scholarly journals Identification of a New HIV-1 BC Intersubtype Circulating Recombinant Form (CRF108_BC) in Spain

Viruses ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 93
Author(s):  
Javier E. Cañada ◽  
Elena Delgado ◽  
Horacio Gil ◽  
Mónica Sánchez ◽  
Sonia Benito ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Basque Country ◽  
Recent Common Ancestor ◽  
Subtype C ◽  
Northern Spain ◽  
Most Recent Common Ancestor ◽  
Phylogenetic Cluster ◽  
Subtype B ◽  
Definition Of ◽  
Hiv 1

The extraordinary genetic variability of human immunodeficiency virus type 1 (HIV-1) group M has led to the identification of 10 subtypes, 102 circulating recombinant forms (CRFs) and numerous unique recombinant forms. Among CRFs, 11 derived from subtypes B and C have been identified in China, Brazil, and Italy. Here we identify a new HIV-1 CRF_BC in Northern Spain. Originally, a phylogenetic cluster of 15 viruses of subtype C in protease-reverse transcriptase was identified in an HIV-1 molecular surveillance study in Spain, most of them from individuals from the Basque Country and heterosexually transmitted. Analyses of near full-length genome sequences from six viruses from three cities revealed that they were BC recombinant with coincident mosaic structures different from known CRFs. This allowed the definition of a new HIV-1 CRF designated CRF108_BC, whose genome is predominantly of subtype C, with four short subtype B fragments. Phylogenetic analyses with database sequences supported a Brazilian ancestry of the parental subtype C strain. Coalescent Bayesian analyses estimated the most recent common ancestor of CRF108_BC in the city of Vitoria, Basque Country, around 2000. CRF108_BC is the first CRF_BC identified in Spain and the second in Europe, after CRF60_BC, both phylogenetically related to Brazilian subtype C strains.

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.

scholarly journals The changing HIV-1 genetic characteristics and transmitted drug resistance among recently infected population in Yunnan, China

2018 ◽  
Vol 146 (6) ◽  
pp. 775-781 ◽  
Author(s):  
M. Chen ◽  
M. H. Jia ◽  
Y. L. Ma ◽  
H. B. Luo ◽  
H. C. Chen ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Management Strategies ◽  
Recent Common Ancestor ◽  
Transmitted Drug Resistance ◽  
Subtype C ◽  
Effective Population ◽  
Genetic Characteristics ◽  
Infected Population ◽  
Subtype B ◽  
Hiv 1

AbstractMultiple human immunodeficiency virus (HIV)-1 genotypes in China were first discovered in Yunnan Province before disseminating throughout the country. As the HIV-1 epidemic continues to expand in Yunnan, genetic characteristics and transmitted drug resistance (TDR) should be further investigated among the recently infected population. Among 2828 HIV-positive samples newly reported in the first quarter of 2014, 347 were identified as recent infections with BED-captured enzyme immunoassay (CEIA). Of them, 291 were successfully genotyped and identified as circulating recombinant form (CRF)08_BC (47.4%), unique recombinant forms (URFs) (18.2%), CRF01_AE (15.8%), CRF07_BC (14.4%), subtype C (2.7%), CRF55_01B (0.7%), subtype B (0.3%) and CRF64_BC (0.3%). CRF08_BC and CRF01_AE were the predominant genotypes among heterosexual and homosexual infections, respectively. CRF08_BC, URFs, CRF01_AE and CRF07_BC expanded with higher prevalence in central and eastern Yunnan. The recent common ancestor of CRF01_AE, CRF07_BC and CRF08_BC dated back to 1983.1, 1992.1 and 1989.5, respectively. The effective population sizes (EPS) for CRF01_AE and CRF07_BC increased exponentially during 1991–1999 and 1994–1999, respectively. The EPS for CRF08_BC underwent two exponential growth phases in 1994–1998 and 2001–2002. Lastly, TDR-associated mutations were identified in 1.8% of individuals. These findings not only enhance our understanding of HIV-1 evolution in Yunnan but also have implications for vaccine design and patient management strategies.

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 Population-Level Immune-Mediated Adaptation in HIV-1 Polymerase during the North American Epidemic

2015 ◽  
Vol 90 (3) ◽  
pp. 1244-1258 ◽  
Author(s):  
Natalie N. Kinloch ◽  
Daniel R. MacMillan ◽  
Anh Q. Le ◽  
Laura A. Cotton ◽  
David R. Bangsberg ◽  
...  
Keyword(s):  
North America ◽  
North American ◽  
Consensus Sequence ◽  
Hla Class I ◽  
Class I ◽  
Recent Common Ancestor ◽  
Most Recent Common Ancestor ◽  
Subtype B ◽  
Hiv 1 ◽  
Over Time

