Characterization of Three Novel HIV-1 Second-Generation Recombinants (CRF01_AE/CRF07_BC) Identified in Shenzhen, China

The prevalence of recombinant forms has greatly enhanced HIV-1 genetic diversity. Under co-circulation of major epidemic HIV-1 strains (CRF01_AE and CRF07_BC) in China, more CRF01_AE and CRF07_BC as the backbone of HIV-1 second-generation recombinants (SGRs) are also emerging. In this study, we identified three similar novel HIV-1 SGR strains composed of CRF01_AE and CRF07_BC from HIV-1 positive individuals in Shenzhen, China. Near full-length genome phylogenetic and recombinant analysis confirmed that these unique recombination forms were CRF01_AE and CRF07_BC strains recombined. Further subregion phylogenetic analysis indicated that all CRF01_AE fragments were from CRF01_AE cluster 4 prevalent among men who have sex with men, and all subtype B and C fragments derived from CRF07_BC. The emergence of novel recombinants of CRF01_AE/CRF07_BC indicates the increased genetic diversity of the HIV epidemic in Shenzhen. It is necessary to monitor HIV-1 SGR strains among high-risk populations for the epidemic dynamics of HIV-1 in Shenzhen, China.

Near Full-Length Genomic Characterization of Two Novel HIV-1 Unique Recombinant Forms (CRF01_AE/CRF07_BC) Among Men Who Have Sex with Men in Shijiazhuang City, Hebei Province, China

Unique recombinant forms (URFs) are more likely developed among HIV-1 infections through men who have sex with men (MSM) because of cocirculation of multiple subtypes. In this study, two novel URFs deriving from two HIV-positive subjects (HB010014, HB010063) were identified in Shijiazhuang, Hebei province, China, and two sequences formed a distinct monophyletic cluster. Further recombination analysis showed that of two new URFs were consisted of circulating recombinant form (CRF)01_AE and CRF07_BC. The subregion phylogenetic analysis indicated that CRF01_AE segments were traced back to cluster 4 of CRF01_AE strains, which were prevalent among HIV-1 infections through MSM in China. New URFs being developing gradually and spreading released that more and more novel recombinant strains of HIV-1 could be developed, which means that the past prevention strategies need to be adjusted.

Identification of a Novel HIV-1 CRF55_01B/B Recombinant Isolate in Guangxi, China

Dynamic recombination is the driving force in the genetic diversity of human immunodeficiency virus type 1 (HIV-1). When multiple subtypes are circulating in the same area of a population, new HIV-1 strains are likely to be generated through recombination. In this study, we report a novel recombinant strain (2018GXQZLSHET001) of HIV-1, isolated from a HIV-1-positive heterosexual individual infected in Guangdong province, who recently lived in Guangxi province, China. Phylogenetic analysis of the near full-length genome suggested that 2018GXQZLSHET001 was a recombinant of strains CRF55_01B and subtype B. Similarity plotting and bootscaning showed that a subtype B segment was inserted into the CRF55_01B genome with one breakpoint in the nef and 3' long terminal repeat regions. Further subregion phylogenetic analysis demonstrated that the CRF55_01B segment originated from Guangdong. The subtype B segment was similar to a Thai B lineage. This indicated that the strain might be a novel recombinant, comprising sequences of both CRF55_01B and B. The emergence of this unique recombinant strain illustrated the complexity of the HIV-1 epidemic, and the need to strengthen molecular epidemiological surveillance and measures to reduce its spread.

Estimating HIV-1 Genetic Diversity in Brazil Through Next-Generation Sequencing

Approximately 36.7 million people were living with the human immunodeficiency virus (HIV) at the end of 2016 according to UNAIDS, representing a global prevalence rate of 0.8%. In Brazil, an HIV prevalence of 0.24% has been estimated, which represents approximately 830,000 individuals living with the virus. As a touristic and commercial hub in Latin America, Brazil harbors an elevated HIV genetic variability, further contributed by the selective pressure exerted by the host immune system and by antiretroviral treatment. Through the progress of the next-generation sequencing (NGS) techniques, it has been possible to expand the study of HIV genetic diversity, evolutionary, and epidemic processes, allowing the generation of HIV complete or near full-length genomes (NFLG) and improving the characterization of intra- and interhost diversity of viral populations. Greater sensitivity in the detection of viral recombinant forms represents one of the major improvements associated with this development. It is possible to identify unique or circulating recombinant forms using the near full-length viral genomes with increasing accuracy. It also permits the characterization of multiple viral infections within individual hosts. Previous Brazilian studies using NGS to analyze HIV diversity were able to identify several distinct unique and circulating recombinant forms and evidenced dual infections. These data unveiled unprecedented high rates of viral recombination and highlighted that novel recombinants are continually arising in the Brazilian epidemic. In the pooled analysis depicted in this report, HIV subtypes have been determined from HIV-positive patients in five states of Brazil with some of the highest HIV prevalence, three in the Southeast (Rio de Janeiro, São Paulo, and Minas Gerais), one in the Northeast (Pernambuco) and one in the South (Rio Grande do Sul). Combined data analysis showed a significant prevalence of recombinant forms (29%; 101/350), and a similar 26% when only NFLGs were considered. Moreover, the analysis was able to evidence the occurrence of multiple infections in some individuals. Our data highlight the great HIV genetic diversity found in Brazil and unveils a more accurate scenario of the HIV evolutionary dynamics in the region.

