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

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.

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Molecular epidemiology of HIV-1 in Oryol Oblast, Russia

10.1101/2021.10.26.21265513 ◽

2021 ◽

Author(s):

Ksenia R Safina ◽

Yulia Sidorina ◽

Natalya Efendieva ◽

Elena Belonosova ◽

Darya Saleeva ◽

...

Keyword(s):

Molecular Epidemiology ◽

Drug Users ◽

Geographic Region ◽

Female Ratio ◽

Multiple Introductions ◽

Aids Epidemic ◽

Subtype B ◽

Subtype A ◽

Male To Female ◽

Hiv 1

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.

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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

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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.

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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.

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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.

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Molecular epidemiology of HIV-1 subtype A in former Soviet Union countries

PLoS ONE ◽

10.1371/journal.pone.0191891 ◽

2018 ◽

Vol 13 (2) ◽

pp. e0191891 ◽

Cited By ~ 8

Author(s):

Lazzat Aibekova ◽

Brian Foley ◽

Gonzalo Hortelano ◽

Muhammad Raees ◽

Sabit Abdraimov ◽

...

Keyword(s):

Soviet Union ◽

Molecular Epidemiology ◽

Former Soviet Union ◽

Subtype A ◽

Hiv 1

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Structure-Guided Redesign Increases the Propensity of HIV Env To Generate Highly Stable Soluble Trimers

Journal of Virology ◽

10.1128/jvi.02652-15 ◽

2015 ◽

Vol 90 (6) ◽

pp. 2806-2817 ◽

Cited By ~ 69

Author(s):

Javier Guenaga ◽

Viktoriya Dubrovskaya ◽

Natalia de Val ◽

Shailendra K. Sharma ◽

Barbara Carrette ◽

...

Keyword(s):

Neutralizing Antibodies ◽

Small Animal ◽

Subtype C ◽

Disulfide Linkage ◽

Vaccine Candidates ◽

Subtype B ◽

Subtype A ◽

Induced Changes ◽

Hiv 1 ◽

Hiv Diversity

ABSTRACTDue to high viral diversity, an effective HIV-1 vaccine will likely require Envs derived from multiple subtypes to generate broadly neutralizing antibodies (bNAbs). Soluble Env mimics, like the native flexibly linked (NFL) and SOSIP trimers, derived from the subtype A BG505 Env, form homogeneous, stable native-like trimers. However, other Env sequences, such as JRFL and 16055 from subtypes B and C, do so to a lesser degree. The high-resolution BG505 SOSIP crystal structures permit the identification and redesign of Env elements involved in trimer stability. Here, we identified structure trimer-derived (TD) residues that increased the propensity of the subtype B JRFL and subtype C 16055 Env sequences to form well-ordered, homogenous, and highly stable soluble trimers. The generation of these spike mimics no longer required antibody-based selection, positive or negative. Using the redesigned subtype B and C trimer representatives as respective foundations, we further stabilized the NFL TD trimers by engineering an intraprotomer disulfide linkage in the prebridging sheet, I201C-A433C (CC), that locks the gp120 in the receptor nontriggered state. We demonstrated that this disulfide pair prevented CD4 induced-conformational rearrangements in NFL trimers derived from the prototypic subtype A, B, and C representatives. Coupling the TD-based design with the engineered disulfide linkage, CC, increased the propensity of Env to form soluble highly stable spike mimics that are resistant to CD4-induced changes. These advances will allow testing of the hypothesis that such stabilized immunogens will more efficiently elicit neutralizing antibodies in small-animal models and primates.IMPORTANCEHIV-1 displays unprecedented global diversity circulating in the human population. Since the envelope glycoprotein (Env) is the target of neutralizing antibodies, Env-based vaccine candidates that address such diversity are needed. Soluble well-ordered Env mimics, typified by NFL and SOSIP trimers, are attractive vaccine candidates. However, the current designs do not allow most Envs to form well-ordered trimers. Here, we made design modifications to increase the propensity of representatives from two of the major HIV subtypes to form highly stable trimers. This approach should be applicable to other viral Envs, permitting the generation of a repertoire of homogeneous, highly stable trimers. The availability of such an array will allow us to assess if sequential or cocktail immune strategies can overcome some of the vaccine challenges presented by HIV diversity.

