, Sleckman C, Millard K, Butler AL, Dizon JP, Belblidia SA, Witmer-Pack M, Shimeliovich I, Gulick RM, Seaman MS, Jankovic M, Caskey M, Nussenzweig MC. Relationship between latent and rebound viruses in a clinical trial of anti-HIV-1 antibody 3BNC117. J Exp Med 2018; 215:2311-2324. [PMID: 30072495 PMCID: PMC6122972 DOI: 10.1084/jem.20180936] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 06/19/2018] [Accepted: 07/17/2018] [Indexed: 11/04/2022] Open
Abstract
A clinical trial was performed to evaluate 3BNC117, a potent anti-HIV-1 antibody, in infected individuals during suppressive antiretroviral therapy and subsequent analytical treatment interruption (ATI). The circulating reservoir was evaluated by quantitative and qualitative viral outgrowth assay (Q2VOA) at entry and after 6 mo. There were no significant quantitative changes in the size of the reservoir before ATI, and the composition of circulating reservoir clones varied in a manner that did not correlate with 3BNC117 sensitivity. 3BNC117 binding site amino acid variants found in rebound viruses preexisted in the latent reservoir. However, only 3 of 217 rebound viruses were identical to 868 latent viruses isolated by Q2VOA and near full-length sequencing. Instead, 63% of the rebound viruses appeared to be recombinants, even in individuals with 3BNC117-resistant reservoir viruses. In conclusion, viruses emerging during ATI in individuals treated with 3BNC117 are not the dominant species found in the circulating latent reservoir, but frequently appear to represent recombinants of latent viruses.
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Affiliation(s)
- Yehuda Z Cohen
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Julio C C Lorenzi
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Lisa Krassnig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - John P Barton
- Department of Physics and Astronomy, University of California, Riverside, CA
| | - Leah Burke
- Division of Infectious Diseases, Weill Cornell Medicine, New York, NY
| | - Joy Pai
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Ching-Lan Lu
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Pilar Mendoza
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Thiago Y Oliveira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | | | - Katrina Millard
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Allison L Butler
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Juan P Dizon
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Shiraz A Belblidia
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Maggi Witmer-Pack
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Irina Shimeliovich
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Roy M Gulick
- Division of Infectious Diseases, Weill Cornell Medicine, New York, NY
| | - Michael S Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA
| | - Mila Jankovic
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Marina Caskey
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY .,Howard Hughes Medical Institute, Chevy Chase, MD
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24
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Guo J, Yan Y, Zhang J, Ji J, Ge Z, Ge R, Zhang X, Wang H, Chen Z, Luo J. Genetic characterization and antiretroviral resistance mutations among treatment-naive HIV-infected individuals in Jiaxing, China. Oncotarget 2017; 8:18271-18279. [PMID: 28407682 PMCID: PMC5392326 DOI: 10.18632/oncotarget.15382] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2016] [Accepted: 01/11/2017] [Indexed: 12/23/2022] Open
Abstract
The aim of this study was to characterize HIV-1 genotypes and antiretroviral resistance mutations among treatment-naive HIV-infected individuals in Jiaxing, China. The HIV-1 partial polymerase (pol) genes in 93 of the 99 plasma samples were successfully amplified and analyzed. Phylogenetic analysis revealed the existence of five HIV-1 genotypes, of which the most prevalent genotype was CRF01_AE (38.7%), followed by CRF07_BC (34.4%), CRF08_BC (16.1%), subtype B/B' (5.4%), and CRF55_01B (2.1%). Besides, three types of unique recombination forms (URFs) were also observed, including C/F2/A1, CRF01_AE/B, and CRF08_BC/CRF07_BC. Among 93 amplicons, 46.2% had drug resistance-associated mutations, including 23.7% for protease inhibitors (PIs) mutations, 1.1% for nucleoside reverse transcriptase inhibitors (NRTIs) mutations, and 20.4% for non-nucleoside reverse transcriptase inhibitors (NNRTIs) mutations. Six (6.5%) out of 93 treatment-naive subjects were identified to be resistant to one or more NNRTIs, while resistance to NRTIs or PIs was not observed. Our study showed the genetic diversity of HIV-1 strains circulating in Jiaxing and a relative high proportion of antiretroviral resistance mutations among treatment-naive patients, indicating a serious challenge for HIV prevention and treatment program.
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Affiliation(s)
- Jinlei Guo
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Municipal Center for Disease Control and Prevention, Jiaxing 314001, PR China
| | - Yong Yan
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Municipal Center for Disease Control and Prevention, Jiaxing 314001, PR China
| | - Jiafeng Zhang
- Institute of AIDS Control and Prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, PR China
| | - Jimei Ji
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Municipal Center for Disease Control and Prevention, Jiaxing 314001, PR China
| | - Zhijian Ge
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Municipal Center for Disease Control and Prevention, Jiaxing 314001, PR China
| | - Rui Ge
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Municipal Center for Disease Control and Prevention, Jiaxing 314001, PR China
| | - Xiaofei Zhang
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Municipal Center for Disease Control and Prevention, Jiaxing 314001, PR China
| | - Henghui Wang
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Municipal Center for Disease Control and Prevention, Jiaxing 314001, PR China
| | - Zhongwen Chen
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Municipal Center for Disease Control and Prevention, Jiaxing 314001, PR China
| | - Jianyong Luo
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Municipal Center for Disease Control and Prevention, Jiaxing 314001, PR China
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25
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Arenas M, Araujo NM, Branco C, Castelhano N, Castro-Nallar E, Pérez-Losada M. Mutation and recombination in pathogen evolution: Relevance, methods and controversies. INFECTION GENETICS AND EVOLUTION 2017; 63:295-306. [PMID: 28951202 DOI: 10.1016/j.meegid.2017.09.029] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 09/20/2017] [Accepted: 09/21/2017] [Indexed: 02/06/2023]
Abstract
Mutation and recombination drive the evolution of most pathogens by generating the genetic variants upon which selection operates. Those variants can, for example, confer resistance to host immune systems and drug therapies or lead to epidemic outbreaks. Given their importance, diverse evolutionary studies have investigated the abundance and consequences of mutation and recombination in pathogen populations. However, some controversies persist regarding the contribution of each evolutionary force to the development of particular phenotypic observations (e.g., drug resistance). In this study, we revise the importance of mutation and recombination in the evolution of pathogens at both intra-host and inter-host levels. We also describe state-of-the-art analytical methodologies to detect and quantify these two evolutionary forces, including biases that are often ignored in evolutionary studies. Finally, we present some of our former studies involving pathogenic taxa where mutation and recombination played crucial roles in the recovery of pathogenic fitness, the generation of interspecific genetic diversity, or the design of centralized vaccines. This review also illustrates several common controversies and pitfalls in the analysis and in the evaluation and interpretation of mutation and recombination outcomes.
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Affiliation(s)
- Miguel Arenas
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain; Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal; Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal.
| | - Natalia M Araujo
- Laboratory of Molecular Virology, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil.
| | - Catarina Branco
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal; Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal.
| | - Nadine Castelhano
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal; Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal.
| | - Eduardo Castro-Nallar
- Universidad Andrés Bello, Center for Bioinformatics and Integrative Biology, Facultad de Ciencias Biológicas, Santiago, Chile.
| | - Marcos Pérez-Losada
- Computational Biology Institute, Milken Institute School of Public Health, George Washington University, Ashburn, VA 20147, Washington, DC, United States; CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão 4485-661, Portugal.
