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Lebedev A, Kim K, Ozhmegova E, Antonova A, Kazennova E, Tumanov A, Kuznetsova A. Rev Protein Diversity in HIV-1 Group M Clades. Viruses 2024; 16:759. [PMID: 38793640 PMCID: PMC11125641 DOI: 10.3390/v16050759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 05/03/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
The HIV-1 Rev protein expressed in the early stage of virus replication is involved in the nuclear export of some forms of virus RNA. Naturally occurring polymorphisms in the Rev protein could influence its activity. The association between the genetic features of different virus variants and HIV infection pathogenesis has been discussed for many years. In this study, Rev diversity among HIV-1 group M clades was analyzed to note the signatures that could influence Rev activity and, subsequently, clinical characteristics. From the Los Alamos HIV Sequence Database, 4962 Rev sequences were downloaded and 26 clades in HIV-1 group M were analyzed for amino acid changes, conservation in consensus sequences, and the presence of clade-specific amino acid substitutions (CSSs) and the Wu-Kabat protein variability coefficient (WK). Subtypes G, CRF 02_AG, B, and A1 showed the largest amino acid changes and diversity. The mean conservation of the Rev protein was 80.8%. In consensus sequences, signatures that could influence Rev activity were detected. In 15 out of 26 consensus sequences, an insertion associated with the reduced export activity of the Rev protein, 95QSQGTET96, was identified. A total of 32 CSSs were found in 16 clades, wherein A6 had the 41Q substitution in the functionally significant region of Rev. The high values of WK coefficient in sites 51 and 82, located on the Rev interaction surface, indicate the susceptibility of these positions to evolutionary replacements. Thus, the noted signatures require further investigation.
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Affiliation(s)
- Aleksey Lebedev
- Gamaleya National Research Center for Epidemiology and Microbiology, 123098 Moscow, Russia; (K.K.); (E.O.); (A.A.); (E.K.); (A.T.)
- Mechnikov Scientific Research Institute of Vaccines and Serums, 105064 Moscow, Russia
| | - Kristina Kim
- Gamaleya National Research Center for Epidemiology and Microbiology, 123098 Moscow, Russia; (K.K.); (E.O.); (A.A.); (E.K.); (A.T.)
| | - Ekaterina Ozhmegova
- Gamaleya National Research Center for Epidemiology and Microbiology, 123098 Moscow, Russia; (K.K.); (E.O.); (A.A.); (E.K.); (A.T.)
| | - Anastasiia Antonova
- Gamaleya National Research Center for Epidemiology and Microbiology, 123098 Moscow, Russia; (K.K.); (E.O.); (A.A.); (E.K.); (A.T.)
| | - Elena Kazennova
- Gamaleya National Research Center for Epidemiology and Microbiology, 123098 Moscow, Russia; (K.K.); (E.O.); (A.A.); (E.K.); (A.T.)
| | - Aleksandr Tumanov
- Gamaleya National Research Center for Epidemiology and Microbiology, 123098 Moscow, Russia; (K.K.); (E.O.); (A.A.); (E.K.); (A.T.)
| | - Anna Kuznetsova
- Gamaleya National Research Center for Epidemiology and Microbiology, 123098 Moscow, Russia; (K.K.); (E.O.); (A.A.); (E.K.); (A.T.)
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2
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Klink GV, Kalinina OV, Bazykin GA. Changing selection on amino acid substitutions in Gag protein between major HIV-1 subtypes. Virus Evol 2024; 10:veae036. [PMID: 38808036 PMCID: PMC11131029 DOI: 10.1093/ve/veae036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 12/27/2023] [Accepted: 04/28/2024] [Indexed: 05/30/2024] Open
Abstract
Amino acid preferences at a protein site depend on the role of this site in protein function and structure as well as on external constraints. All these factors can change in the course of evolution, making amino acid propensities of a site time-dependent. When viral subtypes divergently evolve in different host subpopulations, such changes may depend on genetic, medical, and sociocultural differences between these subpopulations. Here, using our previously developed phylogenetic approach, we describe sixty-nine amino acid sites of the Gag protein of human immunodeficiency virus type 1 (HIV-1) where amino acids have different impact on viral fitness in six major subtypes of the type M. These changes in preferences trigger adaptive evolution; indeed, 32 (46 per cent) of these sites experienced strong positive selection at least in one of the subtypes. At some of the sites, changes in amino acid preferences may be associated with differences in immune escape between subtypes. The prevalence of an amino acid in a protein site within a subtype is only a poor predictor for whether this amino acid is preferred in this subtype according to the phylogenetic analysis. Therefore, attempts to identify the factors of viral evolution from comparative genomics data should integrate across multiple sources of information.
