scholarly journals First complete-genome documentation of HIV-1 intersubtype superinfection with transmissions of diverse recombinants over time to five recipients

2021 ◽  
Vol 17 (2) ◽  
pp. e1009258
Author(s):  
Yang Gao ◽  
Shan He ◽  
Wen Tian ◽  
Dan Li ◽  
Minghui An ◽  
...  
Keyword(s):  
Sexual Behaviors ◽  
Phylogenetic Trees ◽  
Evolutionary Relationship ◽  
Recent Common Ancestor ◽  
Monophyletic Cluster ◽  
Most Recent Common Ancestor ◽  
Immunodeficiency Virus ◽  
Sex With Men ◽  
Full Length Genome ◽  
Hiv 1

Human immunodeficiency virus type 1 (HIV-1) recombinants in the world are believed to be generated through recombination between distinct HIV-1 strains among coinfection or superinfection cases. However, direct evidence to support transmission of HIV-1 recombinants from a coinfected/superinfected donor to putative recipient is lacking. Here, we report on the origin and evolutionary relationship between a set of recombinants from a CRF01_AE/CRF07_BC superinfected putative donor and diverse CRF01_AE/CRF07_BC recombinants from five putative recipients. Interviews on sociodemographic characteristics and sexual behaviors for these six HIV-1-infected men who have sex with men showed that they had similar ways of partner seeking: online dating sites and social circles. Phylogenetic and recombination analyses demonstrated that the near-full-length genome sequences from six patients formed a monophyletic cluster different from known HIV-1 genotypes in maximum likelihood phylogenetic trees, were all composed of CRF01_AE and CRF07_BC fragments with two common breakpoints on env, and shared 4–7 breakpoints with each other. Moreover, 3’ half-genomes of recombinant strains from five recipients had identical/similar recombinant structures with strains at longitudinal samples from the superinfected donor. Recombinants from the donor were paraphyletic, whereas five recipients were monophyletic or polyphyletic in the maximum clade credibility tree. Bayesian analyses confirmed that the estimated time to the most recent common ancestor (tMRCA) of CRF01_AE and CRF07_BC strains of the donor was 2009.2 and 2010.7, respectively, and all were earlier than the emergence of recombinants from five recipients. Our results demonstrated that the closely related unique recombinant forms of HIV-1 might be the descendent of a series of recombinants generated gradually in a superinfected patient. This finding highlights the importance of early initiation of antiretroviral therapy as well as tracing and testing of partners in patients with multiple HIV-1 infection.

scholarly journals Identification of CRF66_BF, a new HIV-1 circulating recombinant form of South American origin

2021 ◽  
Author(s):  
Joan Bacque ◽  
Elena Delgado ◽  
Sonia Benito ◽  
Maria Moreno-Lorenzo ◽  
Vanessa Montero ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Recent Common Ancestor ◽  
South American ◽  
Most Recent Common Ancestor ◽  
Phylogenetic Cluster ◽  
Subtype B ◽  
Sex With Men ◽  
Full Length Genome ◽  
South American Origin ◽  
Hiv 1