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26
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Li X, Liu H, Liu L, Feng Y, Kalish ML, Ho SYW, Shao Y. Tracing the epidemic history of HIV-1 CRF01_AE clusters using near-complete genome sequences. Sci Rep 2017; 7:4024. [PMID: 28642469 PMCID: PMC5481428 DOI: 10.1038/s41598-017-03820-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Human immunodeficiency virus (HIV) has a number of circulating recombinant forms that are the product of recombination between different HIV subtypes. The first circulating recombinant form of HIV-1 to be identified was CRF01_AE, which originated in Central Africa and is now most prevalent in Southeast and East Asia. In this study, we investigated the timescale, evolutionary history, and population genetics of the HIV-1 CRF01_AE strains primarily responsible for the epidemic in Asia. A further aim of our study was to define and standardize the nomenclature and provide well-characterized reference sequences for the phylogenetic transmission clusters of CRF01_AE. We analysed a data set of 334 near-complete genome sequences from various risk groups, sampled between 1990 and 2011 from nine countries. Phylogenetic analyses of these sequences were performed using maximum likelihood and Bayesian methods. Our study confirms that the diversity of HIV-1 CRF01_AE originated in Central Africa in the mid-1970s, was introduced into Thailand between 1979 and 1982, and began expanding there shortly afterwards (1982-1984). Subsequently, multiple clusters significantly contributed to China's HIV epidemic. A Bayesian skyline plot revealed the rapid expansion of CRF01_AE in China around 1999-2000. We identified at least eight different clusters of HIV-1 CRF01_AE formed by rapid expansion into different risk groups and geographic regions in China since the late 1980s.
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Affiliation(s)
- Xingguang Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, Zhejiang, China
| | - Haizhou Liu
- Centre for Emerging Infectious Diseases, The State Key Laboratory of Virology, Wuhan Institute of Virology, University of Chinese Academy of Sciences, Wuhan, China
| | - Lu Liu
- Shantou University Medical College, Shantou, 515041, China
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Yi Feng
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, Zhejiang, China
| | - Marcia L Kalish
- Vanderbilt Institute for Global Health, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, 2006, Australia
| | - Yiming Shao
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, Zhejiang, China.
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Lipsitch M, Siller S, Nowak MA. THE EVOLUTION OF VIRULENCE IN PATHOGENS WITH VERTICAL AND HORIZONTAL TRANSMISSION. Evolution 2017; 50:1729-1741. [PMID: 28565576 DOI: 10.1111/j.1558-5646.1996.tb03560.x] [Citation(s) in RCA: 162] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/1995] [Accepted: 12/11/1995] [Indexed: 11/30/2022]
Abstract
The idea that vertical transmission of parasites selects for lower virulence is widely accepted. However, little theoretical work has considered the evolution of virulence for parasites with mixed horizontal plus vertical transmission. Many human, animal, and plant parasites are transmitted both vertically and horizontally, and some horizontal transmission is generally necessary to maintain parasites at all. We present a population-dynamical model for the evolution of virulence when both vertical and horizontal transmission are present. In the simplest such model, up to two infectious strains can coexist within one host population. Virulent, vertically transmitted pathogens can persist in a population when they provide protection against more virulent, horizontally transmitted strains. When virulence is maintained by a correlation with horizontal transmission rates, increased levels of vertical transmission always lower the evolutionarily stable (ESS) level of virulence. Contrary to existing theory, however, increases in opportunities for horizontal transmission also lower the ESS level of virulence. We explain these findings in light of earlier work and confirm them in simulations including imperfect vertical transmission. We describe further simulations, in which both vertical and horizontal transmission rates are allowed to evolve. The outcome of these simulations depends on whether high levels of vertical transmission are possible with low virulence. Finally, we argue against the notion of a virulence-avirulence continuum between horizontal and vertical transmission, and discuss our results in relation to empirical studies of transmission and virulence.
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Affiliation(s)
- Marc Lipsitch
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
| | - Steven Siller
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Martin A Nowak
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
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28
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Gregory AC, Solonenko SA, Ignacio-Espinoza JC, LaButti K, Copeland A, Sudek S, Maitland A, Chittick L, Dos Santos F, Weitz JS, Worden AZ, Woyke T, Sullivan MB. Genomic differentiation among wild cyanophages despite widespread horizontal gene transfer. BMC Genomics 2016; 17:930. [PMID: 27852226 PMCID: PMC5112629 DOI: 10.1186/s12864-016-3286-x] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 11/09/2016] [Indexed: 12/21/2022] Open
Abstract
Background Genetic recombination is a driving force in genome evolution. Among viruses it has a dual role. For genomes with higher fitness, it maintains genome integrity in the face of high mutation rates. Conversely, for genomes with lower fitness, it provides immediate access to sequence space that cannot be reached by mutation alone. Understanding how recombination impacts the cohesion and dissolution of individual whole genomes within viral sequence space is poorly understood across double-stranded DNA bacteriophages (a.k.a phages) due to the challenges of obtaining appropriately scaled genomic datasets. Results Here we explore the role of recombination in both maintaining and differentiating whole genomes of 142 wild double-stranded DNA marine cyanophages. Phylogenomic analysis across the 51 core genes revealed ten lineages, six of which were well represented. These phylogenomic lineages represent discrete genotypic populations based on comparisons of intra- and inter- lineage shared gene content, genome-wide average nucleotide identity, as well as detected gaps in the distribution of pairwise differences between genomes. McDonald-Kreitman selection tests identified putative niche-differentiating genes under positive selection that differed across the six well-represented genotypic populations and that may have driven initial divergence. Concurrent with patterns of recombination of discrete populations, recombination analyses of both genic and intergenic regions largely revealed decreased genetic exchange across individual genomes between relative to within populations. Conclusions These findings suggest that discrete double-stranded DNA marine cyanophage populations occur in nature and are maintained by patterns of recombination akin to those observed in bacteria, archaea and in sexual eukaryotes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3286-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ann C Gregory
- Department of Soil, Water and Environmental Science, University of Arizona, Tucson, AZ, 85721, USA.,Present Address: Departments of Microbiology, Ohio State University, Columbus, OH, 43210, USA
| | - Sergei A Solonenko
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA.,Present Address: Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus, OH, 43210, USA
| | - J Cesar Ignacio-Espinoza
- Department of Molecular & Cellular Biology, University of Arizona, Tucson, AZ, 85721, USA.,Present Address: Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Kurt LaButti
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Alex Copeland
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Sebastian Sudek
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, 95039, USA
| | - Ashley Maitland
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Lauren Chittick
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Filipa Dos Santos
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Joshua S Weitz
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA.,School of Physics, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Alexandra Z Worden
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, 95039, USA.,Integrated Microbial Biodiversity Program, Canadian Institute for Advanced Research, Toronto, M5G 1Z8, Canada
| | - Tanja Woyke
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Matthew B Sullivan
- Department of Soil, Water and Environmental Science, University of Arizona, Tucson, AZ, 85721, USA. .,Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA. .,Department of Molecular & Cellular Biology, University of Arizona, Tucson, AZ, 85721, USA. .,Present Address: Departments of Microbiology, Ohio State University, Columbus, OH, 43210, USA. .,Present Address: Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus, OH, 43210, USA. .,Present Address: Department of Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, OH, 43210, USA.
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29
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Lebedev AV, Neshumaev DA, Kazennova EV, Lapovok IA, Laga VY, Tumanov AS, Glushchenko NV, Plotnikova YK, Ponomareva OA, Yarygina EI, Bobkova MR. [Comparative analysis of genetic variants of the HIV-1 circulating in the Irkutsk region in 1999 and 2012]. Vopr Virusol 2016; 61:112-118. [PMID: 36494944 DOI: 10.18821/0507-4088-2016-61-3-112-118] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Accepted: 07/12/2020] [Indexed: 12/13/2022]
Abstract
The pol and env genome regions of the HIV-1 genetic variants circulating in the irkutsk region of russia in 1999 and 2012 were compared. The results of this work showed the dominance of the HIV-1 subtype a IDU-A genetic variant (100%) in this region. No primary resistance mutations in the pol gene in the treatment-naive patients were found. The heterogeneity of the viral population was found to be significantly increased based on the pol and env analysis among HIV-variants isolated in 2012 (12.88% and 2.16%) from the intravenous drug users as compared to HIV-variants that caused the outbreak of the HIV infection in 1999 (1.64% and 0.47%). In addition, the comparison of genetic distances of the pol and env gene sequences in the viruses isolated in 2012 from the HIV-positive persons infected through heterosexual intercourse and intravenous drug use demonstrated that the transmission route influenced the variability of the virus population. Among the viruses of IDU-A variant circulating in the area in 2012 the prevalence of X4-tropic variants was 24.7%.