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Determination of Human Immunodeficiency Virus Type 1 Subtypes in Taiwan by vpu Gene Analysis

Journal of Clinical Microbiology ◽

10.1128/jcm.38.7.2468-2474.2000 ◽

2000 ◽

Vol 38 (7) ◽

pp. 2468-2474 ◽

Cited By ~ 12

Author(s):

Chun-Nan Lee ◽

Wei-Kung Wang ◽

Wen-Sheng Fan ◽

Shing-Jer Twu ◽

Shou-Chien Chen ◽

...

Keyword(s):

Human Immunodeficiency Virus ◽

Gene Analysis ◽

Heterosexual Transmission ◽

Subtype B ◽

Genetic Subtypes ◽

Immunodeficiency Virus ◽

Subtype A ◽

Hiv 1

The genetic diversity of human immunodeficiency virus (HIV) type 1 (HIV-1) has been characterized mainly by analysis of theenv and gag genes. Information on thevpu genes in the HIV sequence database is very limited. In the present study, the nucleotide sequences of the vpugenes were analyzed, and the genetic subtypes determined by analysis of the vpu gene were compared with those previously determined by analysis of the gag and env genes. Thevpu genes were amplified by nested PCR of proviral DNA extracted from 363 HIV-1-infected individuals and were sequenced directly by use of the PCR products. HIV-1 subtypes were determined by sequence alignment and phylogenetic analysis with reference strains. The strains in all except one of the samples analyzed could be classified as subtype A, B, C, E, or G. The vpu subtype of one strain could not be determined. Of the strains analyzed, genetic subtypes of 247 (68.0%) were also determined by analysis of theenv or gag gene. The genetic subtypes determined by vpu gene analysis were, in general, consistent with those determined by gag and/orenv gene analysis except for those for two AG recombinant strains. All the strains that clustered with a Thailand subtype E strain in the vpu phylogenetic analyses were subtype E byenv gene analysis and subtype A by gag gene analysis. In summary, our genetic typing revealed that subtype B strains, which constituted 73.8% of all strains analyzed, were most prevalent in Taiwan. While subtype E strains constituted about one-quarter of the viruses, they were prevalent at a higher proportion in the group infected by heterosexual transmission. Genetic analysis ofvpu may provide an alternate method for determination of HIV-1 subtypes for most of the strains, excluding those in which intersubtype recombination has occurred.

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Genomic diversity of human immunodeficiency virus type-1 in India

International Journal of STD & AIDS ◽

10.1258/0956462021924749 ◽

2002 ◽

Vol 13 (2) ◽

pp. 115-118 ◽

Cited By ~ 36

Author(s):

A K Sahni ◽

V V S P Prasad ◽

P Seth

Keyword(s):

Genomic Diversity ◽

New Delhi ◽

Subtype C ◽

Medical Sciences ◽

Clear Cut ◽

Reference Centre ◽

Subtype B ◽

History Of ◽

Subtype A ◽

Hiv 1

Surveillance of HIV-1 subtypes has important implications for the development of candidate vaccine and understanding the possible differences in the transmission and natural history of different subtypes. In this study, HIV-1 subtypes were determined for homologies in the C2-V3-V5 region by heteroduplex mobility assay (HMA) in HIV-1 seropositive patients referred to the National HIV/AIDS Reference Centre, All India Institute of Medical Sciences in New Delhi, India. Of the 125 samples analysed, 98 (78.4%) were HIV-1 subtype C, 11 (8.8%) were subtype B′, 3 (2.4%) were subtype A and 2 (1.6%) were subtype E. In 11 samples, subtype determination was not clear-cut. It is possible that these individuals may be infected with recombinant strains of HIV-1. These findings may have significant implications for the designing and testing of effective HIV-1 vaccine candidate in India.

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