Circulating recombinant forms (CRFs) are important components of the HIV-1 pandemic. Among 108 reported in the literature, 17 are BF1 intersubtype recombinant, most of which are of South American origin. Among these, all 5 identified in the Southern Cone and neighboring countries, except Brazil, derive from a common recombinant ancestor related to CRF12_BF, which circulates widely in Argentina, as deduced from coincident breakpoints and clustering in phylogenetic trees. In a HIV-1 molecular epidemiological study in Spain, we identified a phylogenetic cluster of 20 samples from 3 separate regions which were of F1 subsubtype, related to the Brazilian strain, in protease-reverse transcriptase (Pr-RT) and of subtype B in integrase. Remarkably, 14 individuals from this cluster (designated BF9) were Paraguayans and only 4 were native Spaniards. HIV-1 transmission was predominantly heterosexual, except for a subcluster of 6 individuals, 5 of which were men who have sex with men. Ten additional database sequences, from Argentina (n=4), Spain (n=3), Paraguay (n=1), Brazil (n=1), and Italy (n=1), branched within the BF9 cluster. To determine whether it represents a new CRF, near full-length genome (NFLG) sequences were obtained for 6 viruses from 3 Spanish regions. Bootscan analyses showed a coincident BF1 recombinant structure, with 5 breakpoints, located in p17gag, integrase, gp120, gp41-rev overlap, and nef, which was identical to that of two BF1 recombinant viruses from Paraguay previously sequenced in NFLGs. Interestingly, none of the breakpoints coincided with those of CRF12_BF. In a maximum likelihood phylogenetic tree, all 8 NFLG sequences grouped in a strongly supported clade segregating from previously identified CRFs and from the CRF12_BF family clade. These results allow us to identify a new HIV-1 CRF, designated CRF66_BF. Through a Bayesian coalescent analysis, the most recent common ancestor of CRF66_BF was estimated around 1984 in South America, either in Paraguay or Argentina. Among Pr-RT sequences obtained by us from HIV-1-infected Paraguayans living in Spain, 14 (20.9%) of 67 were of CRF66_BF, suggesting that CRF66_BF may be one of the major HIV-1 genetic forms circulating in Paraguay. CRF66_BF is the first reported non-Brazilian South American HIV-1 CRF_BF unrelated to CRF12_BF

scholarly journals Identification of CRF66_BF, a New HIV-1 Circulating Recombinant Form of South American Origin

2021 ◽  
Vol 12 ◽  
Author(s):  
Joan Bacqué ◽  
Elena Delgado ◽  
Sonia Benito ◽  
María Moreno-Lorenzo ◽  
Vanessa Montero ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Recent Common Ancestor ◽  
South American ◽  
Most Recent Common Ancestor ◽  
Phylogenetic Cluster ◽  
Subtype B ◽  
Sex With Men ◽  
Full Length Genome ◽  
South American Origin ◽  
Hiv 1

Circulating recombinant forms (CRFs) are important components of the HIV-1 pandemic. Among 110 reported in the literature, 17 are BF1 intersubtype recombinant, most of which are of South American origin. Among these, all 5 identified in the Southern Cone and neighboring countries, except Brazil, derive from a common recombinant ancestor related to CRF12_BF, which circulates widely in Argentina, as deduced from coincident breakpoints and clustering in phylogenetic trees. In a HIV-1 molecular epidemiological study in Spain, we identified a phylogenetic cluster of 20 samples from 3 separate regions which were of F1 subsubtype, related to the Brazilian strain, in protease-reverse transcriptase (Pr-RT) and of subtype B in integrase. Remarkably, 14 individuals from this cluster (designated BF9) were Paraguayans and only 4 were native Spaniards. HIV-1 transmission was predominantly heterosexual, except for a subcluster of 6 individuals, 5 of which were men who have sex with men. Ten additional database sequences, from Argentina (n = 4), Spain (n = 3), Paraguay (n = 1), Brazil (n = 1), and Italy (n = 1), branched within the BF9 cluster. To determine whether it represents a new CRF, near full-length genome (NFLG) sequences were obtained for 6 viruses from 3 Spanish regions. Bootscan analyses showed a coincident BF1 recombinant structure, with 5 breakpoints, located in p17gag, integrase, gp120, gp41-rev overlap, and nef, which was identical to that of two BF1 recombinant viruses from Paraguay previously sequenced in NFLGs. Interestingly, none of the breakpoints coincided with those of CRF12_BF. In a maximum likelihood phylogenetic tree, all 8 NFLG sequences grouped in a strongly supported clade segregating from previously identified CRFs and from the CRF12_BF “family” clade. These results allow us to identify a new HIV-1 CRF, designated CRF66_BF. Through a Bayesian coalescent analysis, the most recent common ancestor of CRF66_BF was estimated around 1984 in South America, either in Paraguay or Argentina. Among Pr-RT sequences obtained by us from HIV-1-infected Paraguayans living in Spain, 14 (20.9%) of 67 were of CRF66_BF, suggesting that CRF66_BF may be one of the major HIV-1 genetic forms circulating in Paraguay. CRF66_BF is the first reported non-Brazilian South American HIV-1 CRF_BF unrelated to CRF12_BF.