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Affiliation(s)
- A V Lebedev
- D.I. Ivanovsky Institute of Virology «Federal Research Centre of Epidemilogy and Microbiology named after the honorary academician N.F. Gamaleya».,Moscow State Academy of Veterinary Medicine and Biotechnology
| | | | - E V Kazennova
- D.I. Ivanovsky Institute of Virology «Federal Research Centre of Epidemilogy and Microbiology named after the honorary academician N.F. Gamaleya»
| | - I A Lapovok
- D.I. Ivanovsky Institute of Virology «Federal Research Centre of Epidemilogy and Microbiology named after the honorary academician N.F. Gamaleya»
| | - V Y Laga
- D.I. Ivanovsky Institute of Virology «Federal Research Centre of Epidemilogy and Microbiology named after the honorary academician N.F. Gamaleya»
| | - A S Tumanov
- D.I. Ivanovsky Institute of Virology «Federal Research Centre of Epidemilogy and Microbiology named after the honorary academician N.F. Gamaleya»
| | - N V Glushchenko
- D.I. Ivanovsky Institute of Virology «Federal Research Centre of Epidemilogy and Microbiology named after the honorary academician N.F. Gamaleya»
| | | | | | - E I Yarygina
- Moscow State Academy of Veterinary Medicine and Biotechnology
| | - M R Bobkova
- D.I. Ivanovsky Institute of Virology «Federal Research Centre of Epidemilogy and Microbiology named after the honorary academician N.F. Gamaleya»
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30
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Abstract
The enzyme reverse transcriptase (RT) was discovered in retroviruses almost 50 years ago. The demonstration that other types of viruses, and what are now called retrotransposons, also replicated using an enzyme that could copy RNA into DNA came a few years later. The intensity of the research in both the process of reverse transcription and the enzyme RT was greatly stimulated by the recognition, in the mid-1980s, that human immunodeficiency virus (HIV) was a retrovirus and by the fact that the first successful anti-HIV drug, azidothymidine (AZT), is a substrate for RT. Although AZT monotherapy is a thing of the past, the most commonly prescribed, and most successful, combination therapies still involve one or both of the two major classes of anti-RT drugs. Although the basic mechanics of reverse transcription were worked out many years ago, and the first high-resolution structures of HIV RT are now more than 20 years old, we still have much to learn, particularly about the roles played by the host and viral factors that make the process of reverse transcription much more efficient in the cell than in the test tube. Moreover, we are only now beginning to understand how various host factors that are part of the innate immunity system interact with the process of reverse transcription to protect the host-cell genome, the host cell, and the whole host, from retroviral infection, and from unwanted retrotransposition.
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31
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Abstract
Antibodies (Abs) are a critical component of the human immune response against viral infections. In HIV-infected patients, a robust Ab response against the virus develops within months of infection; however, due to numerous strategies, the virus usually escapes the biological effects of the various Abs. Here we provide an overview of the different viral evasion mechanisms, including glycosylation, high mutation rate, and conformational masking by the envelope glycoproteins of the virus. In response to virus infection and to its evolution within a host, "conventional Abs" are generated, and these can also be induced by immunization; generally, these Abs are limited in their neutralization breadth and potency. In contrast, "exceptional Abs" require extended exposure to virus to generate the required hypermutation in the immunoglobulin variable regions, and they occur only in rare HIV-infected individuals, but they display impressive breadth and potency. In this review, we describe the major regions of the HIV envelope spike that are targeted by conventional and exceptional Abs. These include the first, second, and third variable loops (V1, V2, and V3) located at the apex of the envelope trimer, the CD4 binding site, and the membrane-proximal external region of the gp41 ectodomain. Lastly, we discuss the challenging task of HIV immunogen design and approaches for choosing which immunogens might be used to elicit protective Abs.
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32
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Hameed A, Abdullah MI, Ahmed E, Sharif A, Irfan A, Masood S. Anti-HIV cytotoxicity enzyme inhibition and molecular docking studies of quinoline based chalcones as potential non-nucleoside reverse transcriptase inhibitors (NNRT). Bioorg Chem 2016; 65:175-82. [PMID: 26964017 DOI: 10.1016/j.bioorg.2016.02.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Revised: 02/24/2016] [Accepted: 02/25/2016] [Indexed: 11/20/2022]
Abstract
A series of fourteen (A1 - A14) qunioline based chalcones were screened for reverse transcriptase inhibitors (RT) and found potentially active against RT. Bioassay, theoretical and dockings studies with RT (the enzyme required for reverse transcription of viral RNA) results showed that the type and positions of the substituents seemed to be critical for their inhibition against RT. The bromo and chloro substituted chalcone displayed high degree of inhibition against RT. The A4 andA6 showed high interaction with RT, contributing high free binding energy (ΔG -9.30 and -9.13kcal) and RT inhibition value (IC50 0.10μg/ml and 0.11μg/ml).
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Affiliation(s)
- Asima Hameed
- Institute of Chemistry, University of the Punjab, Lahore, P.O 54590, Pakistan
| | | | - Ejaz Ahmed
- Institute of Chemistry, University of the Punjab, Lahore, P.O 54590, Pakistan.
| | - Ahsan Sharif
- Institute of Chemistry, University of the Punjab, Lahore, P.O 54590, Pakistan
| | - Ahmad Irfan
- Department of Chemistry, Faculty of Science, King Khalid University, Abha 61413, P.O. Box 9004, Saudi Arabia; Research Center for Advanced Materials Science (RCAMS), King Khalid University, Abha 61413, P.O. Box 9004, Saudi Arabia
| | - Sara Masood
- Sheikh Zayed Madical College & Hospital Rahim Yar Khan, Pakistan
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33
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Dudas G, Rambaut A. MERS-CoV recombination: implications about the reservoir and potential for adaptation. Virus Evol 2016; 2:vev023. [PMID: 27774293 PMCID: PMC4989901 DOI: 10.1093/ve/vev023] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Recombination is a process that unlinks neighboring loci allowing for independent evolutionary trajectories within genomes of many organisms. If not properly accounted for, recombination can compromise many evolutionary analyses. In addition, when dealing with organisms that are not obligately sexually reproducing, recombination gives insight into the rate at which distinct genetic lineages come into contact. Since June 2012, Middle East respiratory syndrome coronavirus (MERS-CoV) has caused 1,106 laboratory-confirmed infections, with 421 MERS-CoV-associated deaths as of 16 April 2015. Although bats are considered as the likely ultimate source of zoonotic betacoronaviruses, dromedary camels have been consistently implicated as the source of current human infections in the Middle East. In this article, we use phylogenetic methods and simulations to show that MERS-CoV genome has likely undergone numerous recombinations recently. Recombination in MERS-CoV implies frequent co-infection with distinct lineages of MERS-CoV, probably in camels given the current understanding of MERS-CoV epidemiology.
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Affiliation(s)
- Gytis Dudas
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK,; Centre for Immunology, Infection and Evolution at the University of Edinburgh, Edinburgh, UK and; Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
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34
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Chan LG, Ho MJ, Kaur P, Singh J, Ng OT, Lee CC, Leo YS, Carvalhal A. Differences in clinical and psychiatric outcomes between prevalent HIV-1 molecular subtypes in a multiethnic Southeast Asian sample. Gen Hosp Psychiatry 2016; 38:4-8. [PMID: 26380875 DOI: 10.1016/j.genhosppsych.2015.07.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 07/24/2015] [Accepted: 07/27/2015] [Indexed: 12/16/2022]
Abstract
OBJECTIVE In Southeast Asia, subtypes B and CRF01_AE are the prevalent human immunodeficiency virus-1 (HIV-1) subtypes. This study examines the intersubtype differences in clinical indicators and psychiatric symptoms in a multiethnic sample. METHODS The study site was a national HIV treatment center. Data were extracted from the Molecular Epidemiology Research study and the HIV-Psychiatry Integrated Mental Health Project, and analyzed according to groups defined by viral subtype. RESULTS Of 177 subjects, 54.8% were infected with subtype CRF01_AE; 42.9% screened positive on the Hospital Anxiety and Depression Scale (HADS). The CRF01_AE group was significantly older (mean 38.29 years vs. 34.62 years, P=.031) and had advanced immunosuppression (CD4 <200) just prior to HADS screening (33.0% vs. 13.5%, P=.003). By multivariate logistic regression, homosexual transmission [odds ratio (OR) 0.388, 95% confidence interval (CI) 0.158-0.951, P=.038], subtype CRF01_AE (OR 2.898, 95% CI 1.199-7.001, P=.018) and positive HADS screening (OR 2.859, 95% CI 1.261-8.484, P=.012) were associated with advanced immunosuppression; and only advanced immunosuppression was associated with screening positive on the HADS (OR 3.270, 95% CI 1.299-8.227, P=.012). CONCLUSION Subtype CRF01_AE is associated with advanced immunosuppression but not with symptoms of anxiety and depression. The results suggest that psychiatric symptoms are associated with advanced HIV disease regardless of subtype.