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Affiliation(s)
- Galya V Klink
- Laboratory of Molecular Evolution, Institute for Information Transmission Problems (Kharkevich Institute) of the Russian Academy of Sciences, Bolshoy Karetny per. 19, build.1, Moscow 127051, Russia
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoy Boulevard, 30, p.1, Skolkovo 121205, Russia
| | - Olga V Kalinina
- Drug Bioinformatics, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)/Helmholtz Centre for Infection Research (HZI), Campus E8.1, Saarbrücken 66123, Germany
- Center for Bioinformatics, Saarland University, Campus E2.1, Saarbrücken 66123, Germany
- Medical Faculty, Saarland University, Kirrberger Str. 100, Homburg 66421, Germany
| | - Georgii A Bazykin
- Laboratory of Molecular Evolution, Institute for Information Transmission Problems (Kharkevich Institute) of the Russian Academy of Sciences, Bolshoy Karetny per. 19, build.1, Moscow 127051, Russia
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3
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Li QH, Zhang YQ, Li EL, Guo Q, Chen XH, Wang FX, Wang JY. Characterization of an imported HIV-1 A1/A7/G recombinant in China. Virol J 2024; 21:3. [PMID: 38178224 PMCID: PMC10768240 DOI: 10.1186/s12985-023-02274-x] [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: 10/07/2023] [Accepted: 12/20/2023] [Indexed: 01/06/2024] Open
Abstract
BACKGROUND International migration has accelerated the HIV-1 spread across national borders, gradually reducing the restrictions on the geographical distribution of HIV-1 subtypes. Subtypes A and G are globally recognized as the third and sixth most dominant HIV-1 genotypes, mainly prevalent in Africa, but rarely detected in China. Here we reported an imported HIV-1 recombinant which was composed of sub-subtypes A1 and A7 of subtype A and subtype G genes in a Chinese female. This virus was the first HIV-1 recombinant including A7 genes reported in the world. CASE PRESENTATION The near full-length genome (NFLG) was obtained from the plasma sample of the female in an HIV-1 molecular epidemiological survey with 853 participants in China. Phylogenetic analyses showed that this NFLG sequence contains three A7 segments, four G segments and one A1 segment with seven breakpoints, and all these segments were closely related to HIV-1 references circulating in Africa. The evidence from epidemiological investigation indicated that this female participant had a more-than-two-years heterosexual contact history with a fixed partner from Nigeria, a country in west Africa, which further supported the results of phylogenetic analyses. By the Bayesian phylogenetic analyses, the times of most recent common ancestors (tMRCA) of the partial pol gene (nt2308-3284, A7 region) and full-length vpr-vpu plus partial env gene (nt5534-6858, G region) were estimated around 1989 and 1984, respectively. CONCLUSIONS In this study, by using the NFLG sequencing, we identified an imported HIV-1 A1/A7/G recombinant which was estimated to originate around 1980s in Africa and introduced into China with international migration. This study highlighted the complexity of the global HIV-1 epidemic, the necessity of using genome sequences to determine HIV-1 genotypes and the importance of real-time monitoring of HIV-1 infection among international migrants and travelers.
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Affiliation(s)
- Qing-Hai Li
- Genomics Research Center, College of Pharmacy, Harbin Medical University, Harbin, China
| | - Yun-Qi Zhang
- Department of Microbiology, Harbin Medical University, 157 Baojian Road, 150001, Harbin, China
- Heilongjiang Provincial Key Laboratory of Infection and Immunity, Harbin, China
| | - En-Long Li
- Department of Microbiology, Harbin Medical University, 157 Baojian Road, 150001, Harbin, China
- Heilongjiang Provincial Key Laboratory of Infection and Immunity, Harbin, China
| | - Qi Guo
- Genomics Research Center, College of Pharmacy, Harbin Medical University, Harbin, China
| | - Xiao-Hong Chen
- Department of Infectious Diseases, the Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Fu-Xiang Wang
- Department of Infectious Diseases, the Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
- Department of Infectious Diseases, the Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, China
| | - Jia-Ye Wang
- Department of Microbiology, Harbin Medical University, 157 Baojian Road, 150001, Harbin, China.
- Heilongjiang Provincial Key Laboratory of Infection and Immunity, Harbin, China.
- Heilongjiang Academy of Medical Sciences, Harbin, China.
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Zarudnaya MI, Potyahaylo AL, Kolomiets IM, Gorb LG. Genome sequence analysis suggests coevolution of the DIS, SD, and Psi hairpins in HIV-1 genomes. Virus Res 2022; 321:198910. [PMID: 36070810 DOI: 10.1016/j.virusres.2022.198910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 08/28/2022] [Accepted: 08/31/2022] [Indexed: 12/24/2022]
Abstract
HIV-1 RNA dimerization is a critical step in viral life cycle. It is a prerequisite for genome packaging and plays an important role in reverse transcription and recombination. Dimerization is promoted by the DIS (dimerization initiation site) hairpin located in the 5' leader of HIV-1 genome. Despite the high genetic diversity in HIV-1 group M, only five apical loops (AAGCGCGCA, AAGUGCGCA, AAGUGCACA, AGGUGCACA and AGUGCAC) are commonly found in DIS hairpins. We refer to the parent DISes with these apical loops as DISLai, DISTrans, DISF, DISMal, and DISC, respectively. Based on identity or similarity of DIS hairpins to parent DISes, we distributed HIV-1 M genomes into five dimerization groups. Comparison of the primary and secondary structures of DIS, SD and Psi hairpins in about 3000 HIV-1 M genomes showed that the mutation frequencies at particular nucleotide positions of these hairpins differ among the dimerization groups, and DISF may be an origin of other parent DISes. We found that DIS, SD and Psi hairpins have hundreds of variants, only some of them occurring rather frequently. The lower part of DIS hairpin with G x AGG internal loop is highly conserved in both HIV-1 and SIV genomes. We supposed that the G-quadruplex, located 56 nts downstream of the Gag start codon, may participate in switching of HIV-1 leader RNA from BMH (branched multiple hairpins) to LDI (long distance interaction) conformation.
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Affiliation(s)
- Margarita I Zarudnaya
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Akademika Zabolotnoho Str, Kyiv 03143, Ukraine
| | - Andriy L Potyahaylo
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Akademika Zabolotnoho Str, Kyiv 03143, Ukraine
| | - Iryna M Kolomiets
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Akademika Zabolotnoho Str, Kyiv 03143, Ukraine
| | - Leonid G Gorb
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Akademika Zabolotnoho Str, Kyiv 03143, Ukraine.
