Molecular epidemiology of HIV-1 in Oryol Oblast, Russia

The HIV/AIDS epidemic in Russia is growing, with approximately 100,000 people infected annually. Molecular epidemiology can provide insight on the structure and dynamics of the epidemic. However, its applicability in Russia is limited by the weakness of genetic surveillance, as viral genetic data is only available for <1% of cases. Here, we provide a detailed description of the HIV-1 epidemic for one geographic region of Russia, Oryol Oblast, by collecting and sequencing viral samples from about a third of its HIV-positive population. We identify multiple introductions of HIV-1 into Oryol Oblast, resulting in 82 transmission lineages that together comprise 66% of the samples. Most introductions are of subtype A, the predominant HIV-1 subtype in Russia, followed by CRF63 and subtype B. Bayesian analysis estimates the effective reproduction number Re for subtype A at 2.8 [1.7-4.4], in line with a growing epidemic. The frequency of CRF63 has been growing more rapidly, with the median Re of 11.8 [4.6-28.7], in agreement with recent reports of this variant rising in frequency in some regions of Russia. In contrast to the patterns described previously in European and North American countries, we see no overrepresentation of males in transmission lineages; meanwhile, injecting drug users are overrepresented in transmission lineages. This likely reflects the structure of the HIV-1 epidemic in Russia dominated by heterosexual and, to smaller extent, IDU transmission. Samples attributed to MSM transmission are associated with subtype B and are less prevalent than expected from the male-to-female ratio for this subtype, suggesting underreporting of this transmission route. Together, our results provide a high-resolution description of the HIV-1 epidemic in Oryol Oblast, Russia, characterized by frequent interregional transmission, rapid growth of the epidemic and rapid displacement of subtype A with the recombinant CRF63 variant.

Download Full-text

Molecular Epidemiology of an HIV-1 Subtype A Subcluster among Injection Drug Users in the Southern Ukraine

AIDS Research and Human Retroviruses ◽

10.1089/aid.1998.14.1079 ◽

1998 ◽

Vol 14 (12) ◽

pp. 1079-1085 ◽

Cited By ~ 51

Author(s):

VLADIMIR A. NOVITSKY ◽

MONTY A. MONTANO ◽

MAX ESSEX

Keyword(s):

Molecular Epidemiology ◽

Injection Drug Users ◽

Drug Users ◽

Injection Drug ◽

Subtype A ◽

Southern Ukraine ◽

Hiv 1

Download Full-text

Molecular Epidemiology of HIV-1 Subtype B, CRF01_AE, and CRF07_BC Infection Among Injection Drug Users in Taiwan

JAIDS Journal of Acquired Immune Deficiency Syndromes ◽

10.1097/qai.0b013e3181ccba1a ◽

2010 ◽

Vol 53 (4) ◽

pp. 425-439 ◽

Cited By ~ 12

Author(s):

Yen-Ju Chen ◽

Yu-Huei Huang ◽

Shao-Yuan Chuang ◽

Diana Yu-Ting Kao ◽

Yu-Ching Lan ◽

...

Keyword(s):

Molecular Epidemiology ◽

Injection Drug Users ◽

Drug Users ◽

Injection Drug ◽

Subtype B ◽

Hiv 1

Download Full-text

Molecular epidemiology and HIV-1 variant evolution in Poland between 2015 and 2019

Scientific Reports ◽

10.1038/s41598-021-96125-w ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Karol Serwin ◽

Anna Urbańska ◽

Kaja Scheibe ◽

Magdalena Witak-Jędra ◽

Maria Jankowska ◽

...

Keyword(s):

Molecular Epidemiology ◽

Temporal Trends ◽

Gene Fragment ◽

Molecular Surveillance ◽

Subtype B ◽

Subtype A ◽

Hiv 1

AbstractThe occurrence of HIV-1 subtypes differs worldwide and within Europe, with non-B variants mainly found across different exposure groups. In this study, we investigated the distribution and temporal trends in HIV-1 subtype variability across Poland between 2015 and 2019. Sequences of the pol gene fragment from 2518 individuals were used for the analysis of subtype prevalence. Subtype B was dominant (n = 2163, 85.90%). The proportion of subtype B-infected individuals decreased significantly, from 89.3% in 2015 to 80.3% in 2019. This was related to the increasing number of subtype A infections. In 355 (14.10%) sequences, non-B variants were identified. In 65 (2.58%) samples, recombinant forms (RFs) were noted. Unique recombinant forms (URFs) were found in 30 (1.19%) sequences. Three A/B recombinant clusters were identified of which two were A6/B mosaic viruses not previously described. Non-B clades were significantly more common among females (n = 81, 22.8%, p = 0.001) and heterosexually infected individuals (n = 45, 32.4%, p = 0.0031). The predominance of subtype B is evident, but the variability of HIV-1 in Poland is notable. Almost half of RFs (n = 65, 2.58%) was comprised of URFs (n = 30, 1.19%); thus those forms were common in the analyzed population. Hence, molecular surveillance of identified variants ensures recognition of HIV-1 evolution in Poland.

