scholarly journals HIV-1 molecular diversity in Brazil unveiled by 10 years of sampling by the national genotyping network

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Tiago Gräf ◽  
Gonzalo Bello ◽  
Paula Andrade ◽  
Ighor Arantes ◽  
João Marcos Pereira ◽  
...  
Keyword(s):  
Temporal Dynamics ◽  
Pearson Correlation ◽  
Demographic Data ◽  
Viral Transmission ◽  
Western World ◽  
Female Ratio ◽  
Highly Educated ◽  
Molecular Features ◽  
Sex With Men ◽  
Hiv 1

AbstractHIV-1 has diversified into several subtypes and recombinant forms that are heterogeneously spread around the world. Understanding the distribution of viral variants and their temporal dynamics can help to design vaccines and monitor changes in viral transmission patterns. Brazil has one of the largest HIV-1 epidemics in the western-world and the molecular features of the virus circulating in the country are still not completely known. Over 50,000 partial HIV-1 genomes sampled between 2008 and 2017 by the Brazilian genotyping network (RENAGENO) were analyzed. Sequences were filtered by quality, duplicate sequences per patient were removed and subtyping was performed with online tools and molecular phylogeny. Association between patients’ demographic data and subtypes were performed by calculating the relative risk in a multinomial analysis and trends in subtype prevalence were tested by Pearson correlation. HIV-1B was found to be the most prevalent subtype throughout the country except in the south, where HIV-1C prevails. An increasing trend in the proportion of HIV-1C and F1 was observed in several regions of the country, while HIV-1B tended to decrease. Men and highly educated individuals were more frequently infected by HIV-1B and non-B variants were more prevalent among women with lower education. Our results suggest that socio-demographic factors partially segregate HIV-1 diversity in Brazil while shaping viral transmission networks. Historical events could explain a preferential circulation of HIV-1B among men who have sex with men (MSM) and non-B variants among heterosexual individuals. In view of an increasing male/female ratio of AIDS cases in Brazil in the last 10–15 years, the decrease of HIV-1B prevalence is surprising and suggests a greater penetrance of non-B subtypes in MSM transmission chains.

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

2004 ◽  
Vol 132 (4) ◽  
pp. 693-698 ◽  
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.

scholarly journals Recently acquired HIV infection in men who have sex with men (MSM) in France, 2003-2008

2009 ◽  
Vol 14 (48) ◽  
Author(s):  
C Semaille ◽  
F Cazein ◽  
F Lot ◽  
J Pillonel ◽  
S Le Vu ◽  
...  
Keyword(s):  
Clinical Symptoms ◽  
Economic Status ◽  
Life Time ◽  
Newly Diagnosed ◽  
Highly Educated ◽  
Paris Area ◽  
Sex With Men ◽  
Case Notification ◽  
Reporting Delay ◽  
Hiv 1

An increase in the number of new HIV diagnoses among men who have sex with men (MSM) was observed in several countries in the early 2000s. In this article, we explore the trends among MSM in France between 2003 and 2008. To estimate the number of MSM newly diagnosed with HIV, we take into account the reporting delay, underreporting and missing data for HIV case notification. To identify recent infections (RI) (acquired an average of six months before diagnosis), we used an enzyme immunoassay for recent HIV-1 infections (EIA-RI) which has been performed routinely for new HIV diagnoses since 2003. Multivariate analysis was used to identify factors associated with RI. We estimate that between 1,900 and 2,400 MSM have been newly diagnosed with HIV every year: the proportion of MSM among all newly diagnosed with HIV cases has increased from 25.2% (95% confidence interval (CI): 23.3-27.1) in 2003 to 37.0% (95% CI: 35.2-38.7) in 2008 and was stable during the period 2006-2008. In 2008, the rate of newly diagnosed HIV cases per 10,000 MSM living in France was 72.5. The proportion of non-B subtypes of HIV-1 among cases diagnosed in MSM was 11.7% (2003-2008). The assessment of RI was performed for 4,819 MSM newly diagnosed with HIV in 2003-2008. Of these, 47.6% (95%CI = 46.2-49.0) (2,295 cases) were shown to have been recently infected. The risk of RI was greater for those of French nationality (adjusted odds ratio (aOR) =1.6 [95% CI: 1.4-1.9]), those with high economic status (aOR =1.4 [95% CI: 1.2-1.8]), those tested after a risk exposure (aOR =1.6[95% CI: 1.3-1.8]) or after presenting with clinical symptoms or abnormal biological markers (aOR =1.8 [95% CI: 1.5-2.0]), those who had tested for HIV three or more times during their life-time (aOR =4.2 [95% CI: 3.4-5.2]) and those living in the Paris area (aOR =1.2 [95% CI: 1.0-1.3]). The risk of RI decreased with age. The HIV situation among MSM living in France is a cause of concern, despite the prevention campaigns dedicated to this highly educated sub-population.

scholarly journals A8 Epidemiological study of transmission clusters in a local HIV-1 cohort