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Da Silva RKM, Morais J, Foley BT, Bello G, Morgado MG, Guimarães ML. Identification of a new circulating recombinant form of human immunodeficiency virus type 1, CRF124_cpx involving subtypes A, G, H, and CRF27_cpx in Angola. Front Microbiol 2022; 13:992640. [PMID: 36325024 PMCID: PMC9619209 DOI: 10.3389/fmicb.2022.992640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 09/14/2022] [Indexed: 12/03/2022] Open
Abstract
Angola, located in Central Africa, has around 320,000 (270,000–380,000) people living with human immunodeficiency virus (HIV)/AIDS, equivalent to 1% of the country’s population at the end of 2021. A previous study conducted in 2012, using Angolan samples collected between 2008 and 2010 revealed a high prevalence of HIV-1 recombinants, around 42% of sequences, with 21% showing the same UH profile in partial pol region which were grouped into a monophyletic cluster with high bootstrap support. Thus, the objective of the present work was to obtain complete genomes of those sequences and characterize them, aiming at a description of a new circulating recombinant form (CRF). Whole blood from nine HIV-1 UH pol-infected individuals had their genomic DNA extracted, and nested PCR was used to amplify seven overlapping fragments targeting the full-length HIV-1 genome. The final classification was based on maximum likelihood trees, and recombination analyses were performed using a bootscan from the Simplot program. BLAST and Los Alamos Database inspections were used to search other similar H-like pol sequences. Complete genome amplification was possible for three samples, partial genomes were obtained for the other three, and only pol was available for the remaining three sequences. Bootscan analysis of the two whole-genome and three partial genome sequences retrieved from people living with HIV/AIDS (PLHIVA) without epidemiological linkage showed the same complex recombination profile involving HIV-1 subtypes A/G/H/CRF27_cpx, with a total of six recombinant breakpoints, aiming to classify a new HIV-1 CRF124_cpx. We found no other full-length HIV-1 genomes with the same mosaic profile; however, we identified 33 partial pol sequences, mainly sampled from Angola between 2001 to 2019, with the same H-like profile. Bayesian analysis of H and H-like pol sequences indicates that CRF124_cpx probably originated in Angola at mid-1970s, indicating that this CRF has been circulating in the country for a long time. In summary, our study describes a new CRF circulating principally in Angola and highlights the importance of continuing molecular surveillance studies, especially in countries with high molecular diversity of HIV.
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Affiliation(s)
| | - Joana Morais
- Laboratório de Biologia Molecular, Instituto Nacional de Investigação em Saúde, Ministério da Saúde de Angola, Luanda, Angola
- Departamento de Bioquímica, Faculdade de Medicina, Universidade Agostinho Neto, Luanda, Angola
| | - Brian Thomas Foley
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Gonzalo Bello
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Mariza Gonçalves Morgado
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Monick Lindenmeyer Guimarães
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
- *Correspondence: Monick Lindenmeyer Guimarães,
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6
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Preda M, Manolescu LCS. Romania, a Harbour of HIV-1 Subtype F1: Where Are We after 33 Years of HIV-1 Infection? Viruses 2022; 14:v14092081. [PMID: 36146886 PMCID: PMC9503723 DOI: 10.3390/v14092081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/09/2022] [Accepted: 09/16/2022] [Indexed: 11/16/2022] Open
Abstract
Infection with the human immunodeficiency virus (HIV) has been a major public health concern worldwide for more than 30 years, including in Romania. The F1 HIV-1 subtype was exported from Angola to Romania most probably because of the two countries' close political connections. Patients infected with HIV-1 via re-used and improperly sterilized injection equipment and through transfusions of unscreened blood, also known as the "Romanian cohort", were the most common type of HIV-1 infection in Romania in the early 1990s, when the virus's presence was recognized. Recently, subtype B started to increase in our country, mostly diagnosed in people using intravenous drugs or in men having sex with men. The evolution of the HIV-1 infection in Romania has been unique, with a dominance of the subtype F1, making it different from other countries in Europe.
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Affiliation(s)
- Mădălina Preda
- Department of Microbiology, Parasitology and Virology, Faculty of Midwives and Nursing, "Carol Davila" University of Medicine and Pharmacy, 020021 Bucharest, Romania
- Research Department, Marius Nasta Institute of Pneumology, 050159 Bucharest, Romania
| | - Loredana Cornelia Sabina Manolescu
- Department of Microbiology, Parasitology and Virology, Faculty of Midwives and Nursing, "Carol Davila" University of Medicine and Pharmacy, 020021 Bucharest, Romania
- Department of Virology, Institute of Virology "Stefan S. Nicolau", 030304 Bucharest, Romania
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7
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Revisiting the recombinant history of HIV-1 group M with dynamic network community detection. Proc Natl Acad Sci U S A 2022; 119:e2108815119. [PMID: 35500121 PMCID: PMC9171507 DOI: 10.1073/pnas.2108815119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Recombination is a major mechanism through which HIV type 1 (HIV-1) maintains genetic diversity and interferes with viral eradication efforts. There is growing evidence demonstrating a recombinant origin of primate lentiviruses including HIV-1 group M (HIV-1/M). Inferring the extent of recombination across the entire HIV-1/M genome is of great importance as it provides deeper insights into the origin, dynamics, and evolution of the global pandemic. Here we propose an alternative method that can reconstruct the extent of genome-wide recombination in HIV-1, uncover reticulate patterns, and serve as a framework for HIV-1 classification. Our method provides an alternative approach for understanding the roles of virus recombination in the early evolutionary history of zoonosis for other emerging viruses. The prevailing abundance of full-length HIV type 1 (HIV-1) genome sequences provides an opportunity to revisit the standard model of HIV-1 group M (HIV-1/M) diversity that clusters genomes into largely nonrecombinant subtypes, which is not consistent with recent evidence of deep recombinant histories for simian immunodeficiency virus (SIV) and other HIV-1 groups. Here we develop an unsupervised nonparametric clustering approach, which does not rely on predefined nonrecombinant genomes, by adapting a community detection method developed for dynamic social network analysis. We show that this method (dynamic stochastic block model [DSBM]) attains a significantly lower mean error rate in detecting recombinant breakpoints in simulated data (quasibinomial generalized linear model (GLM), P<8×10−8), compared to other reference-free recombination detection programs (genetic algorithm for recombination detection [GARD], recombination detection program 4 [RDP4], and RDP5). When this method was applied to a representative sample of n = 525 actual HIV-1 genomes, we determined k = 29 as the optimal number of DSBM clusters and used change-point detection to estimate that at least 95% of these genomes are recombinant. Further, we identified both known and undocumented recombination hotspots in the HIV-1 genome and evidence of intersubtype recombination in HIV-1 subtype reference genomes. We propose that clusters generated by DSBM can provide an informative framework for HIV-1 classification.