ABSTRACTHuman leukocyte antigen (HLA) class I-associated polymorphisms in HIV-1 that persist upon transmission to HLA-mismatched hosts may spread in the population as the epidemic progresses. Transmission of HIV-1 sequences containing such adaptations may undermine cellular immune responses to the incoming virus in future hosts. Building upon previous work, we investigated the extent of HLA-associated polymorphism accumulation in HIV-1 polymerase (Pol) through comparative analysis of linked HIV-1/HLA class I genotypes sampled during historic (1979 to 1989;n= 338) and modern (2001 to 2011;n= 278) eras from across North America (Vancouver, BC, Canada; Boston, MA; New York, NY; and San Francisco, CA). Phylogenies inferred from historic and modern HIV-1 Pol sequences were star-like in shape, with an inferred most recent common ancestor (epidemic founder virus) sequence nearly identical to the modern North American subtype B consensus sequence. Nevertheless, modern HIV-1 Pol sequences exhibited roughly 2-fold-higher patristic (tip-to-tip) genetic distances than historic sequences, with HLA pressures likely driving ongoing diversification. Moreover, the frequencies of published HLA-associated polymorphisms in individuals lacking the selecting HLA class I allele was on average ∼2.5-fold higher in the modern than in the historic era, supporting their spread in circulation, though some remained stable in frequency during this time. Notably, polymorphisms restricted by protective HLA alleles appear to be spreading to a greater relative extent than others, though these increases are generally of modest absolute magnitude. However, despite evidence of polymorphism spread, North American hosts generally remain at relatively low risk of acquiring an HIV-1 polymerase sequence substantially preadapted to their HLA profiles, even in the present era.IMPORTANCEHLA class I-restricted cytotoxic T-lymphocyte (CTL) escape mutations in HIV-1 that persist upon transmission may accumulate in circulation over time, potentially undermining host antiviral immunity to the transmitted viral strain. We studied >600 experimentally collected HIV-1 polymerase sequences linked to host HLA information dating back to 1979, along with phylogenetically reconstructed HIV-1 sequences dating back to the virus' introduction into North America. Overall, our results support the gradual spread of many—though not all—HIV-1 polymerase immune escape mutations in circulation over time. This is consistent with recent observations from other global regions, though the extent of polymorphism accumulation in North America appears to be lower than in populations with high seroprevalence, older epidemics, and/or limited HLA diversity. Importantly, the risk of acquiring an HIV-1 polymerase sequence at transmission that is substantially preadapted to one's HLA profile remains relatively low in North America, even in the present era.

scholarly journals Comprehensive Characterization of HIV-1 Molecular Epidemiology and Demographic History in the Brazilian Region Most Heavily Affected by AIDS

2016 ◽  
Vol 90 (18) ◽  
pp. 8160-8168 ◽  
Author(s):  
Tiago Gräf ◽  
Hegger Machado Fritsch ◽  
Rúbia Marília de Medeiros ◽  
Dennis Maletich Junqueira ◽  
Sabrina Esteves de Matos Almeida ◽  
...  
Keyword(s):  
Molecular Epidemiology ◽  
Demographic History ◽  
Phylogenetic Analyses ◽  
Viral Population ◽  
Subtype C ◽  
Capital Cities ◽  
Subtype B ◽  
High Prevalence ◽  
Hiv 1 ◽  
South Brazil

ABSTRACTThe high incidence of AIDS cases and the dominance of HIV-1 subtype C infections are two features that distinguish the HIV-1 epidemic in the two southernmost Brazilian states (Rio Grande do Sul [RS] and Santa Catarina [SC]) from the epidemic in other parts of the country. Nevertheless, previous studies on HIV molecular epidemiology were conducted mainly in capital cities, and a more comprehensive understanding of factors driving this unique epidemic in Brazil is necessary. Blood samples were collected from individuals in 13 municipalities in the Brazilian southern region. HIV-1envandpolgenes were submitted to phylogenetic analyses for assignment of subtype, and viral population phylodynamics were reconstructed by applying Skygrid and logistic coalescent models in a Bayesian analysis. A high prevalence of subtype C was observed in all sampled locations; however, an increased frequency of recombinant strains was found in RS, with evidence for new circulating forms (CRFs). In the SC state, subtype B and C epidemics were associated with distinct exposure groups. Although logistic models estimated similar growth rates for HIV-1 subtype C (HIV-1C) and HIV-1B, a Skygrid plot reveals that the former epidemic has been expanding for a longer time. Our results highlight a consistent expansion of HIV-1C in south Brazil, and we also discuss how heterosexual and men who have sex with men (MSM) transmission chains might have impacted the current prevalence of HIV-1 subtypes in this region.IMPORTANCEThe AIDS epidemic in south Brazil is expanding rapidly, but the circumstances driving this condition are not well known. A high prevalence of HIV-1 subtype C was reported in the capital cities of this region, in contrast to the subtype B dominance in the rest of the country. This study sought to comparatively investigate the HIV-1 subtype B and C epidemics by sampling individuals from several cities in the two states with the highest AIDS incidences in Brazil. Our analyses showed distinct epidemic growth curves for the two epidemics, and we also found evidence suggesting that separate transmission chains may be impacting the viral phylodynamics and the emergence of new recombinant forms.