Download Full-text

022 A heterosexual outbreak in Doncaster involving subtype B of HIV-1: molecular epidemiology as a supplement to contact tracing

HIV Medicine ◽

10.1046/j.1468-1293.2000.00024-43.x ◽

2000 ◽

Vol 1 (3) ◽

pp. 172-172

Author(s):

A Hayman ◽

T Moss ◽

C Arnold ◽

l Naylor-Adamson ◽

J Hawkswell ◽

...

Keyword(s):

Molecular Epidemiology ◽

Contact Tracing ◽

Subtype B ◽

Hiv 1

Download Full-text

HIV Prevalence and Frequency of Risk Behavior in Injecting Drug Users Entering Treatment and Out of Treatment: A Cross-Sectional Study in Five Italian Cities

Journal of Drug Issues ◽

10.1177/002204269402400312 ◽

1994 ◽

Vol 24 (3) ◽

pp. 527-535 ◽

Cited By ~ 6

Author(s):

Giovanni Rezza ◽

Stefania Salmaso ◽

Damiano Abeni ◽

Giovanna Brancato ◽

Alessandra Anemona ◽

...

Keyword(s):

Risk Behavior ◽

Drug Users ◽

Injecting Drug Users ◽

Cross Sectional Study ◽

Hiv Prevalence ◽

Sectional Study ◽

Cross Sectional ◽

Female Ratio ◽

Outreach Programs ◽

Male To Female

We conducted a study to describe current patterns of drug-related behaviors, and to identify characteristics that may distinguish injecting drug users entering treatment from those out of treatment, in five Italian cities. Overall, 1,180 subjects were recruited — 568 entering treatment and 612 out of treatment. Male to female ratio was 6.6:1. The median age was similar in the two groups. A high proportion of injecting drug users recruited out of treatment had been in treatment at least once. HIV prevalence among injecting drug users entering treatment was not higher than that of those who were out of treatment. Furthermore, a large proportion of injecting drug users who still were out of treatment reported having adopted safe behaviors. The results of the study emphasize the need to implement outreach programs aimed at harm reduction.

Download Full-text

Efficiencies of Four Versions of the AMPLICOR HIV-1 MONITOR Test for Quantification of Different Subtypes of Human Immunodeficiency Virus Type 1

Journal of Clinical Microbiology ◽

10.1128/jcm.37.1.110-116.1999 ◽

1999 ◽

Vol 37 (1) ◽

pp. 110-116 ◽

Cited By ~ 74

Author(s):

K. Triques ◽

J. Coste ◽

J. L. Perret ◽

C. Segarra ◽

E. Mpoudi ◽

...

Keyword(s):

Human Immunodeficiency Virus ◽

Viral Load ◽

Pcr Primers ◽

Load Test ◽

Subtype C ◽

Subtype B ◽

Immunodeficiency Virus ◽

Subtype A ◽

Hiv 1

Three versions of a commercial human immunodeficiency virus (HIV) type 1 (HIV-1) load test (the AMPLICOR HIV-1 MONITOR Test versions 1.0, 1.0+, and 1.5; Roche Diagnostics, Branchburg, N.J.) were evaluated for their ability to detect and quantify HIV-1 RNA of different genetic subtypes. Plasma samples from 96 patients infected with various subtypes of HIV-1 (55 patients infected with subtype A, 9 with subtype B, 21 with subtype C, 2 with subtype D, 7 with subtype E, and 2 with subtype G) and cultured virus from 29 HIV-1 reference strains (3 of subtype A, 6 of subtype B, 5 of subtype C, 3 of subtype D, 8 of subtype E, 3 of subtype F, and 1 of subtype G) were tested. Detection of subtypes A and E was significantly improved with versions 1.0+ and 1.5 compared to that with version 1.0, whereas detection of subtypes B, C, D, and G was equivalent with the three versions. Versions 1.0, 1.0+, and 1.5 detected 65, 98, and 100% of the subtype A-infected samples from patients, respectively, and 71, 100, and 100% of the subtype E-infected samples from patients, respectively. Version 1.5 yielded a significant increase in viral load for samples infected with subtypes A and E (greater than 1 log10 HIV RNA copies/ml). For samples infected with subtype B, C, and D and tested with version 1.5, only a slight increase in viral load was observed (<0.5 log10). We also evaluated a prototype automated version of the test that uses the same PCR primers as version 1.5. The results with the prototype automated test were highly correlated with those of the version 1.5 test for all subtypes, but were lower overall. The AMPLICOR HIV-1 MONITOR Test, version 1.5, yielded accurate measurement of the HIV load for all HIV-1 subtypes tested, which should allow the test to be used to assess disease prognosis and response to antiretroviral treatment in patients infected with a group M HIV-1 subtype.