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8
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Giovanetti M, Farcomeni S, Sernicola L, Virtuoso S, Sulekova LF, Maggiorella MT, Buttò S, Taliani G, Ciccozzi M, Borsetti A. Analysis of HIV‐1 integrase genotypes and polymorphisms among integrase inhibitors‐based antiretroviral treatment naïve patients in South Sudan. J Med Virol 2022; 94:3320-3327. [DOI: 10.1002/jmv.27713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 02/16/2022] [Accepted: 03/09/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Marta Giovanetti
- Reference Laboratory of Flavivirus, Oswaldo Cruz Institute, Fundação Oswaldo CruzRio de JaneiroBrazil
- Laboratório de Genética Celular e Molecular, ICBUniversidade Federal de Minas GeraisBelo HorizonteMinas GeraisBrazil
- Medical Statistics and Molecular EpidemiologyUniversity Campus Bio‐Medico of RomeRomeItaly
| | - Stefania Farcomeni
- National HIV/AIDS Research Center, Istituto Superiore di SanitàV. le Regina Elena 29900161RomeItaly
| | - Leonardo Sernicola
- National HIV/AIDS Research Center, Istituto Superiore di SanitàV. le Regina Elena 29900161RomeItaly
| | - Sara Virtuoso
- National HIV/AIDS Research Center, Istituto Superiore di SanitàV. le Regina Elena 29900161RomeItaly
| | | | - Maria T. Maggiorella
- National HIV/AIDS Research Center, Istituto Superiore di SanitàV. le Regina Elena 29900161RomeItaly
| | - Stefano Buttò
- National HIV/AIDS Research Center, Istituto Superiore di SanitàV. le Regina Elena 29900161RomeItaly
| | - Gloria Taliani
- Chronic Infectious Diseases Unit, Policlinico Umberto I“Sapienza” University of RomeRomeItaly
| | - Massimo Ciccozzi
- Medical Statistics and Molecular EpidemiologyUniversity Campus Bio‐Medico of RomeRomeItaly
| | - Alessandra Borsetti
- National HIV/AIDS Research Center, Istituto Superiore di SanitàV. le Regina Elena 29900161RomeItaly
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9
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Wagner T, Zuckerman NS, Halperin T, Chemtob D, Levy I, Elbirt D, Shachar E, Olshtain-Pops K, Elinav H, Chowers M, Itsomin V, Riesenberg K, Wax M, Shirazi R, Gozlan Y, Matus N, Girshengorn S, Marom R, Mendelson E, Turner D, Mor O. Epidemiology and Transmitted HIV-1 Drug Resistance among Treatment-Naïve Individuals in Israel, 2010-2018. Viruses 2021; 14:v14010071. [PMID: 35062274 PMCID: PMC8779053 DOI: 10.3390/v14010071] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 12/27/2021] [Accepted: 12/28/2021] [Indexed: 01/22/2023] Open
Abstract
Despite the low prevalence of HIV-1 in Israel, continuous waves of immigration may have impacted the local epidemic. We characterized all people diagnosed with HIV-1 in Israel in 2010–2018. The demographics and clinical data of all individuals (n = 3639) newly diagnosed with HIV-1 were retrieved. Subtypes, transmitted drug-resistance mutations (TDRM), and phylogenetic relations, were determined in >50% of them. In 39.1%, HIV-1 transmission was through heterosexual contact; 34.3% were men who have sex with men (MSM); and 10.4% were people who inject drugs. Many (>65%) were immigrants. Israeli-born individuals were mostly (78.3%) MSM, whereas only 9% of those born in Sub-Saharan Africa (SSA), Eastern Europe and Central Asia (EEU/CA), were MSM. The proportion of individuals from SSA decreased through the years 2010–2018 (21.1% in 2010–2012; 16.8% in 2016–2018) whereas those from EEU/CA increased significantly (21% in 2010–2012; 27.8% in 2016–2018, p < 0.001). TDRM were identified in 12.1%; 3.7, 3.3 and 6.6% had protease inhibitors (PI), nucleotide reverse transcriptase inhibitors (NRTI), and non-nucleoside reverse transcriptase inhibitors (NNRTI) TDRM, respectively, with the overall proportion remaining stable in the studied years. None had integrase TDRM. Subtype B was present in 43.9%, subtype A in 25.2% (A6 in 22.8 and A1 in 2.4%) and subtype C in 17.1% of individuals. Most MSM had subtype B. Subtype C carriers formed small clusters (with one unexpected MSM cluster), A1 formed a cluster mainly of locally-born patients with NNRTI mutations, and A6 formed a looser cluster of individuals mainly from EEU. Israelis, <50 years old, carrying A1, had the highest risk for having TDRM. In conclusion, an increase in immigrants from EEU/CA and a decrease in those from SSA characterized the HIV-1 epidemic in 2010–2018. Baseline resistance testing should still be recommended to identify TDRM, and improve surveillance and care.
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Affiliation(s)
- Tali Wagner
- Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 6997801, Israel; (T.W.); (I.L.); (M.C.); (E.M.); (D.T.)
- Chaim Sheba Medical Center, National HIV-1 and Viral Hepatitis Reference Laboratory, Ramat Gan 5262112, Israel; (N.S.Z.); (M.W.); (R.S.); (Y.G.)
| | - Neta S. Zuckerman
- Chaim Sheba Medical Center, National HIV-1 and Viral Hepatitis Reference Laboratory, Ramat Gan 5262112, Israel; (N.S.Z.); (M.W.); (R.S.); (Y.G.)
| | - Tami Halperin
- Tel-Aviv Sourasky Medical Center, Crusaid Kobler AIDS Center, Tel Aviv 6423906, Israel; (T.H.); (N.M.); (S.G.); (R.M.)
| | - Daniel Chemtob
- Faculty of Medicine, Braun School of Public Health & Community Medicine, Hebrew University-Hadassah Medical School, Jerusalem 9112102, Israel; (D.C.); (D.E.); (H.E.)
- Tuberculosis and AIDS Department, Ministry of Health, Jerusalem 9101002, Israel
| | - Itzchak Levy
- Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 6997801, Israel; (T.W.); (I.L.); (M.C.); (E.M.); (D.T.)