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Affiliation(s)
- Lai Gwen Chan
- Department of Psychological Medicine, Tan Tock Seng Hospital, 11 Jalan Tan Tock Seng, Singapore, 308433.
| | - Mei Jing Ho
- Department of Psychological Medicine, Tan Tock Seng Hospital, 11 Jalan Tan Tock Seng, Singapore, 308433.
| | - Palvinder Kaur
- Institute of Infectious Disease and Epidemiology, Tan Tock Seng Hospital, 11 Jalan Tan Tock Seng, Singapore, 308433.
| | - Jaspal Singh
- Department of Psychological Medicine, Tan Tock Seng Hospital, 11 Jalan Tan Tock Seng, Singapore, 308433; Psychological Wellness Program, Tan Tock Seng Hospital, 11 Jalan Tan Tock Seng, Singapore, 308433.
| | - Oon Tek Ng
- Institute of Infectious Disease and Epidemiology, Tan Tock Seng Hospital, 11 Jalan Tan Tock Seng, Singapore, 308433.
| | - Cheng Chuan Lee
- Institute of Infectious Disease and Epidemiology, Tan Tock Seng Hospital, 11 Jalan Tan Tock Seng, Singapore, 308433; Yong Loo Lin School of Medicine, National University of Singapore, 11 Jalan Tan Tock Seng, Singapore, 308433.
| | - Yee Sin Leo
- Yong Loo Lin School of Medicine, National University of Singapore, 11 Jalan Tan Tock Seng, Singapore, 308433; Communicable Disease Centre, Tan Tock Seng Hospital, 11 Jalan Tan Tock Seng, Singapore, 308433; Lee Kong Chian School of Medicine, Nanyang Technological University, 11 Jalan Tan Tock Seng, Singapore, 308433; Saw Swee Hock School of Public Health, National University of Singapore, 11 Jalan Tan Tock Seng, Singapore, 308433.
| | - Adriana Carvalhal
- Medical Psychiatry Consultation Service, Department of Psychiatry, St Michael's Hospital, 20 Bond Street, Toronto, ON, M5B 1W8, Canada; Department of Psychiatry, University of Toronto, 20 Bond Street, Toronto, ON, M5B 1W8, Canada; Li Kah Shing, St Michael's Hospital, 20 Bond Street, Toronto, ON, M5B 1W8, Canada.
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35
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Love TMT, Park SY, Giorgi EE, Mack WJ, Perelson AS, Lee HY. SPMM: estimating infection duration of multivariant HIV-1 infections. Bioinformatics 2015; 32:1308-15. [PMID: 26722117 DOI: 10.1093/bioinformatics/btv749] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 12/17/2015] [Indexed: 12/20/2022] Open
Abstract
MOTIVATION Illustrating how HIV-1 is transmitted and how it evolves in the following weeks is an important step for developing effective vaccination and prevention strategies. It is currently possible through DNA sequencing to account for the diverse array of viral strains within an infected individual. This provides an unprecedented opportunity to pinpoint when each patient was infected and which viruses were transmitted. RESULTS Here we develop a mathematical tool for early HIV-1 evolution within a subject whose infection originates either from a single or multiple viral variants. The shifted Poisson mixture model (SPMM) provides a quantitative guideline for segregating viral lineages, which in turn enables us to assess when a subject was infected. The infection duration estimated by SPMM showed a statistically significant linear relationship with that by Fiebig laboratory staging (P = 0.00059) among 37 acutely infected subjects. Our tool provides a functional approach to understanding early genetic diversity, one of the most important parameters for deciphering HIV-1 transmission and predicting the rate of disease progression. AVAILABILITY AND IMPLEMENTATION SPMM, webserver, is available at http://www.hayounlee.org/web-tools.html. CONTACT hayoun@usc.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Tanzy M T Love
- Department of Biostatistics and Computational Biology, University of Rochester, Rochester, New York, 14642, USA
| | - Sung Yong Park
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, 90089, USA
| | - Elena E Giorgi
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA and
| | - Wendy J Mack
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, 90089, USA
| | - Alan S Perelson
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA and
| | - Ha Youn Lee
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA and
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36
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Jia L, Gui T, Li L, Liu S, Li H, Bao Z, Wang X, Zhuang D, Li T, Han J, Liu Y, Li J. A considerable proportion of CRF01_AE strains in China originated from circulating intrasubtype recombinant forms (CIRF). BMC Infect Dis 2015; 15:528. [PMID: 26572485 PMCID: PMC4647519 DOI: 10.1186/s12879-015-1273-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 11/05/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In this study, the prevalence of HIV-1 CRF01_AE intrasubtype recombinants in China is estimated and their contributions to the epidemic are explored. METHODS Available HIV-1 complete genomes of CRF01_AE were retrieved from the HIV database. The two alignments were evaluated with RDP3. Recombinants were defined as cases in which the recombination signal was supported by at least 3 methods with P-values of ≤0.05 after Bonferroni correction for multiple comparisons implemented in RDP3. Phylogenetic analysis was performed to further investigate the role of intrasubtype recombinants in epidemics. RESULTS Here, 124 out of the 339 sequences from around the world (36.6 %) showed significant evidence of recombination. Here, 84 of these recombinants were from China, accounting for 54.9 % of local total sequences (84 out of 153). The results indicated non-negligible levels of intrasubtype recombination. Subsequent phylogenetic analysis indicated that a considerable proportion of CRF01_AE strains in China originated from circulating intrasubtype recombinant forms. Three large, well-supported intrasubtype recombinants clusters were identified here. Through a survey of risk factors and sampling cities and provinces, cluster I and cluster II were found to be prevalent primarily among men who have sex with men in major northern cities. Cluster III was prevalent among heterosexuals and intravenous drug users in southern and southwestern provinces. CONCLUSIONS The current work highlighted the remarkable prevalence of intrasubtype recombination within the CRF01_AE epidemic and emphasized the value of intrasubtype recombinants, which came to circulate in the same manner as intersubtype recombinants.
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Affiliation(s)
- Lei Jia
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dongda Street, Fengtai District, Beijing, 100071, China.
| | - Tao Gui
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dongda Street, Fengtai District, Beijing, 100071, China.
| | - Lin Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dongda Street, Fengtai District, Beijing, 100071, China.
| | - Siyang Liu
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dongda Street, Fengtai District, Beijing, 100071, China.
| | - Hanping Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dongda Street, Fengtai District, Beijing, 100071, China.
| | - Zuoyi Bao
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dongda Street, Fengtai District, Beijing, 100071, China.
| | - Xiaolin Wang
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dongda Street, Fengtai District, Beijing, 100071, China.
| | - Daomin Zhuang
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dongda Street, Fengtai District, Beijing, 100071, China.
| | - Tianyi Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dongda Street, Fengtai District, Beijing, 100071, China.
| | - Jingwan Han
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dongda Street, Fengtai District, Beijing, 100071, China.
| | - Yongjian Liu
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dongda Street, Fengtai District, Beijing, 100071, China.
| | - Jingyun Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dongda Street, Fengtai District, Beijing, 100071, China.
