Genomic characterization and molecular evolution analysis of subtype B and BF recombinant HIV-1 strains among Argentinean men who have sex with men reveal a complex scenario

Abstract Human immunodeficiency virus-1 (HIV-1) is characterised by a vast genetic diversity classified into distinct phylogenetic strains and recombinant forms. We describe the HIV-1 molecular epidemiology and evolution of 129 consecutive HIV-1 positive migrants living in Milan (northern Italy). Polymerase gene sequences of 116 HIV-1 subtype-B positive patients were aligned with HIV-1 reference sequences (https://www.ncbi.nlm.nih.gov/) by using MAFFT alignment and edited by using Bioedit software. A maximum likelihood (ML) phylogenetic tree was performed by MEGA7 and was visualised by using FigTree v1.4.3. Of 129 migrants, 35 were born in Europe (28 in Eastern Europe), 70 in the Americas (67 in South America), 15 in Africa and nine in Asia; 76.4% were men who have sex with men (MSM). The serotype HIV-1-B prevailed (89.9%), followed by -C, -F1, -D and -A. Compared with 116 HIV-B patients, the 13 with HIV-non-B showed lower Nadir of CD4+ cell/mmc (P = 0.043), more frequently had sub Saharan origin (38.5 vs. 1.72%, P = 0.0001) and less frequently were MSM (40 vs. 74.5%, P = 0.02). The ML phylogenetic tree of the 116 HIV-1 subtype-B positive patients showed 13 statistically supported nodes (bootstrap > 70%). Most of the sequences included in these nodes have been isolated from male patients from the Americas and the most common risk factor was MSM. The low number of HIV-1 non-B subtype patients did not allow to perform this analysis. These results suggest a shift of HIV-1 prevention projects' focus and a continuous monitoring of HIV-1 molecular epidemiology among entry populations. Prevention efforts based on HIV molecular epidemiology may improve public health surveillance setting.

Download Full-text

Evolutionary History of HIV-1 Subtype B and CRF01_AE Transmission Clusters among Men Who Have Sex with Men (MSM) in Kuala Lumpur, Malaysia

PLoS ONE ◽

10.1371/journal.pone.0067286 ◽

2013 ◽

Vol 8 (6) ◽

pp. e67286 ◽

Cited By ~ 12

Author(s):

Kim Tien Ng ◽

Lai Yee Ong ◽

Sin How Lim ◽

Yutaka Takebe ◽

Adeeba Kamarulzaman ◽

...

Keyword(s):

Evolutionary History ◽

Kuala Lumpur ◽

Subtype B ◽

History Of ◽

Sex With Men ◽

Hiv 1

Download Full-text

Epidemiological and Molecular Characteristics of HIV-1 Infection in a Sample of Men Who Have Sex With Men in Brazil: Phylogeography of Major Subtype B and F1 Transmission Clusters

Frontiers in Microbiology ◽

10.3389/fmicb.2020.589937 ◽

2020 ◽

Vol 11 ◽

Author(s):

Ágabo Macêdo da Costa e Silva ◽

Mônica Nogueira da Guarda Reis ◽

Thaís Augusto Marinho ◽

Nara Rúbia de Freitas ◽

Sheila Araújo Teles ◽

...

Keyword(s):