- Chaim Sheba Medical Center, Infectious Disease Unit, Ramat Gan 5262112, Israel
| | - Daniel Elbirt
- Faculty of Medicine, Braun School of Public Health & Community Medicine, Hebrew University-Hadassah Medical School, Jerusalem 9112102, Israel; (D.C.); (D.E.); (H.E.)
- Immunology, Kaplan Medical Center, Rehovot 76100, Israel
| | - Eduardo Shachar
- Immunology Unit, Rambam Health Care Campus, Haifa 3109601, Israel;
- Rappaport Faculty of Medicine, Institute of Technology, Technion, Haifa 3200003, Israel
| | | | - Hila Elinav
- Faculty of Medicine, Braun School of Public Health & Community Medicine, Hebrew University-Hadassah Medical School, Jerusalem 9112102, Israel; (D.C.); (D.E.); (H.E.)
- Hadassah Medical Center, Jerusalem 9112102, Israel;
| | - Michal Chowers
- Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 6997801, Israel; (T.W.); (I.L.); (M.C.); (E.M.); (D.T.)
- Infectious Diseases, Meir Medical Center, Kfar Saba 4428164, Israel
| | | | - Klaris Riesenberg
- Faculty of Health Sciences, Goldman Medical School, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel;
- Soroka Medical Center, Infectious Disease Institute, Beer-Sheva 84101, Israel
| | - Marina Wax
- Chaim Sheba Medical Center, National HIV-1 and Viral Hepatitis Reference Laboratory, Ramat Gan 5262112, Israel; (N.S.Z.); (M.W.); (R.S.); (Y.G.)
| | - Rachel Shirazi
- Chaim Sheba Medical Center, National HIV-1 and Viral Hepatitis Reference Laboratory, Ramat Gan 5262112, Israel; (N.S.Z.); (M.W.); (R.S.); (Y.G.)
| | - Yael Gozlan
- Chaim Sheba Medical Center, National HIV-1 and Viral Hepatitis Reference Laboratory, Ramat Gan 5262112, Israel; (N.S.Z.); (M.W.); (R.S.); (Y.G.)
| | - Natasha Matus
- Tel-Aviv Sourasky Medical Center, Crusaid Kobler AIDS Center, Tel Aviv 6423906, Israel; (T.H.); (N.M.); (S.G.); (R.M.)
| | - Shirley Girshengorn
- Tel-Aviv Sourasky Medical Center, Crusaid Kobler AIDS Center, Tel Aviv 6423906, Israel; (T.H.); (N.M.); (S.G.); (R.M.)
| | - Rotem Marom
- Tel-Aviv Sourasky Medical Center, Crusaid Kobler AIDS Center, Tel Aviv 6423906, Israel; (T.H.); (N.M.); (S.G.); (R.M.)
| | - Ella Mendelson
- Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 6997801, Israel; (T.W.); (I.L.); (M.C.); (E.M.); (D.T.)
- Chaim Sheba Medical Center, National HIV-1 and Viral Hepatitis Reference Laboratory, Ramat Gan 5262112, Israel; (N.S.Z.); (M.W.); (R.S.); (Y.G.)
| | - Dan Turner
- Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 6997801, Israel; (T.W.); (I.L.); (M.C.); (E.M.); (D.T.)
- Tel-Aviv Sourasky Medical Center, Crusaid Kobler AIDS Center, Tel Aviv 6423906, Israel; (T.H.); (N.M.); (S.G.); (R.M.)
| | - Orna Mor
- Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 6997801, Israel; (T.W.); (I.L.); (M.C.); (E.M.); (D.T.)
- Chaim Sheba Medical Center, National HIV-1 and Viral Hepatitis Reference Laboratory, Ramat Gan 5262112, Israel; (N.S.Z.); (M.W.); (R.S.); (Y.G.)
- Correspondence: ; Tel.: +972-3-530-2458
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10
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Abstract
Background HIV outbreaks in the Former Soviet Union (FSU) countries were characterized by repeated transmission of the HIV variant AFSU, which is now classified as a distinct subtype A sub-subtype called A6. The current study used phylogenetic/phylodynamic and signature mutation analyses to determine likely evolutionary relationship between subtype A6 and other subtype A sub-subtypes. Methods For this study, an initial Maximum Likelihood phylogenetic analysis was performed using a total of 553 full-length, publicly available, reverse transcriptase sequences, from A1, A2, A3, A4, A5, and A6 sub-subtypes of subtype A. For phylogenetic clustering and signature mutation analysis, a total of 5961 and 3959 pol and env sequences, respectively, were used. Results Phylogenetic and signature mutation analysis showed that HIV-1 sub-subtype A6 likely originated from sub-subtype A1 of African origin. A6 and A1 pol and env genes shared several signature mutations that indicate genetic similarity between the two subtypes. For A6, tMRCA dated to 1975, 15 years later than that of A1. Conclusion The current study provides insights into the evolution and diversification of A6 in the backdrop of FSU countries and indicates that A6 in FSU countries evolved from A1 of African origin and is getting bridged outside the FSU region.
