Global molecular epidemiology of HIV-1: the chameleon challenge

Detection of Antiretroviral Drug-Resistant Mutations and HIV-1 Subtypes in Circulation Among Men Who Have Sex With Men, SEM Females, and Female Sex Workers: Results of Vietnam's HIV Sentinel Surveillance Plus System, 2018-2020

BACKGROUND

HIV drug resistance can reduce the effectiveness of antiretroviral drugs in preventing morbidity and mortality, limit options for treatment, and prevention. Our study aimed to assess HIV-1 subtypes and HIV drug resistance among key populations in HIV Sentinel Surveillance Plus Behavior in 2018 and 2020.

METHODS

One-stage venue-based cluster sampling was used to recruit participants at hotspots identified for men who have sex with men (MSM) in 7 provinces and sexual minority females and female sex workers (FSW) in 13 provinces. Participants completed a standard questionnaire about risk and preventive behaviors, and antiretroviral therapy history, and provided intravenous blood for HIV testing. HIV drug resistance testing was conducted on HIV-positive samples with viral load >1000 copies/mL.

RESULTS

A total of 185 of 435 (42.5%) HIV-positive samples had viral load ≥1000 copies/mL, of which 130 of 136 from MSM and 26 of 49 from FSW were successfully sequenced. Six HIV-1 subtypes were detected (CRF01_AE, A, CRF07/08_BC, B, C, CRF25_cpx), with CRF01_AE (82.7%, 129/156) the most common. Drug resistance mutations were detected in 16.7% of participants overall (26/156), in 15.4% (20/130) of MSM, and in 23.1% (6/26) of FSW. Mutations associated with resistance to non-nucleoside reverse transcriptase inhibitor (NNRTI) were the most frequently detected (73.1%, 19/26). The high level of resistance was presented in NNRTI and nucleoside reverse transcriptase inhibitors classes. There are 10 major resistance mutations detected with nucleoside reverse transcriptase inhibitors (M184VI-25.0%, K65KR-50.0%, Y115F-25%), NNRTI (K103N-21.1%, E138A-10.5%, V106M-5.3%, K101E-5.3%, G190A-5.3%), protease inhibitors (L33F-40.0%, M46L-20.0%).

CONCLUSIONS

Vietnam's HIV Sentinel Surveillance Plus system identified an emerging strain of HIV-1 and mutations associated with resistance to multiple drug classes among MSM and FSW.

Evaluation of the MAGLUMI HIV Ab/Ag combi test for the detection of HIV infection

BACKGROUND

Human immunodeficiency virus (HIV) infection screening and diagnosis are critical to control the HIV epidemic. Testing for anti-HIV antibodies (Ab) and antigens (Ag) in blood samples is the first step to screen people who have been potentially exposed to the virus. This study aimed to evaluate the performance of the MAGLUMI HIV Ab/Ag Combi for detection of HIV antibodies and antigens.

METHODS

We used residual samples to assess the diagnostic specificity and sensitivity of the MAGLUMI HIV Ab/Ag Combi retrospectively. All samples that met the test criteria were tested with the MAGLUMI HIV Ab/Ag Combi according to manufacturer's instruction. Results of the MAGLUMI HIV Ab/Ag Combi were compared with the Architect HIV Ag/Ab Combo test.

RESULTS

The specificity of the MAGLUMI HIV Ab/Ag Combi was 99.85% in 5,057 unselected blood donors and 100.00% in 213 hospitalized patient samples, respectively. The sensitivity of the Test in 614 HIV-1 Ab, HIV-1 Ag or HIV-2 Ab positive samples was 100.00%. Seroconversion sensitivity from results of 30 panels was comparable between the MAGLUMI HIV Ab/Ag Combi and the Architect assay.

CONCLUSIONS

The reactivity of the MAGLUMI HIV Ab/Ag Combi test is comparable to the Architect HIV Ag/Ab Combo assay.

Design of multivalent-epitope vaccine models directed toward the world's population against HIV-Gag polyprotein: Reverse vaccinology and immunoinformatics

Significant progress has been made in HIV-1 research; however, researchers have not yet achieved the objective of eradicating HIV-1 infection. Accordingly, in this study, eucaryotic and procaryotic in silico vaccines were developed for HIV-Gag polyproteins from 100 major HIV subtypes and CRFs using immunoinformatic techniques to simulate immune responses in mice and humans. The epitopes located in the conserved domains of the Gag polyprotein were evaluated for allergenicity, antigenicity, immunogenicity, toxicity, homology, topology, and IFN-γ induction. Adjuvants, linkers, CTLs, HTLs, and BCL epitopes were incorporated into the vaccine models. Strong binding affinities were detected between HLA/MHC alleles, TLR-2, TLR-3, TLR-4, TLR-7, and TLR-9, and vaccine models. Immunological simulation showed that innate and adaptive immune cells elicited active and consistent responses. The human vaccine model was matched with approximately 93.91% of the human population. The strong binding of the vaccine to MHC/HLA and TLR molecules was confirmed through molecular dynamic stimulation. Codon optimization ensured the successful translation of the designed constructs into human cells and E. coli hosts. We believe that the HIV-1 Gag vaccine formulated in our research can reduce the challenges faced in developing an HIV-1 vaccine. Nevertheless, experimental verification is necessary to confirm the effectiveness of these vaccines in these models.

Insights into the molecular network characteristics of major HIV-1 subtypes in developed Eastern China: a study based on comprehensive molecular surveillance data

PURPOSE

This study aimed to conduct a comprehensive molecular epidemiology study of major HIV-1 subtypes in developed Eastern China (Zhejiang Province).

