Near-Full-Length Genomic Characterization of Two Novel HIV-1 Unique Recombinants (CRF01_AE/CRF07_BC) and (CRF01_AE/CRF68_01B) in Shijiazhuang, Hebei Province, China.

Heterosexual transmission (HETE) represents the predominant method of transmission for the human immunodeficiency virus type 1 (HIV-1) in Shijiazhuang, Hebei Province, China. The number of circulating recombinant forms (CRFs) and unique recombinant forms (URFs) continues to increase in this region. In the present study, two novel URFs (TFH010919 and TFH010944) were identified, both derived from HETEs in the Shijiazhuang area.

The origin and transmission of HIV-1 CRF80_0107 among two major first-tier cities in China.

Background: CRF01_AE and CRF07_BC are the two most prevalent HIV-1 genotypes in China, and the co-circulation of these two genotypes has led to the continuous generation of CRF_0107 viruses in recent years. However, little is known about the origin and spread of CRF_0107 viruses thus far. This study focused on HIV-1 CRF80_0107, which we previously identified among the MSM population in Beijing and Hebei Province, to explore the demographic distribution, transmission links, and temporal-spatial evolutionary features of the HIV-1 CRF80_0107 strain in China.

Identification of a Novel HIV-1 Second-Generation Circulating Recombinant Form (CRF117_0107) in China.

Under the background of the main epidemic HIV strains (CRF01_AE and CRF07_BC) co-circulation in China, more HIV second-generation recombinant (SGR) strains with CRF01_AE and CRF07_BC as the backbone were also emerging. In this study, we characterize a novel HIV-1 second-generation circulating recombinant form (CRF117_0107) consisting of CRF01_AE and CRF07_BC fragments from three epidemiologically unrelated HIV-1-infected individuals. One near full-length genome (NFLG) sequence was amplified, sequenced, and spliced in two halves using RNA extracted from the plasma of a homosexual in Shenzhen, Guangdong Province.

HIV-1 viral decay in blood and semen in antiretroviral-naïve adults initiating dolutegravir/lamivudine vs. bictegravir/emtricitabine/tenofovir alafenamide.

Background: Co-formulated dolutegravir and lamivudine (DTG/3TC) is recommended as the first-line antiretroviral therapy (ART); however, the data on the viral decay in seminal plasma (SP) and blood plasma (BP), as well as changes in inflammatory biomarkers in BP, remain limited among antiretroviral-naïve people with HIV (PWH) receiving DTG/3TC. A prospective observational cohort study was conducted to compare the impact of DTG/3TC vs. bictegravir/emtricitabine/tenofovir alafenamide (BIC/FTC/TAF) on viral decay kinetics and changes in inflammatory biomarkers in antiretroviral-naïve PWH.

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.

TaNAC1 boosts powdery mildew resistance by phosphorylation-dependent regulation of TaSec1a and TaCAMTA4 via PP2Ac/CDPK20.

The integrity of wheat (Triticum aestivum) production is increasingly jeopardized by the fungal pathogen Blumeria graminis f. sp. tritici (Bgt), particularly amid the vicissitudes of climate change.

Identification of Two Novel HIV-1 Unique Recombinant Forms (CRF01_AE/CRF07_BC) and Genomic Characterization in Tongzhou District of Beijing, China.

Continuous recombination and variation during replication could lead to rapid evolution and genetic diversity of HIV-1. Some studies had identified that it was easy to develop new recombinant strains of HIV-1 among the populations of men who have sex with men (MSM). Surveillance of genetic variants of HIV-1 in key populations was crucial for comprehending the development of regional HIV-1 epidemics.

Comprehensive Identification and Characterization of HML-9 Group in Chimpanzee Genome.

Endogenous retroviruses (ERVs) are related to long terminal repeat (LTR) retrotransposons, comprising gene sequences of exogenous retroviruses integrated into the host genome and inherited according to Mendelian law. They are considered to have contributed greatly to the evolution of host genome structure and function. We previously characterized HERV-K HML-9 in the human genome.

A unified classification system for HIV-1 5' long terminal repeats.

The HIV-1 provirus mainly consists of internal coding region flanked by 1 long terminal repeats (LTRs) at each terminus. The LTRs play important roles in HIV-1 reverse transcription, integration, and transcription. However, despite of the significant study advances of the internal coding regions of HIV-1 by using definite reference classification, there are no systematic and phylogenetic classifications for HIV-1 5' LTRs, which hinders our elaboration on 5' LTR and a better understanding of the viral origin, spread and therapy.

Sequence Note: Characterization of Two HIV-1 Strains with Novel Unique Recombinant Genome in Hebei, China.

In China, the proportion of HIV-1 infections due to men who have sex with men (MSM) has increased rapidly. More and more new subtypes are found among the MSM population besides known CRF01_AE, CRF07_BC, and B. The co-circulation of several HIV subtypes in the same population provides the opportunity to develop a new circulating recombinant form (CRF) and unique recombinant form (URF).

Near Full-Length Genome Characterization of Two Novel Unique Recombinants (CRF01_AE/CRF07_BC) in Beijing, China.

With the prevalence of human immunodeficiency virus type 1 (HIV-1) CRF01_AE and CRF07_BC subtypes in China, the co-circulation of multiple subtypes in the HIV-1-positive population may result in dual infection or superinfection in the population, leading to the emergence of unique recombinant forms (URFs) of the HIV-1 virus. In this study, two second-generation unique recombinant strains, BI0114 and BI0116, were identified, and their near full-length genome sequences were obtained. Recombination analysis showed that both sequences were isoforms of URF_0107, and they were second-generation unique recombinant strains formed by the recombination of CRF01_AE and CRF07_BC, with the isoforms being CRF01_AE and CRF0107_BC, respectively.