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11
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Zhao Z, Fagerlund R, Tossavainen H, Hopfensperger K, Lotke R, Srinivasachar Badarinarayan S, Kirchhoff F, Permi P, Sato K, Sauter D, Saksela K. Evolutionary plasticity of SH3 domain binding by Nef proteins of the HIV-1/SIVcpz lentiviral lineage. PLoS Pathog 2021; 17:e1009728. [PMID: 34780577 PMCID: PMC8629392 DOI: 10.1371/journal.ppat.1009728] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 11/29/2021] [Accepted: 10/28/2021] [Indexed: 11/18/2022] Open
Abstract
The accessory protein Nef of human and simian immunodeficiency viruses (HIV and SIV) is an important pathogenicity factor known to interact with cellular protein kinases and other signaling proteins. A canonical SH3 domain binding motif in Nef is required for most of these interactions. For example, HIV-1 Nef activates the tyrosine kinase Hck by tightly binding to its SH3 domain. An archetypal contact between a negatively charged SH3 residue and a highly conserved arginine in Nef (Arg77) plays a key role here. Combining structural analyses with functional assays, we here show that Nef proteins have also developed a distinct structural strategy—termed the "R-clamp”—that favors the formation of this salt bridge via buttressing Arg77. Comparison of evolutionarily diverse Nef proteins revealed that several distinct R-clamps have evolved that are functionally equivalent but differ in the side chain compositions of Nef residues 83 and 120. Whereas a similar R-clamp design is shared by Nef proteins of HIV-1 groups M, O, and P, as well as SIVgor, the Nef proteins of SIV from the Eastern chimpanzee subspecies (SIVcpzP.t.s.) exclusively utilize another type of R-clamp. By contrast, SIV of Central chimpanzees (SIVcpzP.t.t.) and HIV-1 group N strains show more heterogenous R-clamp design principles, including a non-functional evolutionary intermediate of the aforementioned two classes. These data add to our understanding of the structural basis of SH3 binding and kinase deregulation by Nef, and provide an interesting example of primate lentiviral protein evolution. Viral replication depends on interactions with a plethora of host cell proteins. Cellular protein interactions are typically mediated by specialized binding modules, such as the SH3 domain. To gain access to host cell regulation viruses have evolved to contain SH3 domain binding sites in their proteins, a notable example of which is the HIV-1 Nef protein. Here we show that during the primate lentivirus evolution the structural strategy that underlies the avid binding of Nef to cellular SH3 domains, which we have dubbed the R-clamp, has been generated via alternative but functionally interchangeable molecular designs. These patterns of SH3 recognition depend on the amino acid combinations at the positions corresponding to residues 83 and 120 in the consensus HIV-1 Nef sequence, and are distinctly different in Nef proteins from SIVs of Eastern and Central chimpanzees, gorillas, and the four groups of HIV-1 that have independently originated from the latter two. These results highlight the evolutionary plasticity of viral proteins, and have implications on therapeutic development aiming to interfere with SH3 binding of Nef.
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Affiliation(s)
- Zhe Zhao
- Department of Virology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Riku Fagerlund
- Department of Virology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Helena Tossavainen
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Kristina Hopfensperger
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Tübingen, Germany
| | - Rishikesh Lotke
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Tübingen, Germany
| | | | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Perttu Permi
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
- Department of Chemistry, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Kei Sato
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Daniel Sauter
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Tübingen, Germany
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Kalle Saksela
- Department of Virology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- * E-mail:
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12
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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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13
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Mendes Da Silva RK, Monteiro de Pina Araujo II, Venegas Maciera K, Gonçalves Morgado M, Lindenmeyer Guimarães M. Genetic Characterization of a New HIV-1 Sub-Subtype A in Cabo Verde, Denominated A8. Viruses 2021; 13:v13061093. [PMID: 34201179 PMCID: PMC8230070 DOI: 10.3390/v13061093] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 05/13/2021] [Accepted: 05/15/2021] [Indexed: 12/16/2022] Open
Abstract
Previous molecular characterization of Human immunodeficiency virus (HIV-1) samples from Cabo Verde pointed out a vast HIV-1 pol diversity, with several subtypes and recombinant forms, being 5.2% classified as AU-pol. Thus, the aim of the present study was to improve the characterization of these AU sequences. The genomic DNA of seven HIV-1 AU pol-infected individuals were submitted to four overlapping nested-PCR fragments aiming to compose the full-length HIV-1 genome. The final classification was based on phylogenetic trees that were generated using the maximum likelihood and bootscan analysis. The genetic distances were calculated using Mega 7.0 software. Complete genome amplification was possible for two samples, and partial genomes were obtained for the other five. These two samples grouped together with a high support value, in a separate branch from the other sub-subtypes A and CRF26_A5U. No recombination was verified at bootscan, leading to the classification of a new sub-subtype A. The intragroup genetic distance from the new sub-subtype A at a complete genome was 5.2%, and the intergroup genetic varied from 8.1% to 19.0% in the analyzed fragments. Our study describes a new HIV-1 sub-subtype A and highlights the importance of continued molecular surveillance studies, mainly in countries with high HIV molecular diversity.
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Affiliation(s)
- Rayana Katylin Mendes Da Silva
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-360, Brazil; (R.K.M.D.S.); (K.V.M.); (M.G.M.)
| | | | - Karine Venegas Maciera
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-360, Brazil; (R.K.M.D.S.); (K.V.M.); (M.G.M.)
| | - Mariza Gonçalves Morgado
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-360, Brazil; (R.K.M.D.S.); (K.V.M.); (M.G.M.)
| | - Monick Lindenmeyer Guimarães
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-360, Brazil; (R.K.M.D.S.); (K.V.M.); (M.G.M.)
- Correspondence: ; Tel.: +55-21-3865-8154
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14
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Adhiambo M, Makwaga O, Adungo F, Kimani H, Mulama DH, Korir JC, Mwau M. Human immunodeficiency virus (HIV) type 1 genetic diversity in HIV positive individuals on antiretroviral therapy in a cross-sectional study conducted in Teso, Western Kenya. Pan Afr Med J 2021; 38:335. [PMID: 34046145 PMCID: PMC8140725 DOI: 10.11604/pamj.2021.38.335.26357] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 04/01/2021] [Indexed: 11/16/2022] Open
Abstract
Introduction high HIV-1 infection rates and genetic diversity especially in African population pose significant challenges in HIV-1 clinical management and drug design and development. HIV-1 is a major health challenge in Kenya and causes mortality and morbidity in the country as well as straining the healthcare system and the economy. This study sought to identify HIV-1 genetic subtypes circulating in Teso, Western Kenya which borders the Republic of Uganda. Methods a cross-sectional study was conducted in January 2019 to December 2019. Sequencing of the partial pol gene was carried out on 80 HIV positive individuals on antiretroviral therapy. Subtypes and recombinant forms were generated using the jumping profile hidden Markov model. Alignment of the sequences was done using ClustalW program and phylogenetic tree constructed using MEGA7 neighbor-joining method. Results sixty three samples were successful sequenced. In the analysis of these sequences, it was observed that HIV-1 subtype A1 was predominant 43 (68.3%) followed by D 8 (12.7%) and 1 (1.6%) each of C, G and B and inter-subtype recombinants A1-D 3 (4.8%), A1-B 2 (3.2%) and 1 (1.6%) each of A1-A2, A1-C, BC and BD. Phylogenetic analysis of these sequences showed close clustering of closely related and unrelated sequences with reference sequences. Conclusion there was observed increased genetic diversity of HIV-1 subtypes which not only pose a challenge in disease control and management but also drug design and development. Therefore, there is need for continued surveillance to enhance future understanding of the geographical distribution and transmission patterns of the HIV epidemic.