The identification of a novel HIV-1 second-generation recombinant form (CRF01_AE/CRF07_BC) among men who have sex with men in Jiangsu, China

2020 ◽  
Vol 18 ◽  
Author(s):  
Yin Yueqi ◽  
Zhou Ying ◽  
Lu Jing ◽  
Guo Hongxiong ◽  
Chen Jianshuang ◽  
...  
Keyword(s):  
Maximum Likelihood ◽  
Phylogenetic Trees ◽  
Second Generation ◽  
Emergency Situation ◽  
The World ◽  
Break Points ◽  
Sex With Men ◽  
Full Length Genome ◽  
Virus Strains ◽  
Hiv 1

Background: CRF01_AE and CRF07_BC are the two major HIV-1 virus strains circulating in China. The proportion of dominant subtypes (CRF01_AE and CRF07_BC) among MSM in Jiangsu province was over 80%. A large number of URFs have been found in China in recently years. Objective: This study aimed to report on novel HIV-1 recombinants. Method: We constructed Phylogenetic trees using the maximum likelihood (ML) method with 1000 bootstrap replicates in IQ-TREE 1.6.8 software and determined recombination break points using SimPlot 3.5.1. Results: We identified a novel, second-generation HIV-1 recombinant (JS020202) between CRF01_AE and CRF07_BC. The analysis of near full-length genome (NFLG) showed there were at least 8 breakpoints inner virus, which differed from any previously identified CRF and URF around the world. Conclusion: Novel diverse CRF01_AE/07_BC suggested the complexity trends of HIV-1 genetics. The emergency situation of diverse recombinant strains should be monitored continuously.

scholarly journals Timing and Reconstruction of the Most Recent Common Ancestor of the Subtype C Clade of Human Immunodeficiency Virus Type 1

2004 ◽  
Vol 78 (19) ◽  
pp. 10501-10506 ◽  
Author(s):  
Simon A. A. Travers ◽  
Jonathan P. Clewley ◽  
Judith R. Glynn ◽  
Paul E. M. Fine ◽  
Amelia C. Crampin ◽  
...  
Keyword(s):  
Human Immunodeficiency Virus ◽  
Human Immunodeficiency Virus Type ◽  
Virus Type ◽  
Common Ancestor ◽  
Recent Common Ancestor ◽  
Subtype C ◽  
Most Recent Common Ancestor ◽  
Immunodeficiency Virus ◽  
Hiv 1

ABSTRACT Human immunodeficiency virus type 1 (HIV-1) subtype C is responsible for more than 55% of HIV-1 infections worldwide. When this subtype first emerged is unknown. We have analyzed all available gag (p17 and p24) and env (C2-V3) subtype C sequences with known sampling dates, which ranged from 1983 to 2000. The majority of these sequences come from the Karonga District in Malawi and include some of the earliest known subtype C sequences. Linear regression analyses of sequence divergence estimates (with four different approaches) were plotted against sample year to estimate the year in which there was zero divergence from the reconstructed ancestral sequence. Here we suggest that the most recent common ancestor of subtype C appeared in the mid- to late 1960s. Sensitivity analyses, by which possible biases due to oversampling from one district were explored, gave very similar estimates.

scholarly journals First Detection of a Cluster Novel HIV-1 Second-Generation Recombinant (CRF01_AE/CRF07_BC) among Men Who Have Sex with Men in Nanjing, Eastern China

Intervirology ◽  
2021 ◽  
Vol 64 (2) ◽  
pp. 81-87 ◽  
Author(s):  
Yueqi Yin ◽  
Ying Zhou ◽  
Jing Lu ◽  
Hongxiong Guo ◽  
Jianshuang Chen ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Second Generation ◽  
Eastern China ◽  
Northern China ◽  
Small Scale ◽  
Transmission Networks ◽  
Nanjing City ◽  
Sex With Men ◽  
Full Length Genome ◽  
Hiv 1