Genetic Diversity ◽

Drug Resistance ◽

Reverse Transcriptase ◽

The State ◽

Enzyme Linked Immunosorbent Assay ◽

Molecular Characteristics ◽

Resistance Mutations ◽

Subtype B ◽

Sex With Men ◽

Hiv 1

This study describes human immunodeficiency virus 1 (HIV-1) prevalence, associated factors, viral genetic diversity, transmitted drug resistance (TDR), and acquired drug resistance mutations (DRM) among a population of 522 men who have sex with men (MSM) recruited by the respondent-driven sampling (RDS) method, in Goiânia city, the capital of the State of Goiás, Central-Western Brazil. All serum samples were tested using a four-generation enzyme-linked immunosorbent assay (ELISA), and reactive samples were confirmed by immunoblotting. Plasma RNA or proviral DNA was extracted, and partial polymerase (pol) gene including the protease/reverse transcriptase (PR/RT) region was amplified and sequenced. HIV-1 subtypes were identified by phylogenetic inference and by bootscan analysis. The time and location of the ancestral strains that originated the transmission clusters were estimated by a Bayesian phylogeographic approach. TDR and DRM were identified using the Stanford databases. Overall, HIV-1 prevalence was 17.6% (95% CI: 12.6–23.5). Self-declared black skin color, receptive anal intercourse, sex with drug user partner, and history of sexually transmitted infections were factors associated with HIV-1 infection. Of 105 HIV-1-positive samples, 78 (74.3%) were sequenced and subtyped as B (65.4%), F1 (20.5%), C (3.8%), and BF1 (10.3%). Most HIV-1 subtype B sequences (67%; 34 out of 51) branched within 12 monophyletic clusters of variable sizes, which probably arose in the State of Goiás between the 1980s and 2010s. Most subtype F1 sequences (n = 14, 88%) branched in a single monophyletic cluster that probably arose in Goiás around the late 1990s. Among 78 samples sequenced, three were from patients under antiretroviral therapy (ART); two presented DRM. Among 75 ART-naïve patients, TDR was identified in 13 (17.3%; CI 95%: 9.6–27.8). Resistance mutations to non-nucleoside reverse transcriptase inhibitors (NNRTI) predominated (14.7%), followed by nucleoside reverse transcriptase inhibitor (NRTI) mutations (5.3%) and protease inhibitor (PI) mutations (1.3%). This study shows a high prevalence of HIV-1 associated with sexual risk behaviors, high rate of TDR, and high genetic diversity driven by the local expansion of different subtype B and F1 strains. These findings can contribute to the understanding about the dissemination and epidemiological and molecular characteristics of HIV-1 among the population of MSM living away from the epicenter of epidemics in Brazil.

Download Full-text

HIV-1 subtype in Scotland: the establishment of a national surveillance system

Epidemiology and Infection ◽

10.1017/s095026880400233x ◽

2004 ◽

Vol 132 (4) ◽

pp. 693-698 ◽

Cited By ~ 10

Author(s):

D. L. YIRRELL ◽

L. SHAW ◽

S. M. BURNS ◽

S. O. CAMERON ◽

M. QUIGG ◽

...

Keyword(s):

United Kingdom ◽

Drug Users ◽

Demographic Data ◽

Risk Groups ◽

Heterosexual Contact ◽

The United Kingdom ◽

Subtype B ◽

Route Of Transmission ◽

Sex With Men ◽

Hiv 1

Historically, subtype B viruses in men who have sex with men (MSM) and injecting drug users (IDU) dominated the HIV epidemic in the United Kingdom, whereas non-B heterosexual infections dominate globally. Heterosexual contact is now the most common route of transmission in the United Kingdom. Here we monitor HIV subtype in Scotland, and link it to origin of infection. HIV-1 sequence was generated from new diagnoses and the subtype thus obtained linked with demographic data. Virus was subtyped from 80% (137/171) of all new diagnoses in Scotland. Of 58 individuals infected by heterosexual contact, 74% (43) harboured non-B viruses, contrasting with 7% (5/68) of those infected by IDU or MSM. Eighty-four per cent of non-Bs (46/55) were probably acquired outside the United Kingdom, but nine individuals probably acquired their non-B infection in the United Kingdom. Non-B subtypes of HIV-1 predominate in recently diagnosed, heterosexually acquired infections in Scotland and are present in all risk groups, even those with no exposure outside the United Kingdom.

Download Full-text

Genomic Characterization of Two Novel HIV-1 Second-Generation Recombinant Forms Among Men Who Have Sex with Men in Beijing, China

AIDS Research and Human Retroviruses ◽

10.1089/aid.2014.0307 ◽

2015 ◽

Vol 31 (3) ◽

pp. 342-346 ◽

Cited By ~ 12

Author(s):

Zheng Li ◽

Huamian Wei ◽

Yi Feng ◽

Jia Li ◽

Marcia L. Kalish ◽

...