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Affiliation(s)
- Maureen Adhiambo
- Department of Biological Sciences, Masinde Muliro University of Science and Technology, Kakamega, Kenya.,Department of Infectious Diseases Control Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Olipher Makwaga
- Department of Biological Sciences, Masinde Muliro University of Science and Technology, Kakamega, Kenya.,Department of Infectious Diseases Control Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Ferdinard Adungo
- Department of Infectious Diseases Control Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Humphrey Kimani
- Department of Infectious Diseases Control Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - David Hughes Mulama
- Department of Biological Sciences, Masinde Muliro University of Science and Technology, Kakamega, Kenya
| | - Jackson Cheruiyot Korir
- Department of Biological Sciences, Masinde Muliro University of Science and Technology, Kakamega, Kenya
| | - Matilu Mwau
- Department of Infectious Diseases Control Research, Kenya Medical Research Institute, Nairobi, Kenya
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15
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Parczewski M, Scheibe K, Witak-Jędra M, Pynka M, Aksak-Wąs B, Urbańska A. Infection with HIV-1 subtype D adversely affects the live expectancy independently of antiretroviral drug use. INFECTION GENETICS AND EVOLUTION 2021; 90:104754. [PMID: 33540086 DOI: 10.1016/j.meegid.2021.104754] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 01/20/2021] [Accepted: 01/29/2021] [Indexed: 11/17/2022]
Abstract
INTRODUCTION HIV-1 subtypes have been associated with less favourable clinical profiles, differences in disease progression and higher risk of neurocognitive deficit. In this study we aimed to analyse the long term survival disparities between patients infected with the most common HIV-1 variants observed in Poland. METHODS For the study data from 518 Caucasian non-immigrant patients of Polish origin infected with divergent HIV subtypes and variants [subtype A (n = 35, 6.8%), subtype B (n = 386, 74.5%), subtype C (n = 13, 2.5%), subtype D (n = 58, 11.19%) or other non-A,B,C,D (n = 26, 5.01%)variants] were analysed. Subtyping was performed using the partial pol (reverse transcriptase and protease) sequencing. HIV variant was coupled with clinical, virologic and survival data censored at 20 years of observation. Overall survival and on antiretroviral treatment survival was analysed using Kaplan-Meyer as well as unadjusted and multivariate Cox proportional hazards models. RESULTS Significantly higher mortality was observed among subtype D (28.8%) infected subjects compared to subtype B (11.7%, p = 0.0004). Increased risk of death among subtype D cases remained significant when cART treated individuals were analysed, with on-treatment mortality of 26.9% for subtype D (p = 0.006) compared to 10.73% in subtype B infected cases. Kaplan-Meyer survival estimates differed significantly across all investigated HIV-1 variant groups when overall 20 year mortality was analysed (log rank p = 0.029), being non-significant for the cART treated group. In multivariate model of overall 20 year survival, adjusted for age at diagnosis, gender, HCV and AIDS status, lymphocyte CD4 count, transmission route and HIV viral load, only age and subtype D were independently associated with higher likelihood of death [HR: 1.08 (95%CI: 1.03-1.14, p = 0.002) and HR: 7.91 (95%CI:2.33-26.86), p < 0.001, respectively]. In the on-treatment (cART) multivariate model of 20 year survival adjusted for the same parameters only subtype D remained as the independent factor associated with higher mortality risk [HR: 4.24 (95%CI:1.31-13.7), p = 0.02]. CONCLUSIONS Subtype D has an independent deleterious effect of survival, even in the setting of antiretroviral treatment. Observed effect indicated higher clinical vigilance for patients infected with this subtype even after long time of stable antiretroviral treatment.
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Affiliation(s)
- Miłosz Parczewski
- Department of Infectious, Tropical Diseases and Immune Deficiency, Pomeranian Medical University in Szczecin, Szczecin, Poland.
| | - Kaja Scheibe
- Department of Infectious, Tropical Diseases and Immune Deficiency, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Magdalena Witak-Jędra
- Department of Infectious, Tropical Diseases and Immune Deficiency, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Magdalena Pynka
- Department of Infectious, Tropical Diseases and Immune Deficiency, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Bogusz Aksak-Wąs
- Department of Infectious, Tropical Diseases and Immune Deficiency, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Anna Urbańska
- Department of Infectious, Tropical Diseases and Immune Deficiency, Pomeranian Medical University in Szczecin, Szczecin, Poland
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16
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Santos-Pereira A, Magalhães C, Araújo PMM, Osório NS. Evolutionary Genetics of Mycobacterium tuberculosis and HIV-1: "The Tortoise and the Hare". Microorganisms 2021; 9:147. [PMID: 33440808 PMCID: PMC7827287 DOI: 10.3390/microorganisms9010147] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 12/24/2020] [Accepted: 01/06/2021] [Indexed: 12/16/2022] Open
Abstract
The already enormous burden caused by Mycobacterium tuberculosis and Human Immunodeficiency Virus type 1 (HIV-1) alone is aggravated by co-infection. Despite obvious differences in the rate of evolution comparing these two human pathogens, genetic diversity plays an important role in the success of both. The extreme evolutionary dynamics of HIV-1 is in the basis of a robust capacity to evade immune responses, to generate drug-resistance and to diversify the population-level reservoir of M group viral subtypes. Compared to HIV-1 and other retroviruses, M. tuberculosis generates minute levels of genetic diversity within the host. However, emerging whole-genome sequencing data show that the M. tuberculosis complex contains at least nine human-adapted phylogenetic lineages. This level of genetic diversity results in differences in M. tuberculosis interactions with the host immune system, virulence and drug resistance propensity. In co-infected individuals, HIV-1 and M. tuberculosis are likely to co-colonize host cells. However, the evolutionary impact of the interaction between the host, the slowly evolving M. tuberculosis bacteria and the HIV-1 viral "mutant cloud" is poorly understood. These evolutionary dynamics, at the cellular niche of monocytes/macrophages, are also discussed and proposed as a relevant future research topic in the context of single-cell sequencing.