2019 ◽  
Vol 5 (Supplement_1) ◽  
Author(s):  
Carmen M González Domenech ◽  
Isabel Viciana-Ramos ◽  
Gabriel Sena-Corrales ◽  
Laura Mora Navas ◽  
Guillermo Ojeda ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Demographic Data ◽  
Phylogenetic Reconstruction ◽  
Likelihood Method ◽  
Resistance Mutations ◽  
Primary Resistance ◽  
Number Of Patients ◽  
Sex With Men ◽  
K103n Mutation ◽  
Hiv 1

Abstract Integration of molecular, clinical, and demographic data represents a powerful tool to understand the dynamics of local HIV-1 transmission chains (TCs). The aim of our study was the phylogenetic analysis of the TCs within a HIV-1 cohort and the description of the relevant patient data within a TC. We performed a phylogenetic analysis of 757 sequences from newly HIV-1 diagnosed patients in Málaga (Southern Spain) during the period 2004–15. We used partial pol gene sequences in a preliminary phylogenetic reconstruction using the Neighbour Joining method (MEGA v6.06 program). After eliminating branches with bootstrap values <80 per cent, we constructed a new phylogeny by Maximum likelihood method (FastTree program). We considered as TC any cluster with bootstrap values ≥ 90 per cent. Patient sequences within and outside TCs were compared. Resistance mutations in the protease (PR) and reverse transcriptase (RT) sequences were analyzed using the Stanford algorithm. Four hundred and fifty-one out of 757 patients (59.6%) were grouped into fifty-three TCs, seventeen of them with five or more subjects. The largest number of patients associated within a TC was ninety. Patients younger than 40 years [odds ratio (OR) 1.75, 95% confidence interval (95% CI) 1.2–2.4, P = 0.002], men who have sex with men (MSM) (OR 2.14, 95% CI 1.3–3.2, P < 0.0001), non-Spanish (OR 1.48, 95% CI 1.0–2.1, P = 0.038), with a non-B subtype HIV-1 (OR 3.12, 95% CI 2.0–4.8, P < 0.0001), and presenting primary resistance mutations (OR 14.1, 95% CI 3.1–62.6, P = 0.001) were more likely to be associated within a cluster. Ninety-four out of 118 patients (79.6%) with transmission resistance mutations were included in some TC. The most frequent mutations associated with clusters were T69D/N, L210W, and K219E/Q, for NRTIs, K103N, and G190A/S for NNRTIs, and the I54L/M and L90M mutations for PIs. The prevalence for resistance to NNRTIs in TCs was 13.7 per cent. There were two TCs of rarer non-B subtypes: CRF19_cpx, with twenty-one individuals, sixteen of them (76.2%) with mutation G190A; and CRF51_01B with thirty-nine patients, twenty of them with the K103N mutation. Approximately 60 per cent of newly HIV-1 diagnosed patients were included in a TC. Younger patients, MSM, non-Spanish, with non-B subtype HIV-1 and primary resistance mutations were more likely to belong to a cluster. NNRTI mutations were the most frequent ones among patients in TCs. We observed two TCs represented by infrequent non-B subtypes in our area—CRF19_cpx and CRF51_01B—both of which were associated to the transmission of primary resistance.

scholarly journals HIV subtypes in Scotland, 2000–2006

2007 ◽  
Vol 136 (8) ◽  
pp. 1069-1075 ◽  
Author(s):  
D. L. YIRRELL ◽  
L. SHAW ◽  
E. CAMPBELL ◽  
S. M. BURNS ◽  
S. O. CAMERON ◽  
...  
Keyword(s):  
Drug Users ◽  
Geographical Origin ◽  
Demographic Data ◽  
Risk Groups ◽  
Intravenous Drug Users ◽  
Subtype B ◽  
The Social ◽  
Sex With Men ◽  
Hiv 1 ◽  
Hiv Subtypes

SUMMARYThe purpose of this study was to document the dynamics of HIV-1 subtypes in Scotland over a 6-year period. Viral RNA from all-new diagnoses was amplified by nested PCR and sequenced in the gag and/or env regions. Subtype was assigned by phylogenetic analysis, and aligned with demographic data including likely route and geographical origin of infection. We present data on 80% of all new diagnoses in Scotland between April 2000 and April 2006. Within the background of an expanding epidemic, subtype B predominates in men who have sex with men and intravenous drug users but there is a small but consistent number of UK-acquired infections in these risk groups caused by non-B subtypes. In heterosexuals, non-B subtypes acquired abroad, especially Africa, are still the largest group but again UK-acquired numbers are rising. The social and clinical significance of the spread of non-B subtypes in different ethnic and risk groups remains to be established.