Keyword(s):

Second Generation ◽

Genomic Characterization ◽

Sex With Men ◽

Beijing China ◽

Hiv 1

Download Full-text

Expanding HIV-1 subtype B transmission networks among men who have sex with men in Poland

PLoS ONE ◽

10.1371/journal.pone.0172473 ◽

2017 ◽

Vol 12 (2) ◽

pp. e0172473 ◽

Cited By ~ 13

Author(s):

Miłosz Parczewski ◽

Magdalena Leszczyszyn-Pynka ◽

Magdalena Witak-Jędra ◽

Bartosz Szetela ◽

Jacek Gąsiorowski ◽

...

Keyword(s):

Transmission Networks ◽

Subtype B ◽

Sex With Men ◽

Hiv 1

Download Full-text

Increase in HIV-1-transmitted drug resistance among ART-naïve youths at the China-Myanmar border during 2009 ~ 2017

BMC Infectious Diseases ◽

10.1186/s12879-021-05794-5 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Yibo Ding ◽

Min Chen ◽

Jibao Wang ◽

Yuecheng Yang ◽

Yi Feng ◽

...

Keyword(s):

Drug Resistance ◽

Reverse Transcriptase ◽

Cd4 Count ◽

Transmitted Drug Resistance ◽

Subtype C ◽

Reverse Transcriptase Inhibitors ◽

Recombination Hotspots ◽

Subtype B ◽

Sex With Men ◽

Hiv 1

Abstract Background HIV-transmitted drug resistance (TDR) is found in antiretroviral therapy (ART)-naïve populations infected with HIV-1 with TDR mutations and is important for guiding future first- and second-line ART regimens. We investigated TDR and its effect on CD4 count in ART-naïve youths from the China-Myanmar border near the Golden Triangle to better understand TDR and effectively guide ART. Methods From 2009 to 2017, 10,832 HIV-1 infected individuals were newly reported along the Dehong border of China, 573 ART-naïve youths (16 ~ 25 y) were enrolled. CD4 counts were obtained from whole blood samples. HIV pol gene sequences were amplified from RNA extracted from plasma. The Stanford REGA program and jpHMM recombination prediction tool were used to determine genotypes. TDR mutations (TDRMs) were analyzed using the Stanford Calibrated Population Resistance tool. Results The most common infection route was heterosexuals (70.51%), followed by people who inject drugs (PWID, 19.20%) and men who have sex with men (MSM) (8.90%). The distribution of HIV genotypes mainly included the unique recombinant form (URF) (44.08%), 38.68% were CRFs, 13.24% were subtype C and 4.04% were subtype B. The prevalence of TDR increased significantly from 2009 to 2017 (3.48 to 9.48%) in ART-naïve youths (4.00 to 13.16% in Burmese subjects, 3.33 to 5.93% in Chinese subjects), and the resistance to non-nucleoside reverse transcriptase inhibitors (NNRTIs), nucleoside and nucleotide reverse transcriptase inhibitors (NRTIs), and protease inhibitors (PIs) were 3.49, 2.62, and 0.52%, respectively. Most (94.40%, n = 34) of HIV-1-infected patients with TDRM had mutation that conferred resistance to a single drug class. The most common mutations Y181I/C and K103N, were found in 7 and 9 youths, respectively. The mean CD4 count was significantly lower among individuals with TDRMs (373/mm3 vs. 496/mm3, p = 0.013). Conclusions The increase in the prevalence of HIV-1 TDR increase and a low CD4 count of patients with TDRMs in the China-Myanmar border suggests the need for considering drug resistance before initiating ART in HIV recombination hotspots.

Download Full-text

Molecular Network Analysis Reveals Transmission of HIV-1 Drug-Resistant Strains Among Newly Diagnosed HIV-1 Infections in a Moderately HIV Endemic City in China

Frontiers in Microbiology ◽

10.3389/fmicb.2021.797771 ◽

2022 ◽

Vol 12 ◽

Author(s):

Bin Zhao ◽

Wei Song ◽

Mingming Kang ◽

Xue Dong ◽

Xin Li ◽

...