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Affiliation(s)
- Ana Santos-Pereira
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal; (A.S.-P.); (C.M.); (P.M.M.A.)
- ICVS/3B’s-T Government Associate Laboratory, 4710-057 Braga/Guimarães, Portugal
| | - Carlos Magalhães
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal; (A.S.-P.); (C.M.); (P.M.M.A.)
- ICVS/3B’s-T Government Associate Laboratory, 4710-057 Braga/Guimarães, Portugal
| | - Pedro M. M. Araújo
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal; (A.S.-P.); (C.M.); (P.M.M.A.)
- ICVS/3B’s-T Government Associate Laboratory, 4710-057 Braga/Guimarães, Portugal
| | - Nuno S. Osório
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal; (A.S.-P.); (C.M.); (P.M.M.A.)
- ICVS/3B’s-T Government Associate Laboratory, 4710-057 Braga/Guimarães, Portugal
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17
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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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18
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Capoferri AA, Lamers SL, Grabowski MK, Rose R, Wawer MJ, Serwadda D, Gray RH, Quinn TC, Kigozi G, Kagaayi J, Laeyendecker O, Abeler-Dörner L, Ayles H, Bonsall D, Bowden R, Calvez V, Cohen M, Denis A, Frampton D, de Oliveira T, Essex M, Fidler S, Fraser C, Golubchik T, Hayes R, Herbeck JT, Hoppe A, Kaleebu P, Kellam P, Kityo C, Leigh-Brown A, Lingappa JR, Novitsky V, Paton N, Pillay D, Rambaut A, Ratmann O, Seeley J, Ssemwanga D, Tanser F. Recombination Analysis of Near Full-Length HIV-1 Sequences and the Identification of a Potential New Circulating Recombinant Form from Rakai, Uganda. AIDS Res Hum Retroviruses 2020; 36:467-474. [PMID: 31914792 DOI: 10.1089/aid.2019.0150] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Phylogenetics And Networks for Generalized HIV Epidemics in Africa (PANGEA-HIV) consortium has been vital in the generation and examination of near full-length HIV-1 sequences generated from Sub-Saharan Africa. In this study, we examined a subset (n = 275) of sequences from Rakai, Uganda, collected between August 2011 and January 2015. Sequences were initially screened with COMET for subtyping and then evaluated using bootscanning and phylogenetic inference. Among 275 sequences, 38.6% were subtype D, 19.3% were subtype A, 2.9% were subtype C, and 39.3% were recombinant. The recombinants were structurally diverse in the number of breakpoints observed, the location of recombinant segments, and represented subtypes, with AD recombinants accounting for the majority of all recombinants (29.8%). Within the AD subpopulation, we identified a potential new circulating recombinant form in five individuals where the polymerase gene was subtype D and most of env was subtype A (D-A junctures at HXB2 6760 and 8709). While the breakpoints were identical for the viruses from these individuals, the viral fragments did not cluster together. These results suggest selection for a viral strain where properties of the subtype A and subtype D portions of the virus confer a survival advantage. The continued study of recombinants will increase our breadth of knowledge for the genetic diversity and evolution of HIV-1, which can further contribute to our understanding toward a universal HIV-1 vaccine.
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Affiliation(s)
- Adam A. Capoferri
- The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Mary Kate Grabowski
- The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Rakai Health Sciences Program, Entebbe, Uganda
| | | | - Maria J. Wawer
- The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Rakai Health Sciences Program, Entebbe, Uganda
| | - David Serwadda
- Rakai Health Sciences Program, Entebbe, Uganda
- Makerere University School of Public Health, Kampala, Uganda
| | - Ronald H. Gray
- The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Rakai Health Sciences Program, Entebbe, Uganda
| | - Thomas C. Quinn
- The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Baltimore, Maryland, USA
| | | | | | - Oliver Laeyendecker
- The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Baltimore, Maryland, USA
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High frequency of new recombinant forms in HIV-1 transmission networks demonstrated by full genome sequencing. INFECTION GENETICS AND EVOLUTION 2020; 84:104365. [PMID: 32417307 DOI: 10.1016/j.meegid.2020.104365] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 05/08/2020] [Accepted: 05/12/2020] [Indexed: 11/22/2022]
Abstract
The HIV-1 epidemic in Belgium is primarily driven by MSM. In this patient population subtype B predominates but an increasing presence of non-B subtypes has been reported. We aimed to define to what extent the increasing subtype heterogeneity in a high at risk population induces the formation and spread of new recombinant forms. The study focused on transmission networks that reflect the local transmission to an important extent. One hundred and five HIV-1 transmission clusters were identified after phylogenetic analysis of 2849 HIV-1 pol sequences generated for the purpose of baseline drug resistance testing between 2013 and 2017. Of these 105 clusters, 62 extended in size during the last two years and were therefore considered as representing ongoing transmission. These 62 clusters included 774 patients in total. From each cluster between 1 and 3 representative patients were selected for near full-length viral genome sequencing. In total, the full genome sequence of 101 patients was generated. Indications for the presence of a new recombinant form were found for 10 clusters. These 10 clusters represented 105 patients or 13.6% of the patients covered by the study. The findings clearly show that new recombinant strains highly contribute to local transmission, even in an epidemic that is largely MSM and subtype B driven. This is an evolution that needs to be monitored as reshuffling of genome fragments through recombination may influence the transmissibility of the virus and the pathology of the infection. In addition, important changes in the sequence of the viral genome may challenge the performance of tests used for diagnosis, patient monitoring and drug resistance analysis.
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