<b><i>Introduction:</i></b> A large number of unique recombinant forms have been found in China in recent years. This study aimed to report on a cluster of novel HIV-1 recombinants. <b><i>Methods:</i></b> We constructed phylogenetic trees using the maximum likelihood (ML) method with 1,000 bootstrap replicates in IQ-TREE 1.6.8 software and determined recombination break points using SimPlot 3.5.1. <b><i>Results:</i></b> Overall, 9 near-full-length genome (NFLG) sequences were reported in this study, including 1 circulation recombinant form (CRF)01_AE NFLG sequence and 8 highly similar novel HIV-1 second-generation recombinants composed of CRF01_AE and CRF07_BC (CRF105_0107) isolated from a cluster HIV-positive male subjects infected among men who have sex with men (MSM) in Nanjing, eastern China. The phylogenetic analysis of NFLG showed 1 sequence named “nj16” to have at least 11 breakpoints inner virus and 7 other sequences to have at least 10 breakpoints inner virus. Our findings further showed as follows: first, this is the first time that a cluster of novel CRF105_0107 HIV-1 strains were identified among MSM in Nanjing, Jiangsu. Second, the Chinese “4a” cluster of CRF01_AE which mainly circulating in northern China has spread in Jiangsu for more than 15 years. Third, HIV-1 recombination events were active in Nanjing city, and novel recombinants could spread rapidly through some small-scale transmission networks. <b><i>Conclusion:</i></b> The continued emergence of novel recombinant HIV-1 strains in Nanjing suggests dynamics and complexity in the HIV epidemic among MSM in Jiangsu province. Further investigations and molecular epidemiological research should be taken to monitor and understand transmission networks among MSM.

scholarly journals Nation-Wide Viral Sequence Analysis of HIV-1 Subtype B Epidemic in 2003–2012 Revealed a Contribution of Men Who Have Sex With Men to the Transmission Cluster Formation and Growth in Japan

2020 ◽  
Vol 2 ◽  
Author(s):  
Teiichiro Shiino ◽  
Atsuko Hachiya ◽  
Junko Hattori ◽  
Wataru Sugiura ◽  
Kazuhisa Yoshimura
Keyword(s):  
Recent Common Ancestor ◽  
Bayesian Posterior Probability ◽  
Newly Diagnosed ◽  
Surveillance Network ◽  
Relative Population ◽  
Most Recent Common Ancestor ◽  
Subtype B ◽  
Geographical Regions ◽  
Sex With Men ◽  
Hiv 1

Background: To better understand the epidemiology of human immunodeficiency virus type 1 (HIV-1) subtype B transmission in Japan, phylodynamic analysis of viral pol sequences was conducted on individuals newly diagnosed as HIV-1 seropositive.Methodology: A total of 5,018 patients newly diagnosed with HIV-1 infection and registered in the Japanese Drug Resistance HIV Surveillance Network from 2003 to 2012 were enrolled in the analysis. Using the protease-reverse transcriptase nucleotide sequences, their subtypes were determined, and phylogenetic relationships among subtype B sequences were inferred using three different methods: distance-matrix, maximum likelihood, and Bayesian Markov chain Monte Carlo. Domestically spread transmission clusters (dTCs) were identified based on the following criteria: &gt;95% in interior branch test, &gt;95% in Bayesian posterior probability and &lt;10% in depth-first searches for sub-tree partitions. The association between dTC affiliation and individuals' demographics was analyzed using univariate and multivariate analyses.Results: Among the cases enrolled in the analysis, 4,398 (87.6%) were classified as subtype B. Many of them were Japanese men who had sex with men (MSM), and 3,708 (84.3%) belonged to any of 312 dTCs. Among these dTCs, 243 (77.9%) were small clusters with &lt;10 individuals, and the largest cluster consisted of 256 individuals. Most dTCs had median time of the most recent common ancestor between 1995 and 2005, suggesting that subtype B infection was spread among MSMs in the second half of the 1990s. Interestingly, many dTCs occurred within geographical regions. Comparing with singleton cases, TCs included more MSM, young person, and individuals with high CD4+ T-cell count at the first consultation. Furthermore, dTC size was significantly correlated with gender, age, transmission risks, recent diagnosis and relative population size of the region mainly distributed.Conclusions: Our study clarified that major key population of HIV-1 subtype B epidemic in Japan is local MSM groups. The study suggests that HIV-1 subtype B spread via episodic introductions into the local MSM groups, some of the viruses spread to multiple regions. Many cases in dTC were diagnosed during the early phase of infection, suggesting their awareness to HIV risks.