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Sanborn KB, Somasundaran M, Luzuriaga K, Leitner T. Recombination elevates the effective evolutionary rate and facilitates the establishment of HIV-1 infection in infants after mother-to-child transmission. Retrovirology 2015; 12:96. [PMID: 26573574 PMCID: PMC4647327 DOI: 10.1186/s12977-015-0222-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 11/05/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Previous studies have demonstrated that single HIV-1 genotypes are commonly transmitted from mother to child, but such analyses primarily used single samples from mother and child. It is possible that in a single sample, obtained early after infection, only the most replication competent virus is detected even when other forms may have been transmitted. Such forms may have advantages later in infection, and may thus be detected in follow-up samples. Because HIV-1 frequently recombines, phylogenetic analyses that ignore recombination may miss transmission of multiple forms if they recombine after transmission. Moreover, recombination may facilitate adaptation, thus providing an advantage in establishing infection. The effect of recombination on viral evolution in HIV-1 infected children has not been well defined. RESULTS We analyzed full-length env sequences after single genome amplification from the plasma of four subtype B HIV-1 infected women (11-67 env clones from 1 time point within a month prior to delivery) and their non-breastfed, intrapartum-infected children (3-6 longitudinal time points per child starting at the time of HIV-1 diagnosis). To address the potential beneficial or detrimental effects of recombination, we used a recently developed hierarchical recombination detection method based on the pairwise homoplasy index (PHI)-test. Recombination was observed in 9-67% of the maternal sequences and in 25-60% of the child sequences. In the child, recombination only occurred between variants that had evolved after transmission; taking recombination into account, we identified transmission of only 1 or 2 phylogenetic lineages from mother to child. Effective HIV-1 evolutionary rates of HIV-1 were initially high in the child and slowed over time (after 1000 days). Recombination was associated with elevated evolutionary rates. CONCLUSIONS Our results confirm that 1-2 variants are typically transmitted from mothers to their newborns. They also demonstrate that early abundant recombination elevates the effective evolutionary rate, suggesting that recombination increases the rate of adaptation in HIV-1 evolution.
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Affiliation(s)
- Keri B Sanborn
- Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Worcester, 01605, MA, USA.
| | - Mohan Somasundaran
- Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Worcester, 01605, MA, USA.
| | - Katherine Luzuriaga
- Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Worcester, 01605, MA, USA.
| | - Thomas Leitner
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, 87545, NM, USA.
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Ode H, Matsuda M, Matsuoka K, Hachiya A, Hattori J, Kito Y, Yokomaku Y, Iwatani Y, Sugiura W. Quasispecies Analyses of the HIV-1 Near-full-length Genome With Illumina MiSeq. Front Microbiol 2015; 6:1258. [PMID: 26617593 PMCID: PMC4641896 DOI: 10.3389/fmicb.2015.01258] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Accepted: 10/29/2015] [Indexed: 12/29/2022] Open
Abstract
Human immunodeficiency virus type-1 (HIV-1) exhibits high between-host genetic diversity and within-host heterogeneity, recognized as quasispecies. Because HIV-1 quasispecies fluctuate in terms of multiple factors, such as antiretroviral exposure and host immunity, analyzing the HIV-1 genome is critical for selecting effective antiretroviral therapy and understanding within-host viral coevolution mechanisms. Here, to obtain HIV-1 genome sequence information that includes minority variants, we sought to develop a method for evaluating quasispecies throughout the HIV-1 near-full-length genome using the Illumina MiSeq benchtop deep sequencer. To ensure the reliability of minority mutation detection, we applied an analysis method of sequence read mapping onto a consensus sequence derived from de novo assembly followed by iterative mapping and subsequent unique error correction. Deep sequencing analyses of aHIV-1 clone showed that the analysis method reduced erroneous base prevalence below 1% in each sequence position and discarded only < 1% of all collected nucleotides, maximizing the usage of the collected genome sequences. Further, we designed primer sets to amplify the HIV-1 near-full-length genome from clinical plasma samples. Deep sequencing of 92 samples in combination with the primer sets and our analysis method provided sufficient coverage to identify >1%-frequency sequences throughout the genome. When we evaluated sequences of pol genes from 18 treatment-naïve patients' samples, the deep sequencing results were in agreement with Sanger sequencing and identified numerous additional minority mutations. The results suggest that our deep sequencing method would be suitable for identifying within-host viral population dynamics throughout the genome.
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Affiliation(s)
- Hirotaka Ode
- Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center Nagoya, Japan
| | - Masakazu Matsuda
- Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center Nagoya, Japan
| | - Kazuhiro Matsuoka
- Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center Nagoya, Japan
| | - Atsuko Hachiya
- Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center Nagoya, Japan
| | - Junko Hattori
- Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center Nagoya, Japan
| | - Yumiko Kito
- Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center Nagoya, Japan
| | - Yoshiyuki Yokomaku
- Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center Nagoya, Japan
| | - Yasumasa Iwatani
- Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center Nagoya, Japan ; Department of AIDS Research, Graduate School of Medicine, Nagoya University Nagoya, Japan
| | - Wataru Sugiura
- Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center Nagoya, Japan ; Department of AIDS Research, Graduate School of Medicine, Nagoya University Nagoya, Japan
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Haqqani AA, Marek SL, Kumar J, Davenport M, Wang H, Tilton JC. Central memory CD4+ T cells are preferential targets of double infection by HIV-1. Virol J 2015; 12:184. [PMID: 26559763 PMCID: PMC4642630 DOI: 10.1186/s12985-015-0415-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 11/01/2015] [Indexed: 12/14/2022] Open
Abstract
Background Template switching between two distinct HIV-1 RNA genomes during reverse transcription gives rise to recombinant viruses that greatly expand the genetic diversity of HIV-1 and have adverse implications for drug resistance, immune escape, and vaccine design. Virions with two distinct genomes are produced exclusively from cells infected with two or more viruses, or ‘doubly infected’ cells. Previous studies have revealed higher than expected frequencies of doubly infected cells compared to frequencies based on chance alone, suggesting non-random enhancement of double infection. Methods We investigated double infection of unstimulated primary CD4+ T cells using reporter viruses carrying genes for different fluorescent proteins, EGFP and mCherry, combined with sophisticated modeling techniques based on Poisson distribution. Additionally, through the use of multiparameter flow cytometry we examined the susceptibility of naïve and memory subsets of CD4+ T cells to double infection by HIV. Results Using our double infection system, we confirm non-random enhancement of multiple infection events. Double infection of CD4+ T cells was not found to be a consequence of suboptimal provirus expression rescued by Tat in trans—as has been reported in cell lines—but rather due to a heterogeneous cell population in which only a fraction of primary peripheral blood CD4+ T cells are susceptible to HIV infection regardless of viral titer. Intriguingly, double infection of CD4+ T cells occurred preferentially in memory CD4+ T cells—particularly the central memory (TCM) subset—but was not a consequence of SAMHD1-mediated restriction of HIV infection in naïve cells. Conclusions These findings reveal that double infection in primary CD4+ T cells is primarily a consequences of cellular heterogeneity and not rescue of suboptimal provirus expression by Tat in trans. Additionally, we report a previously unappreciated phenomenon of enhanced double infection within primary TCM cells and suggest that these long-lived cells may serve as an archive that drive ongoing viral recombination events in vivo.
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Affiliation(s)
- Aiman A Haqqani
- Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, 10900 Euclid Ave, BRB 919, Cleveland, OH, 44106, USA.
| | - Samantha L Marek
- Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, 10900 Euclid Ave, BRB 919, Cleveland, OH, 44106, USA.
| | - Jagadish Kumar
- Complex Systems in Biology Group, Center for Vascular Research, University of New South Wales, Sydney, NSW, 2052, Australia.
| | - Miles Davenport
- Complex Systems in Biology Group, Center for Vascular Research, University of New South Wales, Sydney, NSW, 2052, Australia.
| | - Heng Wang
- DDC Clinic-Center for Special Needs Children, Middlefield, OH, 44062, USA.
| | - John C Tilton
- Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, 10900 Euclid Ave, BRB 919, Cleveland, OH, 44106, USA.
