Development of an HIV-1 Subtype Panel in China: Isolation and Characterization of 30 HIV-1 Primary Strains Circulating in China

Characterizing transcripts of HIV-1 different substrains using direct RNA sequencing

Post-transcriptional processing and modification of viral RNA, including alternative splicing, polyadenylation, and methylation, play crucial roles in regulating viral gene expression, enhancing genomic stability, and increasing replication efficiency. These processes have significant implications for viral biology and antiviral therapies. In this study, using Oxford Nanopore Technology (ONT) direct RNA sequencing (DRS), we provided a comprehensive analysis of the transcriptome and epitranscriptome features of the HIV-1 B (NL4-3) subtype strain and, for the first time, characterized these features in the CRF01_AE (GX2005002) subtype strain. We identified 11 novel splicing sites among the 61 RNA isoforms in NL4-3 and defined the splicing sites for GX2005002 based on its 63 RNA isoforms. Furthermore, we identified 74 and 79 chemically modified sites in the transcripts of NL4-3 and GX2005002, respectively. Although differences in poly(A) tail length were observed between the two HIV-1 strains, no specific correlation was detected between poly(A) tail length and the number of modification sites. Additionally, three distinct N6-methyladenosine (m6A) modification sites were identified in both NL4-3 and GX2005002 transcripts. This study provides a detailed analysis of post-transcriptional processing modifications in HIV-1 and suggests promising avenues for future research that could potentially be applied as new therapeutic targets in HIV treatment.

Near Full-Length Genomic Characterization of 16 HIV-1 CRF01_AE Primary Isolates from Guangxi, China

Isolation and culture of human immunodeficiency virus (HIV) are an important basis for acquired immune deficiency syndrome (AIDS) etiology, immunology, drug screening, clinical treatment, and vaccine research. CRF01_AE is one of the predominant strains of HIV-1 in China. However, there are few HIV-1 CRF01_AE isolates that have been reported. In this study, 16 HIV-1 CRF01_AE strains from Guangxi, China, were isolated, and the near full-length genomes were reverse transcribed and amplified in two halves with the 1 kb overlapping region. The polymerase chain reaction products were sequenced directly. The phylogenetic analysis results showed that all of the 16 isolated strains were CRF01_AE recombinant form, and two clusters were set up in the phylogenetic tree. The tropic prediction of 16 strains showed that 2 isolates were CCR5 tropic, and the others are CXCR4 tropic. Eight of the isolated strains are drug resistant according to the genetic prediction. These 16 near full-length characterized CRF01_AE isolates obtained in this study will provide valuable genomic and phenotypic information on HIV-1 strains circulating in China for related researches.

Overview of HIV molecular epidemiology among people who inject drugs in Europe and Asia

HIV strains continuously evolve, tend to recombine, and new circulating variants are being discovered. Novel strains complicate efforts to develop a vaccine against HIV and may exhibit higher transmission efficiency and virulence, and elevated resistance to antiretroviral agents. The United Nations Joint Programme on HIV/AIDS (UNAIDS) set an ambitious goal to end HIV as a public health threat by 2030 through comprehensive strategies that include epidemiological input as the first step of the process. In this context, molecular epidemiology becomes invaluable as it captures trends in HIV evolution rates that shape epidemiological pictures across several geographical areas. This review briefly summarizes the molecular epidemiology of HIV among people who inject drugs (PWID) in Europe and Asia. Following high transmission rates of subtype G and CRF14_BG among PWID in Portugal and Spain, two European countries, Greece and Romania, experienced recent HIV outbreaks in PWID that consisted of multiple transmission clusters including subtypes B, A, F1, and recombinants CRF14_BG and CRF35_AD. The latter was first identified in Afghanistan. Russia, Ukraine, and other Former Soviet Union (FSU) states are still facing the devastating effects of epidemics in PWID produced by A_FSU (also known as IDU-A), B_FSU (known as IDU-B), and CRF03_AB. In Asia, CRF01_AE and subtype B (Western B and Thai B) travelled from PWID in Thailand to neighboring countries. Recombination hotspots in South China, Northern Myanmar, and Malaysia have been generating several intersubtype and inter-CRF recombinants (e.g. CRF07_BC, CRF08_BC, CRF33_01B etc.), increasing the complexity of HIV molecular patterns.