scholarly journals Phylogenetic evidence of HIV-1 transmission linkage between two men who have sex with men

2021 ◽  
Vol 18 (1) ◽  
Author(s):  
Jiafeng Zhang ◽  
Qin Fan ◽  
Mingyu Luo ◽  
Jiaming Yao ◽  
Xiaohong Pan ◽  
...  
Keyword(s):  
Hiv Transmission ◽  
Phylogenetic Analyses ◽  
Recent Common Ancestor ◽  
Hiv Positive ◽  
Most Recent Common Ancestor ◽  
Hiv Seroconversion ◽  
Selective Forces ◽  
Sex With Men ◽  
Hiv 1 ◽  
Control Sequences

Abstract Background In China, an HIV-infected man (complainant; P2) alleged that another man (defendant; P1) had unlawfully infected him with HIV through unprotected homosexual contact in 2018. Methods We employed epidemiological, serological and phylogenetic analyses to investigate the transmission linkage between two men who have sex with men (MSM). Partial segments of three HIV-1 gene regions (gag, pol, and env) were amplified and sequenced by cloning. Maximum-likelihood (ML) and Bayesian methods were used to determine the direction and estimate the timing of transmission. Local control sequences and database control sequences were also used in the phylogenetic analysis. Results It indicated that P2 underwent HIV seroconversion after P1 was diagnosed as HIV positive. The time to the most recent common ancestor (tMRCA) estimates consistently showed that P1 most likely became HIV-1 infected at an earlier date than P2. P1 and P2 were infected with the same HIV-1 CRF01_AE subtype according to segments of all three gene regions (gag, pol, and env). All three genetic regions of P1 have been subject to more potential selective forces than those of P2, indicating a longer evolutionary history. Bayesian and ML trees showed similar paraphyletic-monophyletic topologies of gag and env, with the virus from P1 located at the root, which supported a P1-to-P2 transmission direction. Conclusions Phylogenetic investigations can elucidate HIV transmission linkage and might empower its use in the opposition of the intentional transmission of HIV-1 as a forensic tool.

scholarly journals Phylogenetic and genetic characterization of Treponema pallidum strains from syphilis patients in Japan by whole-genome sequence analysis from global perspectives

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Shingo Nishiki ◽  
Kenichi Lee ◽  
Mizue Kanai ◽  
Shu-ichi Nakayama ◽  
Makoto Ohnishi
Keyword(s):  
Genetic Difference ◽  
Phylogenetic Analyses ◽  
Treponema Pallidum ◽  
Whole Genome Sequence ◽  
Epidemiological Surveillance ◽  
Recent Common Ancestor ◽  
Whole Genome ◽  
Global Perspectives ◽  
Most Recent Common Ancestor ◽  
Sex With Men

AbstractJapan has had a substantial increase in syphilis cases since 2013. However, research on the genomic features of the Treponema pallidum subspecies pallidum (TPA) strains from these cases has been limited. Here, we elucidated the genetic variations and relationships between TPA strains in Japan (detected between 2014 and 2018) and other countries by whole-genome sequencing and phylogenetic analyses, including syphilis epidemiological surveillance data and information on patient sexual orientation. Seventeen of the 20 strains in Japan were SS14- and the remaining 3 were Nichols-lineage. Sixteen of the 17 SS14-lineage strains were classified into previously reported Sub-lineage 1B. Sub-lineage 1B strains in Japan have formed distinct sub-clusters of strains from heterosexuals and strains from men who have sex with men. These strains were closely related to reported TPA strains in China, forming an East-Asian cluster. However, those strains in these countries evolved independently after diverging from their most recent common ancestor and expanded their genetic diversity during the time of syphilis outbreak in each country. The genetic difference between the TPA strains in these countries was characterized by single-nucleotide-polymorphism analyses of their penicillin binding protein genes. Taken together, our results elucidated the detailed phylogenetic features and transmission networks of syphilis.