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Cocirculation of Two env Molecular Variants, of Possible Recombinant Origin, in Gorilla and Chimpanzee Simian Foamy Virus Strains from Central Africa. J Virol 2015; 89:12480-91. [PMID: 26446599 DOI: 10.1128/jvi.01798-15] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 09/28/2015] [Indexed: 12/30/2022] Open
Abstract
UNLABELLED Simian foamy virus (SFV) is a ubiquitous retrovirus in nonhuman primates (NHPs) that can be transmitted to humans, mostly through severe bites. In the past few years, our laboratory has identified more than 50 hunters from central Africa infected with zoonotic SFVs. Analysis of the complete sequences of five SFVs obtained from these individuals revealed that env was the most variable gene. Furthermore, recombinant SFV strains, some of which involve sequences in the env gene, were recently identified. Here, we investigated the variability of the env genes of zoonotic SFV strains and searched for possible recombinants. We sequenced the complete env gene or its surface glycoprotein region (SU) from DNA amplified from the blood of (i) a series of 40 individuals from Cameroon or Gabon infected with a gorilla or chimpanzee foamy virus (FV) strain and (ii) 1 gorilla and 3 infected chimpanzees living in the same areas as these hunters. Phylogenetic analyses revealed the existence of two env variants among both the gorilla and chimpanzee FV strains that were present in zoonotic and NHP strains. These variants differ greatly (>30% variability) in a 753-bp-long region located in the receptor-binding domain of SU, whereas the rest of the gene is very conserved. Although the organizations of the Env protein sequences are similar, the potential glycosylation patterns differ between variants. Analysis of recombination suggests that the variants emerged through recombination between different strains, although all parental strains could not be identified. IMPORTANCE SFV infection in humans is a great example of a zoonotic retroviral infection that has not spread among human populations, in contrast to human immunodeficiency viruses (HIVs) and human T-lymphotropic viruses (HTLVs). Recombination was a major mechanism leading to the emergence of HIV. Here, we show that two SFV molecular envelope gene variants circulate among ape populations in Central Africa and that both can be transmitted to humans. These variants differ greatly in the SU region that corresponds to the part of the Env protein in contact with the environment. These variants may have emerged through recombination between SFV strains infecting different NHP species.
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Tongo M, Dorfman JR, Abrahams MR, Mpoudi-Ngole E, Burgers WA, Martin DP. Near full-length HIV type 1M genomic sequences from Cameroon : Evidence of early diverging under-sampled lineages in the country. EVOLUTION MEDICINE AND PUBLIC HEALTH 2015; 2015:254-65. [PMID: 26354000 PMCID: PMC4600344 DOI: 10.1093/emph/eov022] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 08/25/2015] [Indexed: 12/30/2022]
Abstract
Background: Cameroon is the country in which HIV-1 group M (HIV-1M) likely originated and is today a major hotspot of HIV-1M genetic diversity. It remains unclear, however, whether the highly divergent HIV-1M lineages found in this country arose during the earliest phases of the global HIV-1M epidemic, or whether they arose more recently as a result of recombination events between globally circulating HIV-1M lineages. Methodology: To differentiate between these two possibilities, we performed phylogenetic analyses of the near full genome sequences of nine newly sequenced divergent HIV-1M isolates and 15 previously identified, apparently unique recombinant forms (URFs) from Cameroon. Results: Although two of the new genome sequences were clearly classifiable within subtype G, the remaining seven were highly divergent and phylogenetically branched either outside of, or very near the bases of clades containing the well characterised globally circulating viral lineages that they were most closely related to. Recombination analyses further revealed that these divergent viruses were likely complex URFs. We show, however that substantial portions (>1 Kb) of three of the new genome sequences and 15 of the previously characterised Cameroonian URFs have apparently been derived from divergent parental viruses that branch phylogenetically near the bases of the major HIV-1M clades. Conclusions and implications: Our analyses indicate the presence in Cameroon of contemporary descendants of numerous early-diverging HIV-1M lineages. Further efforts to sample and sequence viruses from such lineages could be crucial both for retracing the earliest evolutionary steps during the emergence of HIV-1M in humans, and accurately reconstructing the ancestral sequences of the major globally circulating HIV-1M lineages.
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Affiliation(s)
- Marcel Tongo
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town, South Africa; Division of Immunology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa; Division of Medical Virology, Department of Pathology and Institute of Medical Research and Study of Medicinal plants (IMPM), Yaoundé, Cameroon
| | - Jeffrey R Dorfman
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town, South Africa; Division of Immunology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | | | - Eitel Mpoudi-Ngole
- Institute of Medical Research and Study of Medicinal plants (IMPM), Yaoundé, Cameroon
| | | | - Darren P Martin
- Division of Computational Biology, Department of Integrated Biology Sciences and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa; and
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Peck KM, Burch CL, Heise MT, Baric RS. Coronavirus Host Range Expansion and Middle East Respiratory Syndrome Coronavirus Emergence: Biochemical Mechanisms and Evolutionary Perspectives. Annu Rev Virol 2015; 2:95-117. [PMID: 26958908 DOI: 10.1146/annurev-virology-100114-055029] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Coronaviruses have frequently expanded their host range in recent history, with two events resulting in severe disease outbreaks in human populations. Severe acute respiratory syndrome coronavirus (SARS-CoV) emerged in 2003 in Southeast Asia and rapidly spread around the world before it was controlled by public health intervention strategies. The 2012 Middle East respiratory syndrome coronavirus (MERS-CoV) outbreak represents another prime example of virus emergence from a zoonotic reservoir. Here, we review the current knowledge of coronavirus cross-species transmission, with particular focus on MERS-CoV. MERS-CoV is still circulating in the human population, and the mechanisms governing its cross-species transmission have been only partially elucidated, highlighting a need for further investigation. We discuss biochemical determinants mediating MERS-CoV host cell permissivity, including virus spike interactions with the MERS-CoV cell surface receptor dipeptidyl peptidase 4 (DPP4), and evolutionary mechanisms that may facilitate host range expansion, including recombination, mutator alleles, and mutational robustness. Understanding these mechanisms can help us better recognize the threat of emergence for currently circulating zoonotic strains.
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Affiliation(s)
| | | | - Mark T Heise
- Genetics.,Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina 27599;
| | - Ralph S Baric
- Epidemiology, and.,Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina 27599;
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Diallo K, Zheng DP, Rottinghaus EK, Bassey O, Yang C. Viral Genetic Diversity and Polymorphisms in a Cohort of HIV-1-Infected Patients Eligible for Initiation of Antiretroviral Therapy in Abuja, Nigeria. AIDS Res Hum Retroviruses 2015; 31:564-75. [PMID: 25582324 DOI: 10.1089/aid.2014.0168] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Studying the genetic diversity and natural polymorphisms of HIV-1 would benefit our understanding of HIV drug resistance (HIVDR) development and predict treatment outcomes. In this study, we have characterized the HIV-1 genetic diversity and natural polymorphisms at the 5' region of the pol gene encompassing the protease (PR) and reverse transcriptase (RT) from 271 plasma specimens collected in 2008 from HIV-1-infected patients who were eligible for initiating antiretroviral therapy in Abuja (Nigeria). The analysis indicated that the predominant subtype was subtype G (31.0%), followed by CRF02-AG (19.2 %), CRF43-02G (18.5%), and A/CRF36-cpx (11.4%); the remaining (19.9%) were other subtypes and circulating (CRF) and unique (URF) recombinant forms. Recombinant viruses (68.6%) were the major viral strains in the region. Eighty-four subtype G sequences were further mainly classified into two major and two minor clusters; sequences in the two major clusters were closely related to the HIV-1 strains in two of the three major subtype G clusters detected worldwide. Those in the two minor clusters appear to be new subtype G strains circulating only in Abuja. The pretreatment DR prevalence was <3%; however, numerous natural polymorphisms were present. Eleven polymorphic mutations (G16E, K20I, L23P, E35D, M36I, N37D/S/T, R57K, L63P, and V82I) were detected in the PR that were subtype or CRF specific while only three mutations (D123N, I135T, and I135V) were identified in the RT. Overall, this study indicates an evolving HIV-1 epidemic in Abuja with recombinant viruses becoming the dominant strains and the emergence of new subtype G strains; pretreatment HIVDR was low and the occurrence of natural polymorphism in the PR region was subtype or CRF dependent.