Increased predominance of HIV-1 CRF01_AE and its recombinants in the Philippines

The growth rate of new HIV infections in the Philippines was the fastest of any countries in the Asia-Pacific region between 2010 and 2016. To date, HIV-1 subtyping results in the Philippines have been determined by characterizing only partial viral genome sequences. It is not known whether recombination occurs in the majority of unsequenced genome regions. Near-full-length genome (NFLG) sequences were obtained by amplifying two overlapping half genomes from plasma samples collected between 2015 and 2017 from 23 newly diagnosed infected individuals in the Philippines. Phylogenetic analysis showed that the newly characterized sequences were CRF01_AE (14), subtype B (3), CRF01/B recombinants (5) and a CRF01/CRF07/B recombinant (1). All 14 CRF01_AE formed a tight cluster, suggesting that they were derived from a single introduction. The time to the most recent common ancestor (tMRCA) for CRF01_AE in the Philippines was 1995 (1992-1998), about 10-15 years later than that of CRF01_AE in China and Thailand. All five CRF01/B recombinants showed distinct recombination patterns, suggesting ongoing recombination between the two predominant circulating viruses. The identification of partial CRF07_BC sequences in one CRF01/CRF07/B recombinant, not reported previously in the Philippines, indicated that CRF07_BC may have been recently introduced into that country from China, where CRF07_BC is prevalent. Our results show that the major epidemic strains may have shifted to an increased predominance of CRF01_AE and its recombinants, and that other genotypes such as CRF07_BC may have been introduced into the Philippines.

Four Closely Related HIV-1 CRF01_AE/CRF07_BC Recombinant Forms Identified in East China

Five near full-length genomes of novel second-generation HIV-1 recombinant virus (JS150021, JS150029, JS150129, JS150132, and AH150183) were identified from five HIV-positive people in Jiangsu and Anhui province, east China. Phylogenic analyses showed that these five sequences are all composed of two well-established circulating recombinant forms (CRFs) CRF07_BC and CRF01_AE, grouped into four new discovered recombinant forms, which show several very similar but not identical recombinant breakpoints. The four recombinant forms are also identified to be a sort of family or related viruses, seems to be the results of different recombination events. The emergence of a serious new closely related CRF07_BC/CRF01_AE recombinant strain indicates the increasing complexity of sexual transmission of the HIV-1 epidemic in China.

Tracing the origin of a singular HIV-1 CRF45_cpx clade identified in Brazil

The HIV-1 epidemiology has changed over the past decade toward a marked increase in the circulation of strains previously restricted to local epidemics. Recent molecular epidemiological surveys identified some HIV-1 strains of probable African origin circulating in Brazil, including the Circulating Recombinant Form (CRF) 45_cpx, a complex A1/K/U recombinant that circulates in Central Africa. Here, we characterize partial genomic sequences and reconstruct the evolutionary history of HIV-1 CRF45_cpx-related recombinant samples identified in independent studies carried out with HIV+ individuals in Brazil. The sequences were obtained by overlapping PCR amplifications followed by direct sequencing. Recombination profiles were determined by phylogenetic and bootscaning analyses. The evolutionary history was estimated by a Bayesian coalescent-based method using datasets representing the gag, pol and env gene fragments. Six of the 10 samples isolated in Rio de Janeiro showed a CRF45_cpx-like pattern throughout the sequenced genome. The remaining were classified as second-generation recombinants, showing the mosaic patterns: CRF45_cpx/B/D/F1/U, CRF45_cpx/B/F1/U, CRF45_cpx/B/U and CRF45_cpx/F1. All Brazilian CRF45_cpx sequences, except one, formed a monophyletic clade (CRF45-BR), which seems to be the result of a single introduction event that has spread to the Rio de Janeiro, São Paulo and Minas Gerais states and is related to sequences from Argentina, Italy and Belgium. The Bayesian analyses pointed out quite consistent onset dates for CRF45-BR clade (~1984: 1976-1996) in the three gene datasets. These results indicate that the CRF45-BR clade has been circulating in the Southeastern Brazilian region for about 30years, although its presence was not detected until recently due to its very low prevalence. This reinforces the relevance of large-scale molecular surveillance data to identify the emergence of new HIV variants and their impact on local epidemics.