Download Full-text

Amino Acid Deletions in p6Gag Domain of HIV-1 CRF07_BC Ameliorate Galectin-3 Mediated Enhancement in Viral Budding

International Journal of Molecular Sciences ◽

10.3390/ijms21082910 ◽

2020 ◽

Vol 21 (8) ◽

pp. 2910 ◽

Cited By ~ 1

Author(s):

Wen-Hung Wang ◽

Chun-Sheng Yeh ◽

Chih-Yen Lin ◽

Ruei-Yu Yuan ◽

Aspiro Nayim Urbina ◽

...

Keyword(s):

Amino Acid ◽

Drug Users ◽

Potential Effect ◽

Promoting Effect ◽

Viral Budding ◽

Subtype B ◽

Infectious Clones ◽

Galectin 3 ◽

Hiv 1

HIV-1 CRF07_BC is a recombinant virus with amino acid (a.a.) deletions in p6Gag, which are overlapped with the Alix-binding domain. Galectin-3 (Gal3), a β-galactose binding lectin, has been reported to interact with Alix and regulate HIV-1 subtype B budding. This study aims to evaluate the role of Gal3 in HIV-1 CRF07_BC infection and the potential effect of a.a. deletions on Gal3-mediated regulation. A total of 38 HIV-1+ injecting drug users (IDUs) were enrolled in the study. Viral characterization and correlation of Gal3 were validated. CRF07_BC containing 7 a.a. deletions and wild-type in the p6Gag (CRF07_BC-7d and -wt) were isolated and infectious clones were generated. Viral growth kinetic and budding assays using Jurkat-CCR5/Jurkat-CCR5-Gal3 cells infected with CRF07_BC were performed. Results indicate that 69.4% (25/38) of the recruited patients were identified as CRF07_BC, and CRF07_BC-7d was predominant. Slow disease progression and significantly higher plasma Gal3 were noted in CRF07_BC patients (p < 0.01). Results revealed that CRF07_BC infection resulted in Gal3 expression, which was induced by Tat. Growth dynamic and budding assays indicated that Gal3 expression in Jurkat-CCR5 cells significantly enhanced CRF07_BC-wt replication and budding (p < 0.05), while the promoting effect was ameliorated in CRF07_BC-7d. Co-immunoprecipitation found that deletions in the p6Gag reduced Gal-3-mediated enhancement of the Alix–Gag interaction.

Download Full-text

Molecular Epidemiology of HIV-1 Infected Migrants Followed Up in Portugal: Trends between 2001–2017

Viruses ◽

10.3390/v12030268 ◽

2020 ◽

Vol 12 (3) ◽

pp. 268 ◽

Cited By ~ 2

Author(s):

Victor Pimentel ◽

Marta Pingarilho ◽

Daniela Alves ◽

Isabel Diogo ◽

Sandra Fernandes ◽

...

Keyword(s):

Drug Resistance ◽

Reverse Transcriptase ◽

Molecular Epidemiology ◽

Nucleoside Reverse Transcriptase Inhibitor ◽

Country Of Origin ◽

Transcriptase Inhibitor ◽

Subtype B ◽

Reverse Transcriptase Inhibitor ◽

Hiv 1 ◽

Over Time

Migration is associated with HIV-1 vulnerability. Objectives: To identify long-term trends in HIV-1 molecular epidemiology and antiretroviral drug resistance (ARV) among migrants followed up in Portugal Methods: 5177 patients were included between 2001 and 2017. Rega, Scuel, Comet, and jPHMM algorithms were used for subtyping. Transmitted drug resistance (TDR) and Acquired drug resistance (ADR) were defined as the presence of surveillance drug resistance mutations (SDRMs) and as mutations of the IAS-USA 2015 algorithm, respectively. Statistical analyses were performed. Results: HIV-1 subtypes infecting migrants were consistent with the ones prevailing in their countries of origin. Over time, overall TDR significantly increased and specifically for Non-nucleoside reverse transcriptase inhibitor (NNRTIs) and Nucleoside reverse transcriptase inhibitor (NRTIs). TDR was higher in patients from Mozambique. Country of origin Mozambique and subtype B were independently associated with TDR. Overall, ADR significantly decreased over time and specifically for NRTIs and Protease Inhibitors (PIs). Age, subtype B, and viral load were independently associated with ADR. Conclusions: HIV-1 molecular epidemiology in migrants suggests high levels of connectivity with their country of origin. The increasing levels of TDR in migrants could indicate an increase also in their countries of origin, where more efficient surveillance should occur.

Download Full-text

Molecular epidemiology of HIV-1 infection in immigrant population in northern Italy

Epidemiology and Infection ◽

10.1017/s0950268819002012 ◽

2020 ◽

Vol 148 ◽

Cited By ~ 3

Author(s):

Caterina Sagnelli ◽

Caterina Uberti-Foppa ◽

Sabrina Bagaglio ◽

Eleonora Cella ◽

Vittoria Scolamacchia ◽

...

Keyword(s):

Phylogenetic Tree ◽

Molecular Epidemiology ◽

Northern Italy ◽

Subtype B ◽

Immunodeficiency Virus ◽

Male Patients ◽

Sub Saharan ◽

Sex With Men ◽

Cd4 Cell ◽

Hiv 1

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