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Affiliation(s)
- Karidia Diallo
- International Laboratory Branch, Division of Global HIV/AIDS, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Du-Ping Zheng
- International Laboratory Branch, Division of Global HIV/AIDS, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Erin K. Rottinghaus
- International Laboratory Branch, Division of Global HIV/AIDS, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Orji Bassey
- Centers for Disease Control and Prevention, Abuja, Nigeria
| | - Chunfu Yang
- International Laboratory Branch, Division of Global HIV/AIDS, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia
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Nazar MF, Abdullah MI, Badshah A, Mahmood A, Rana UA, Khan SUD. Synthesis, structure–activity relationship and molecular docking of cyclohexenone based analogous as potent non-nucleoside reverse-transcriptase inhibitors. J Mol Struct 2015. [DOI: 10.1016/j.molstruc.2014.12.090] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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45
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Acevedo-Sáenz L, Ochoa R, Rugeles MT, Olaya-García P, Velilla-Hernández PA, Diaz FJ. Selection pressure in CD8⁺ T-cell epitopes in the pol gene of HIV-1 infected individuals in Colombia. A bioinformatic approach. Viruses 2015; 7:1313-31. [PMID: 25803098 PMCID: PMC4379572 DOI: 10.3390/v7031313] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 02/23/2015] [Accepted: 02/24/2015] [Indexed: 01/24/2023] Open
Abstract
One of the main characteristics of the human immunodeficiency virus is its genetic variability and rapid adaptation to changing environmental conditions. This variability, resulting from the lack of proofreading activity of the viral reverse transcriptase, generates mutations that could be fixed either by random genetic drift or by positive selection. Among the forces driving positive selection are antiretroviral therapy and CD8+ T-cells, the most important immune mechanism involved in viral control. Here, we describe mutations induced by these selective forces acting on the pol gene of HIV in a group of infected individuals. We used Maximum Likelihood analyses of the ratio of non-synonymous to synonymous mutations per site (dN/dS) to study the extent of positive selection in the protease and the reverse transcriptase, using 614 viral sequences from Colombian patients. We also performed computational approaches, docking and algorithmic analyses, to assess whether the positively selected mutations affected binding to the HLA molecules. We found 19 positively-selected codons in drug resistance-associated sites and 22 located within CD8+ T-cell epitopes. A high percentage of mutations in these epitopes has not been previously reported. According to the docking analyses only one of those mutations affected HLA binding. However, algorithmic methods predicted a decrease in the affinity for the HLA molecule in seven mutated peptides. The bioinformatics strategies described here are useful to identify putative positively selected mutations associated with immune escape but should be complemented with an experimental approach to define the impact of these mutations on the functional profile of the CD8+ T-cells.
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Affiliation(s)
- Liliana Acevedo-Sáenz
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, 050010, Colombia.
| | - Rodrigo Ochoa
- Programa de Estudio y Control de Enfermedades Tropicales-PECET, Universidad de Antioquia, Medellín, 050010, Colombia.
| | - Maria Teresa Rugeles
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, 050010, Colombia.
| | | | - Paula Andrea Velilla-Hernández
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, 050010, Colombia.
| | - Francisco J Diaz
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, 050010, Colombia.
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Pérez-Losada M, Arenas M, Galán JC, Palero F, González-Candelas F. Recombination in viruses: mechanisms, methods of study, and evolutionary consequences. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2015; 30:296-307. [PMID: 25541518 PMCID: PMC7106159 DOI: 10.1016/j.meegid.2014.12.022] [Citation(s) in RCA: 198] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2014] [Revised: 12/15/2014] [Accepted: 12/17/2014] [Indexed: 02/08/2023]
Abstract
Recombination is a pervasive process generating diversity in most viruses. It joins variants that arise independently within the same molecule, creating new opportunities for viruses to overcome selective pressures and to adapt to new environments and hosts. Consequently, the analysis of viral recombination attracts the interest of clinicians, epidemiologists, molecular biologists and evolutionary biologists. In this review we present an overview of three major areas related to viral recombination: (i) the molecular mechanisms that underlie recombination in model viruses, including DNA-viruses (Herpesvirus) and RNA-viruses (Human Influenza Virus and Human Immunodeficiency Virus), (ii) the analytical procedures to detect recombination in viral sequences and to determine the recombination breakpoints, along with the conceptual and methodological tools currently used and a brief overview of the impact of new sequencing technologies on the detection of recombination, and (iii) the major areas in the evolutionary analysis of viral populations on which recombination has an impact. These include the evaluation of selective pressures acting on viral populations, the application of evolutionary reconstructions in the characterization of centralized genes for vaccine design, and the evaluation of linkage disequilibrium and population structure.
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Affiliation(s)
- Marcos Pérez-Losada
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Portugal; Computational Biology Institute, George Washington University, Ashburn, VA 20147, USA
| | - Miguel Arenas
- Centre for Molecular Biology "Severo Ochoa", Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Juan Carlos Galán
- Servicio de Microbiología, Hospital Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain; CIBER en Epidemiología y Salud Pública, Spain
| | - Ferran Palero
- CIBER en Epidemiología y Salud Pública, Spain; Unidad Mixta Infección y Salud Pública, FISABIO-Universitat de València, Valencia, Spain
| | - Fernando González-Candelas
- CIBER en Epidemiología y Salud Pública, Spain; Unidad Mixta Infección y Salud Pública, FISABIO-Universitat de València, Valencia, Spain.
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Arenas M, Lopes JS, Beaumont MA, Posada D. CodABC: a computational framework to coestimate recombination, substitution, and molecular adaptation rates by approximate Bayesian computation. Mol Biol Evol 2015; 32:1109-12. [PMID: 25577191 PMCID: PMC4379410 DOI: 10.1093/molbev/msu411] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The estimation of substitution and recombination rates can provide important insights into the molecular evolution of protein-coding sequences. Here, we present a new computational framework, called "CodABC," to jointly estimate recombination, substitution and synonymous and nonsynonymous rates from coding data. CodABC uses approximate Bayesian computation with and without regression adjustment and implements a variety of codon models, intracodon recombination, and longitudinal sampling. CodABC can provide accurate joint parameter estimates from recombining coding sequences, often outperforming maximum-likelihood methods based on more approximate models. In addition, CodABC allows for the inclusion of several nuisance parameters such as those representing codon frequencies, transition matrices, heterogeneity across sites or invariable sites. CodABC is freely available from http://code.google.com/p/codabc/, includes a GUI, extensive documentation and ready-to-use examples, and can run in parallel on multicore machines.
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Affiliation(s)
- Miguel Arenas
- Centre for Molecular Biology "Severo Ochoa," Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain Departamento de Bioquímica, Genética e Inmunología, Universidad de Vigo, Vigo, Spain
| | - Joao S Lopes
- Instituto Gulbenkian de Ciencia, Oeiras, Portugal
| | - Mark A Beaumont
- School of Mathematical Sciences and School of Biological Sciences, University of Bristol, University Walk, Bristol, United Kingdom
| | - David Posada
- Departamento de Bioquímica, Genética e Inmunología, Universidad de Vigo, Vigo, Spain
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Angelis K, Albert J, Mamais I, Magiorkinis G, Hatzakis A, Hamouda O, Struck D, Vercauteren J, Wensing AMJ, Alexiev I, Åsjö B, Balotta C, Camacho RJ, Coughlan S, Griskevicius A, Grossman Z, Horban A, Kostrikis LG, Lepej S, Liitsola K, Linka M, Nielsen C, Otelea D, Paredes R, Poljak M, Puchhammer-Stöckl E, Schmit JC, Sönnerborg A, Staneková D, Stanojevic M, Boucher CAB, Kaplan L, Vandamme AM, Paraskevis D. Global Dispersal Pattern of HIV Type 1 Subtype CRF01_AE: A Genetic Trace of Human Mobility Related to Heterosexual Sexual Activities Centralized in Southeast Asia. J Infect Dis 2014; 211:1735-44. [PMID: 25512631 DOI: 10.1093/infdis/jiu666] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 11/24/2014] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Human immunodeficiency virus type 1 (HIV-1) subtype CRF01_AE originated in Africa and then passed to Thailand, where it established a major epidemic. Despite the global presence of CRF01_AE, little is known about its subsequent dispersal pattern. METHODS We assembled a global data set of 2736 CRF01_AE sequences by pooling sequences from public databases and patient-cohort studies. We estimated viral dispersal patterns, using statistical phylogeographic analysis run over bootstrap trees estimated by the maximum likelihood method. RESULTS We show that Thailand has been the source of viral dispersal to most areas worldwide, including 17 of 20 sampled countries in Europe. Japan, Singapore, Vietnam, and other Asian countries have played a secondary role in the viral dissemination. In contrast, China and Taiwan have mainly imported strains from neighboring Asian countries, North America, and Africa without any significant viral exportation. DISCUSSION The central role of Thailand in the global spread of CRF01_AE can be probably explained by the popularity of Thailand as a vacation destination characterized by sex tourism and by Thai emigration to the Western world. Our study highlights the unique case of CRF01_AE, the only globally distributed non-B clade whose global dispersal did not originate in Africa.