Keyword(s):

Network Analysis ◽

Molecular Network ◽

Transmitted Drug Resistance ◽

Newly Diagnosed ◽

Subtype B ◽

Sex With Men ◽

Treat All ◽

Few Data ◽

Drug Resistant Strains ◽

Hiv 1

Since the implementation of the “treat all” policy in China in 2016, there have been few data on the prevalence of transmitted drug resistance (TDR) in China. In this study, we describe TDR in patients newly diagnosed with human immunodeficiency virus (HIV) infection between 2016 and 2019 in Shenyang city, China. Demographic information and plasma samples from all newly reported HIV-infected individuals in Shenyang from 2016 to 2019 were collected. The HIV pol gene was amplified and sequenced for subtyping and TDR. The spread of TDR was analyzed by inferring an HIV molecular network based on pairwise genetic distance. In total, 2,882 sequences including CRF01_AE (2019/2,882, 70.0%), CRF07_BC (526/2,882, 18.3%), subtype B (132/2,882, 4.6%), and other subtypes (205/2,882, 7.1%) were obtained. The overall prevalence of TDR was 9.1% [95% confidence interval (CI): 8.1–10.2%]; the prevalence of TDR in each subtype in descending order was CRF07_BC [14.6% (95% CI: 11.7–18.0%)], subtype B [9.1% (95% CI: 4.8–15.3%)], CRF01_AE [7.9% (95% CI: 6.7–9.1%)], and other sequences [7.3% (95% CI: 4.2–11.8%)]. TDR mutations detected in more than 10 cases were Q58E (n = 51), M46ILV (n = 46), K103N (n = 26), E138AGKQ (n = 25), K103R/V179D (n = 20), and A98G (n = 12). Molecular network analysis revealed three CRF07_BC clusters with TDR [two with Q58E (29/29) and one with K103N (10/19)]; and five CRF01_AE clusters with TDR [two with M46L (6/6), one with A98G (4/4), one with E138A (3/3), and one with K103R/V179D (3/3)]. In the TDR clusters, 96.4% (53/55) of individuals were men who have sex with men (MSM). These results indicate that TDR is moderately prevalent in Shenyang (5–15%) and that TDR strains are mainly transmitted among MSM, providing precise targets for interventions in China.

Download Full-text

National molecular surveillance of recently acquired HIV infections in Germany, 2013 to 2014

Eurosurveillance ◽

10.2807/1560-7917.es.2017.22.2.30436 ◽

2017 ◽

Vol 22 (2) ◽

Cited By ~ 22

Author(s):

Andrea Hauser ◽

Alexandra Hofmann ◽

Kirsten Hanke ◽

Viviane Bremer ◽

Barbara Bartmeyer ◽

...

Keyword(s):

Drug Users ◽

Hiv Infections ◽

Heterosexual Transmission ◽

Transmitted Drug Resistance ◽

Robert Koch Institute ◽

Recent Infection ◽

Subtype B ◽

Statutory Duty ◽

Sex With Men ◽

Hiv 1

To enable an up-to-date molecular analysis of human immunodeficiency virus (HIV) genotypes circulating in Germany we have established a surveillance system based on recently acquired HIV infections. New HIV infections are reported to the Robert Koch Institute as a statutory duty for anonymous notification. In 2013 and 2014, a dried serum spot (DSS) sample was received from 6,371 newly diagnosed HIV-cases; their analysis suggested that 1,797 samples originated from a recent infection. Of these, 809 were successfully genotyped in the pol region to identify transmitted drug resistance (TDR) mutations and to determine the HIV-1 subtype. Total TDR was 10.8%, comprising 4.3% with mono-resistance to nucleoside reverse transcriptase inhibitors (NRTIs), 2.6% to non-NRTIs, 3.0% to protease inhibitors and 0.6% and 0.2%, respectively, with dual- and triple-class resistances. HIV-1 subtype B was most prevalent with 77.0%. Non-B infections were identified more often in men and women with heterosexual transmission compared with intravenous drug users or men who have sex with men (79% and 76%, 33%, 12%; all p < 0.05). Non-B subtypes were also more frequently found in patients originating from countries other than Germany (46% vs 14%; p < 0.05) and in patients infected outside of Germany (63% vs 14%; p < 0.05).

Download Full-text