A Comparison of Psychosocial Factors, Substance Use Behaviors, and Sexual Behaviors by Self-Reported HIV Status Among Middle-Aged Hispanic Men Who Have Sex With Men

2020 ◽  
pp. 154041532092356
Author(s):  
Beatriz Valdes ◽  
Deborah Salani ◽  
Joseph P. De Santis
Keyword(s):  
Social Support ◽  
Substance Use ◽  
Depressive Symptoms ◽  
Psychosocial Factors ◽  
Sexual Behaviors ◽  
Hiv Status ◽  
Illicit Substance Use ◽  
Immunodeficiency Virus ◽  
Hispanic Men ◽  
Sex With Men

Introduction: Human immunodeficiency virus (HIV) is a significant health issue among Hispanic men who have sex with men (MSM). Despite existing research, no studies have compared psychosocial factors by self-reported HIV antibody status. Method: Participants ( n = 150) completed measures of social support, loneliness, depressive symptoms, substance use, and sexual behaviors. Results: Participants with a self-reported HIV-antibody positive status reported lower levels of social support and higher levels of illicit substance use. Hispanic MSM with an unknown HIV antibody status reported more sexual partners. Conclusion: More research is needed to address psychosocial factors (social support, loneliness, depressive symptoms), substance use, and sexual behaviors among Hispanic MSM.

scholarly journals Comparisons of Human Immunodeficiency Virus Type 1 Envelope Variants in Blood and Genital Fluids near the Time of Male-to-Female Transmission

2019 ◽  
Vol 93 (13) ◽  
Author(s):  
Corey A. Williams-Wietzikoski ◽  
Mary S. Campbell ◽  
Rachel Payant ◽  
Airin Lam ◽  
Hong Zhao ◽  
...  
Keyword(s):  
Human Immunodeficiency Virus ◽  
Human Immunodeficiency Virus Type ◽  
Virus Type ◽  
Genital Tract ◽  
Recent Common Ancestor ◽  
Female Partners ◽  
Immunodeficiency Virus ◽  
Male To Female ◽  
Hiv 1

ABSTRACTTo better understand the transmission of human immunodeficiency virus type 1 (HIV-1), the genetic characteristics of blood and genital viruses from males were compared to those of the imputed founding virus population in their female partners. Initially serodiscordant heterosexual African couples with sequence-confirmed male-to-female HIV-1 transmission and blood and genital specimens collected near the time of transmission were studied. Single viral templates from blood plasma and genital tract RNA and DNA were sequenced across HIV-1envgp160. Eight of 29 couples examined yielded viral sequences from both tissues. Analysis of these couples’ sequences demonstrated, with one exception, that the women’s founding viral populations arose from a single viral variant and were CCR5 tropic, even though CXCR4 variants were detected within four males. The median genetic distance of the imputed most recent common ancestor of the women’s founder viruses showed that they were closer to the semen viruses than to the blood viruses of their transmitting male partner, but this finding was biased by detection of a greater number of viral clades in the blood. Using multiple assays, the blood and genital viruses were consistently found to be compartmentalized in only two of eight men. No distinct amino acid signatures in the men’s viruses were found to link to the women’s founders, nor did the women’senvsequences have shorter variable loops or fewer N-linked glycosylation sites. The lack of selective factors, except for coreceptor tropism, is consistent with others’ findings in male-to-female and high-risk transmissions. The infrequent compartmentalization between the transmitters’ blood and semen viruses suggests that cell-free blood virus likely includes HIV-1 sequences representative of those of viruses in semen.IMPORTANCEMucosal transmissions account for the majority of HIV-1 infections. Identification of the viral characteristics associated with transmission would facilitate vaccine design. This study of HIV strains from transmitting males and their seroconverting female partners found that the males’ genital tract viruses were rarely distinct from the blood variants. The imputed founder viruses in women were genetically similar to both the blood and genital tract variants of their male partners, indicating a lack of evidence for genital tract-specific lineages. These findings suggest that targeting vaccine responses to variants found in blood are likely to also protect from genital tract variants.

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