The identification of a novel HIV-1 second-generation recombinant form (CRF01_AE/CRF07_BC) among men who have sex with men in Jiangsu, China

2020 ◽  
Vol 18 ◽  
Author(s):  
Yin Yueqi ◽  
Zhou Ying ◽  
Lu Jing ◽  
Guo Hongxiong ◽  
Chen Jianshuang ◽  
...  
Keyword(s):  
Maximum Likelihood ◽  
Phylogenetic Trees ◽  
Second Generation ◽  
Emergency Situation ◽  
The World ◽  
Break Points ◽  
Sex With Men ◽  
Full Length Genome ◽  
Virus Strains ◽  
Hiv 1

Background: CRF01_AE and CRF07_BC are the two major HIV-1 virus strains circulating in China. The proportion of dominant subtypes (CRF01_AE and CRF07_BC) among MSM in Jiangsu province was over 80%. A large number of URFs have been found in China in recently years. Objective: This study aimed to report on novel HIV-1 recombinants. Method: We constructed Phylogenetic trees using the maximum likelihood (ML) method with 1000 bootstrap replicates in IQ-TREE 1.6.8 software and determined recombination break points using SimPlot 3.5.1. Results: We identified a novel, second-generation HIV-1 recombinant (JS020202) between CRF01_AE and CRF07_BC. The analysis of near full-length genome (NFLG) showed there were at least 8 breakpoints inner virus, which differed from any previously identified CRF and URF around the world. Conclusion: Novel diverse CRF01_AE/07_BC suggested the complexity trends of HIV-1 genetics. The emergency situation of diverse recombinant strains should be monitored continuously.

The prevalence of hepatitis B and C co-infections among people with HIV-1 in Bulgaria: 2010–2015

2019 ◽  
Vol 14 (12) ◽  
pp. 791-798
Author(s):  
Ivailo Alexiev ◽  
Elitsa Golkocheva-Markova ◽  
Asya Kostadinova ◽  
Reneta Dimitrova ◽  
Lora Nikolova ◽  
...  
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Hepatitis B ◽  
Hepatitis B Surface Antigen ◽  
Hcv Rna ◽  
B Virus ◽  
Sex With Men ◽  
Multiple Risk Behavior ◽  
Hiv 1 ◽  
Hiv Aids

Aim: To evaluate hepatitis B virus (HBV) and hepatitis C virus (HCV) among individuals with HIV/AIDS in Bulgaria diagnosed between 2010 and 2015. Materials & methods: A total of 1158 individuals were diagnosed with HIV/AIDS during the study period. Different transmission groups were tested with ELISA and real-time PCR for HBV and HCV markers. Results: Hepatitis B surface antigen and hepatitis C virus antiboby were found in 9.3 and 23.2% of the tested. HBV DNA and HCV RNA has been found in 47.4 and 69.6%. Hepatitis B and C co-infections were predominant in multiple risk behavior groups, including people who inject drugs, men who have sex with men, prisoners and Roma individuals. Conclusion: HIV prevalence in Bulgaria is low but the rates of hepatitis B and C co-infections among these patients fall within the upper range reported in Europe.

scholarly journals Estimation of HIV incidence in two Brazilian municipalities, 2013

2016 ◽  
Vol 50 (0) ◽  
Author(s):  
Célia Landmann Szwarcwald ◽  
Orlando da Costa Ferreira Júnior ◽  
Ana Maria de Brito ◽  
Karin Regina Luhm ◽  
Clea Elisa Lopes Ribeiro ◽  
...  
Keyword(s):  
Total Population ◽  
Hiv Infections ◽  
Incidence Rates ◽  
Hiv Incidence ◽  
Female Ratio ◽  
Exposure Category ◽  
Two Cities ◽  
Population Subgroup ◽  
Sex With Men ◽  
Male To Female

ABSTRACT OBJECTIVE To estimate HIV incidence in two Brazilian municipalities, Recife and Curitiba, in the year of 2013. METHODS The method for estimating incidence was based on primary information, resulting from the Lag-Avidity laboratory test for detection of recent HIV infections, applied in a sample of the cases diagnosed in the two cities in 2013. For the estimation of the HIV incidence for the total population of the cities, the recent infections detected in the research were annualized and weighted by the inverse of the probability of HIV testing in 2013 among the infected and not diagnosed cases. After estimating HIV incidence for the total population, the incidence rates were estimated by sex, age group, and exposure category. RESULTS In Recife, 902 individuals aged 13 years and older were diagnosed with HIV infection. From these, 528 were included in the study, and the estimated proportion of recent infections was 13.1%. In Curitiba, 1,013 people aged 13 years and older were diagnosed, 497 participated in the study, and the proportion of recent infections was 10.5%. In Recife, the estimated incidence rate was 53.1/100,000 inhabitants of 13 years and older, while in Curitiba, it was 41.1/100,000, with male-to-female ratio of 3.5 and 2.4, respectively. We observed high rates of HIV incidence among men who have sex with men, of 1.47% in Recife and 0.92% in Curitiba. CONCLUSIONS The results obtained in the two cities showed that the group of men who have sex with men are disproportionately subject to a greater risk of new infections, and indicate that strategies to control the spread of the epidemic in this population subgroup are essential and urgent.

scholarly journals HIV-1 Transmission Networks Among Men Who Have Sex With Men in Asia

2014 ◽  
Vol 59 (6) ◽  
pp. 910-911 ◽  
Author(s):  
K. T. Ng ◽  
K. Y. Ng ◽  
J. H.-K. Chen ◽  
O. T. Ng ◽  
A. Kamarulzaman ◽  
...  
Keyword(s):  
Transmission Networks ◽  
Sex With Men ◽  
Hiv 1
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