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: >95% in interior branch test, >95% in Bayesian posterior probability and <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 <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 Revisiting the recombinant history of HIV-1 group M with dynamic network community detection

2021 ◽  
Author(s):  
Abayomi Samuel Olabode ◽  
Garway Tammy Ng ◽  
Kaitlyn E Wade ◽  
Mikhail Salnikov ◽  
David W Dick ◽  
...  
Keyword(s):  
Community Detection ◽  
Detection Method ◽  
Wilcoxon Test ◽  
Recent Common Ancestor ◽  
Subtype C ◽  
Recombination Detection ◽  
Most Recent Common Ancestor ◽  
Dynamic Social Networks ◽  
History Of ◽  
Hiv 1

In previous work, we used a comprehensive sliding-window molecular clock analysis of near full length HIV-1 genomes to find that different regions of the virus genome yield significantly different estimates of the time to the most recent common ancestor. This finding, together with other evidence of the deep recombinant history of SIV and HIV, is not consistent with the standard model of the evolutionary history of HIV-1/M where non-recombinant subtypes are globally distributed through founder effects, followed by occasional inter-subtype recombination. We propose to re-examine the history of HIV-1/M using recombination detection methods that do not rely on predefined non-recombinant genomes. Here we describe an unsupervised non-parametric clustering approach to this problem by adapting a community detection method developed for the analysis of dynamic social networks. We compared our method to other reference-free recombination detection programs, namely GARD (HyPhy) and RDP (versions 4 and 5). We simulated recombination events by swapping randomly sampled branches in a time-scaled tree, which we reconstructed from subtype reference sequences in BEAST. Extant sequences were simulated for each tree using INDELible, and concatenated segments delimited by randomly sampled breakpoints from the resulting alignments to form the recombinant sequences. We show that our community detection method outperforms GARD, RDP4 and RDP5 in detecting recombinant breakpoints in simulated data, with a significantly lower mean error rate (Wilcoxon test, P < 0:05). Our method groups HIV-1 into 25 communities and detects evidence of inter-subtype recombination in pure subtype reference genomes obtained from Los Alamos HIV sequence database. For instance, we estimate that sub-subtypes A1 and A2 may contain large fragments from subtype C, while subtype C seems to contain fragments from subtype G. Our method provides a new reference-free framework for detecting recombination in viral genomes, and network communities may provide an alternative framework for HIV-1 classification.

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.

Genetic Diversity and Drug Resistance of HIV-1 CRF55_01B in Guangdong, China

2020 ◽  
Vol 18 (3) ◽  
pp. 210-218
Author(s):  
Guolong Yu ◽  
Yan Li ◽  
Xuhe Huang ◽  
Pingping Zhou ◽  
Jin Yan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Drug Resistance ◽  
Reverse Transcriptase ◽  
Phylogenetic Analyses ◽  
Resistance Mutations ◽  
Protease Inhibition ◽  
Subtype B ◽  
Primary Drug Resistance ◽  
Hiv 1 ◽  
Primary Drug

Background: HIV-1 CRF55_01B was first reported in 2013. At present, no report is available regarding this new clade’s polymorphisms in its functionally critical regions protease and reverse transcriptase. Objective: To identify the diversity difference in protease and reverse transcriptase between CRF55_01B and its parental clades CRF01_AE and subtype B; and to investigate CRF55_01B’s drug resistance mutations associated with the protease inhibition and reverse transcriptase inhibition. Methods: HIV-1 RNA was extracted from plasma derived from a MSM population. The reverse transcription and nested PCR amplification were performed following our in-house PCR procedure. Genotyping and drug resistant-associated mutations and polymorphisms were identified based on polygenetic analyses and the usage of the HIV Drug Resistance Database, respectively. Results: A total of 9.24 % of the identified CRF55_01B sequences bear the primary drug resistance. CRF55_01B contains polymorphisms I13I/V, G16E and E35D that differ from those in CRF01_AE. Among the 11 polymorphisms in the RT region, seven were statistically different from CRF01_AE’s. Another three polymorphisms, R211K (98.3%), F214L (98.3%), and V245A/E (98.3 %.), were identified in the RT region and they all were statistically different with that of the subtype B. The V179E/D mutation, responsible for 100% potential low-level drug resistance, was found in all CRF55_01B sequences. Lastly, the phylogenetic analyses demonstrated 18 distinct clusters that account for 35% of the samples. Conclusions: CRF55_01B’s pol has different genetic diversity comparing to its counterpart in CRF55_01B’s parental clades. CRF55_01B has a high primary drug resistance presence and the V179E/D mutation may confer more vulnerability to drug resistance.

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