Near-full-length genome analysis of two novel HIV second recombinant forms in Hebei, China.

The number of individuals infected with HIV-1 among men who have sex with men (MSM) has risen rapidly in recent years in China, and the subtypes CRF01_AE, CRF07_BC, and B, as well as many novel unique recombinant forms (URFs) are prevalent among them. Co-circulation of strains among MSM populations allows the generation of circulating recombinant forms (CRFs) and URFs. In this study, we identified two new URFs from two HIV-1-positive subjects who were infected through homosexual contact in Hebei, China.

Comprehensive characterization of ERV-K (HML-8) in the chimpanzee genome revealed less genomic activity than humans.

Endogenous retroviruses (ERVs) originate from ancestral germline infections caused by exogenous retroviruses. Throughout evolution, they have become fixed within the genome of the animals into which they were integrated. As ERV elements coevolve with the host, they are normally epigenetically silenced and can become upregulated in a series of physiological and pathological processes.

Higher Expression of Human Endogenous Retrovirus-K was Observed in Peripheral B Lymphocytes of Leukemia and Lymphoma Patients.

Hematological malignant tumors (HMTs) are serious diseases that threaten human health and life with high mortality. Therefore, it is necessary to develop novel strategies for diagnosis and treatment. Human endogenous retroviruses (HERVs) have recently attracted increasing attention as potential targets for cancer diagnosis and therapy.

Identification of differentially expressed HERV-K(HML-2) loci in colorectal cancer.

Colorectal cancer is one of the malignant tumors with the highest mortality rate in the world. Survival rates vary significantly among patients at various stages of the disease. A biomarker capable of early diagnosis is required to facilitate the early detection and treatment of colorectal cancer.

Increased prevalence and stable clustering rate of HIV-1 transmitted drug resistance strains after 'treat-all' in a megacity of China.

Objectives: The 'treat-all' strategy was implemented in Shenzhen, China in 2016. The effect of this extensive treatment on transmitted drug resistance (TDR) of HIV is unclear.

Methods: TDR analysis was performed, based on the partial HIV-1 pol gene obtained from the newly reported HIV-1 positive cases from 2011 to 2019 in Shenzhen, China.

The Long Terminal Repeat Sequence of Subtype C and CRF01_AE Recombinants in China.

HIV-1 provirus is flanked by one long terminal repeat (LTR) at each terminal. The 5' LTR plays important roles in HIV-1 life cycle, especially, it determines HIV-1 transcription. However, there are 810 5' LTR entries exist in the HIV-1 sequence database, accounting for only 0.

Identification of Two Novel HIV-1 Second-Generation Recombinant Forms (CRF01_AE/CRF07_BC) in Men Who Have Sex with Men in Hebei, China.

In recent years, men who have sex with men (MSM) have been identified as the primary source of HIV-1 transmission in Hebei Province, China. Co-circulation of multiple subtypes in HIV-1 positive MSM populations may contribute to the emergence of the second generation of recombinant HIV-1 strains, indicating the occurrence of dual infections or superinfections in MSM populations. Thus, the discovery of new recombinant strains is important to indicate the appearance of multiple infected individuals and the prevalence caused by changes in the parent strains.

Endogenous Retrovirus Elements Are Co-Expressed with IFN Stimulation Genes in the JAK-STAT Pathway.

: Endogenous retrovirus (ERV) elements can act as proximal regulatory elements in promoting interferon (IFN) responses. Previous relevant studies have mainly focused on IFN-stimulated genes (ISGs). However, the role of ERV elements as cis-regulatory motifs in regulating genes of the JAK-STAT pathway remains poorly understood.

Identification and Characterization of the HERV-K (HML-8) Group of Human Endogenous Retroviruses in the Genome.

Human endogenous retroviruses (HERVs) can be vertically transmitted in a Mendelian fashion, are stably maintained in the human genome, and are estimated to constitute ∼8% of the genome. HERVs affect human physiology and pathology through their provirus-encoded protein or long terminal repeat (LTR) element effect. Characterization of the genomic distribution is an essential step to understanding the relationships between endogenous retrovirus expression and diseases.

Limited nucleotide changes of HIV-1 subtype B Rev response element in China affect overall Rev-RRE activity and viral replication.

The HIV-1 Rev response element (RRE) is a cis-acting RNA element that facilitates the nuclear export of mRNA-containing introns by binding specifically to the Rev protein, enabling a critical step in the viral replication cycle. This study aims to determine the subtype-specific loci of HIV-1 subtype B RRE circulating in China and to analyze their effects on Rev-RRE function and HIV-1 replication. We amplified 71 HIV-1 subtype B RRE full-length sequences from the HIV patients' blood samples collected in China, analyzed the subtype-specific loci on them by comparing them with subtype B in the United States, and predicted their RNA secondary structures.

Plasma metabolomics provides new insights into the relationship between metabolites and outcomes and left ventricular remodeling of coronary artery disease.

Background: Coronary artery disease (CAD) is a metabolically perturbed pathological condition. However, the knowledge of metabolic signatures on outcomes of CAD and their potential causal effects and impacts on left ventricular remodeling remains limited. We aim to assess the contribution of plasma metabolites to the risk of death and major adverse cardiovascular events (MACE) as well as left ventricular remodeling.

Establishment and application of a method of tagged-amplicon deep sequencing for low-abundance drug resistance in HIV-1.

In the latest HIV-1 global drug resistance report released by WHO, countries are advised to strengthen pre-treatment monitoring of drug resistance in AIDS patients. In this study, we established an NGS-based segmented amplification HIV-1 drug resistance mutation detection method. The region of HIV-1 was divided into three short fragments for NGS.