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Affiliation(s)
- Konstantinos Angelis
- Department of Hygiene, Epidemiology, and Medical Statistics, Medical School, University of Athens, Greece
| | - Jan Albert
- Department of Microbiology, Tumor, and Cell Biology Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Ioannis Mamais
- Department of Hygiene, Epidemiology, and Medical Statistics, Medical School, University of Athens, Greece
| | - Gkikas Magiorkinis
- Department of Hygiene, Epidemiology, and Medical Statistics, Medical School, University of Athens, Greece Department of Zoology, University of Oxford, United Kingdom
| | - Angelos Hatzakis
- Department of Hygiene, Epidemiology, and Medical Statistics, Medical School, University of Athens, Greece
| | | | | | - Jurgen Vercauteren
- Clinical and Epidemiological Virology, Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Belgium
| | | | - Ivailo Alexiev
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | | | | | - Ricardo J Camacho
- Centro de Malária e OutrasDoenças Tropicais and Unidade de Microbiologia, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Portugal
| | | | | | | | | | | | - Snjezana Lepej
- Department of Molecular Diagnostics and Flow Cytometry, University Hospital for Infectious Diseases Dr F. Mihaljevic, Zagreb, Croatia
| | - Kirsi Liitsola
- National Institute of Health and Welfare, Helsinki, Finland
| | - Marek Linka
- National Reference Laboratory of AIDS, National Institute of Health, Prague, Czech Republic
| | | | - Dan Otelea
- National Institute for Infectious Diseases Prof Dr Matei Bals, Bucharest, Romania
| | | | - Mario Poljak
- Faculty of Medicine, Slovenian HIV/AIDS Reference Center, University of Ljubljana, Slovenia
| | | | | | - Anders Sönnerborg
- Division of Infectious Diseases Division of Clinical Virology, Karolinska Institute Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | | | | | | | - Lauren Kaplan
- Alcohol Research Group, University California, Berkeley
| | - Anne-Mieke Vandamme
- Clinical and Epidemiological Virology, Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Belgium Centro de Malária e OutrasDoenças Tropicais and Unidade de Microbiologia, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Portugal
| | - Dimitrios Paraskevis
- Department of Hygiene, Epidemiology, and Medical Statistics, Medical School, University of Athens, Greece
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Faria NR, Rambaut A, Suchard MA, Baele G, Bedford T, Ward MJ, Tatem AJ, Sousa JD, Arinaminpathy N, Pépin J, Posada D, Peeters M, Pybus OG, Lemey P. HIV epidemiology. The early spread and epidemic ignition of HIV-1 in human populations. Science 2014; 346:56-61. [PMID: 25278604 PMCID: PMC4254776 DOI: 10.1126/science.1256739] [Citation(s) in RCA: 370] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Thirty years after the discovery of HIV-1, the early transmission, dissemination, and establishment of the virus in human populations remain unclear. Using statistical approaches applied to HIV-1 sequence data from central Africa, we show that from the 1920s Kinshasa (in what is now the Democratic Republic of Congo) was the focus of early transmission and the source of pre-1960 pandemic viruses elsewhere. Location and dating estimates were validated using the earliest HIV-1 archival sample, also from Kinshasa. The epidemic histories of HIV-1 group M and nonpandemic group O were similar until ~1960, after which group M underwent an epidemiological transition and outpaced regional population growth. Our results reconstruct the early dynamics of HIV-1 and emphasize the role of social changes and transport networks in the establishment of this virus in human populations.
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Affiliation(s)
- Nuno R Faria
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK. KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Minderbroedersstraat 10, B-3000 Leuven, Belgium
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Kings Buildings, West Mains Road, Edinburgh EH9 3JT, UK. Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA. Centre for Immunity, Infection and Evolution, University of Edinburgh, Kings Buildings, West Mains Road, Edinburgh EH9 3JT, UK
| | - Marc A Suchard
- Departments of Biomathematics and Human Genetics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA 90095-1766, USA. Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles, CA 90095-1766, USA
| | - Guy Baele
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Minderbroedersstraat 10, B-3000 Leuven, Belgium
| | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Melissa J Ward
- Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Kings Buildings, West Mains Road, Edinburgh EH9 3JT, UK
| | - Andrew J Tatem
- Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA. Department of Geography and Environment, University of Southampton, Highfield, Southampton, UK
| | - João D Sousa
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Minderbroedersstraat 10, B-3000 Leuven, Belgium. Centro de Malária e outras Doenças Tropicais and Unidade de Microbiologia, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Rua da Junqueira 100, 1349-008 Lisbon, Portugal
| | | | - Jacques Pépin
- Department of Microbiology and Infectious Diseases, Université de Sherbrooke, CHUS, 3001, 12ème Avenue Nord, Sherbrooke, QC J1H 5N4, Canada
| | - David Posada
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo 36310, Spain
| | - Martine Peeters
- Laboratoire Retrovirus, UMI233, Institut de Recherche pour le Développement and University of Montpellier, 911 Avenue Agropolis, BP5045, 34032 Montpellier, France
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK.
| | - Philippe Lemey
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Minderbroedersstraat 10, B-3000 Leuven, Belgium.
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50
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Bulla I, Schultz AK, Chesneau C, Mark T, Serea F. A model-based information sharing protocol for profile Hidden Markov Models used for HIV-1 recombination detection. BMC Bioinformatics 2014; 15:205. [PMID: 24946781 PMCID: PMC4230192 DOI: 10.1186/1471-2105-15-205] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 06/04/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In many applications, a family of nucleotide or protein sequences classified into several subfamilies has to be modeled. Profile Hidden Markov Models (pHMMs) are widely used for this task, modeling each subfamily separately by one pHMM. However, a major drawback of this approach is the difficulty of dealing with subfamilies composed of very few sequences. One of the most crucial bioinformatical tasks affected by the problem of small-size subfamilies is the subtyping of human immunodeficiency virus type 1 (HIV-1) sequences, i.e., HIV-1 subtypes for which only a small number of sequences is known. RESULTS To deal with small samples for particular subfamilies of HIV-1, we introduce a novel model-based information sharing protocol. It estimates the emission probabilities of the pHMM modeling a particular subfamily not only based on the nucleotide frequencies of the respective subfamily but also incorporating the nucleotide frequencies of all available subfamilies. To this end, the underlying probabilistic model mimics the pattern of commonality and variation between the subtypes with regards to the biological characteristics of HI viruses. In order to implement the proposed protocol, we make use of an existing HMM architecture and its associated inference engine. CONCLUSIONS We apply the modified algorithm to classify HIV-1 sequence data in the form of partial HIV-1 sequences and semi-artificial recombinants. Thereby, we demonstrate that the performance of pHMMs can be significantly improved by the proposed technique. Moreover, we show that our algorithm performs significantly better than Simplot and Bootscanning.
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Affiliation(s)
- Ingo Bulla
- Institut für Mathematik und Informatik, Universität Greifswald, Walther-Rathenau-Straße 47, 17487 Greifswald, Germany.
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