METHODS

Plasma samples and epidemiological information were collected from 4180 newly diagnosed HIV-1 positive patients in Zhejiang Province in 2021. Pol sequences were obtained to determine the subtypes via multiple analytical tools. HIV-1 molecular networks were constructed on the basis of genetic distances to analyze transmission patterns among major subtypes. Furthermore, the birth-death skyline (BDSKY) model was utilized to estimate the transmission risks associated with large clusters (LCs).

RESULTS

In 4180 patients, 3699 (88.49%) pol sequences were successfully obtained and classified into four subtype groups. In the networks under an optimal genetic distance of 0.01 substitutions/site, the majority of links (74.52%, 1383/1856) involved individuals within the same city, highlighting the predominant role of local transmission in driving the HIV-1 epidemic. In the CRF07_BC, CRF01_AE, and others/URFs networks, men who have sex with men (MSM) were the primary sexual transmission population, with the younger MSM group (< 30 years old) exhibiting higher linkage frequencies. Within the CRF08_BC network, 93.98% of individuals were infected primarily through heterosexual contact and had a significantly greater risk of localized clustering than other subtypes did. Moreover, fifteen identified LCs were predominantly transmitted through commercial heterosexual contact (CHC), exhibiting localized clustering and high potential for sustained diffusion.

CONCLUSIONS

Overall, our findings reveal a diverse and heterogeneous distribution of HIV-1 subtypes in Zhejiang Province, with noticeable variations in hotspots across different geographic areas and populations.

Rev Protein Diversity in HIV-1 Group M Clades

The HIV-1 Rev protein expressed in the early stage of virus replication is involved in the nuclear export of some forms of virus RNA. Naturally occurring polymorphisms in the Rev protein could influence its activity. The association between the genetic features of different virus variants and HIV infection pathogenesis has been discussed for many years. In this study, Rev diversity among HIV-1 group M clades was analyzed to note the signatures that could influence Rev activity and, subsequently, clinical characteristics. From the Los Alamos HIV Sequence Database, 4962 Rev sequences were downloaded and 26 clades in HIV-1 group M were analyzed for amino acid changes, conservation in consensus sequences, and the presence of clade-specific amino acid substitutions (CSSs) and the Wu-Kabat protein variability coefficient (WK). Subtypes G, CRF 02_AG, B, and A1 showed the largest amino acid changes and diversity. The mean conservation of the Rev protein was 80.8%. In consensus sequences, signatures that could influence Rev activity were detected. In 15 out of 26 consensus sequences, an insertion associated with the reduced export activity of the Rev protein, 95QSQGTET96, was identified. A total of 32 CSSs were found in 16 clades, wherein A6 had the 41Q substitution in the functionally significant region of Rev. The high values of WK coefficient in sites 51 and 82, located on the Rev interaction surface, indicate the susceptibility of these positions to evolutionary replacements. Thus, the noted signatures require further investigation.

Cohort-Specific Peptide Reagents Broaden Depth and Breadth Estimates of the CD8 T Cell Response to HIV-1 Gag Potential T Cell Epitopes

An effective HIV vaccine will need to stimulate immune responses against the sequence diversity presented in circulating virus strains. In this study, we evaluate breadth and depth estimates of potential T-cell epitopes (PTEs) in transmitted founder virus sequence-derived cohort-specific peptide reagents against reagents representative of consensus and global sequences. CD8 T-cells from twenty-six HIV-1+ PBMC donor samples, obtained at 1-year post estimated date of infection, were evaluated. ELISpot assays compared responses to 15mer consensus (n = 121), multivalent-global (n = 320), and 10mer multivalent cohort-specific (n = 300) PTE peptides, all mapping to the Gag antigen. Responses to 38 consensus, 71 global, and 62 cohort-specific PTEs were confirmed, with sixty percent of common global and cohort-specific PTEs corresponding to consensus sequences. Both global and cohort-specific peptides exhibited broader epitope coverage compared to commonly used consensus reagents, with mean breadth estimates of 3.2 (global), 3.4 (cohort) and 2.2 (consensus) epitopes. Global or cohort peptides each identified unique epitope responses that would not be detected if these peptide pools were used alone. A peptide set designed around specific virologic and immunogenetic characteristics of a target cohort can expand the detection of CD8 T-cell responses to epitopes in circulating viruses, providing a novel way to better define the host response to HIV-1 with implications for vaccine development.

Molecular Epidemiology of HIV-1 Subtype G in the Russian Federation

Although HIV-1 subtype A has predominated in Russia since the end of the 20th century, other viral variants also circulate in this country. The dramatic outbreak of HIV-1 subtype G in 1988-1990 represents the origin of this variant spreading in Russia. However, full genome sequencing of the nosocomial viral variant and an analysis of the current circulating variants have not been conducted. We performed near full-length genome sequencing and phylogenetic and recombination analyses of 11 samples; the samples were determined to be subtype G based on an analysis of the pol region. Three samples were reliably obtained from patients infected during the nosocomial outbreak. The other 8 samples were obtained from patients who were diagnosed in 2010-2015. Phylogenetic analysis confirmed that a man from the Democratic Republic of the Congo was the origin of the outbreak. We also found that currently circulating viral variants that were genotyped as subtype G according to their pol region are in fact unique recombinant forms. These recombinant forms are similar to the BG-recombinants from Western Europe, particularly Spain and Portugal. The limitations of subtyping based on the pol region suggest that these viral variants are more widespread in Europe than is currently supposed.