scholarly journals HIV-1 Sub-Subtype A6: Settings for Normalised Identification and Molecular Epidemiology in the Southern Federal District, Russia

Viruses ◽  
2020 ◽  
Vol 12 (4) ◽  
pp. 475 ◽  
Author(s):  
Madita Schlösser ◽  
Vladimir V. Kartashev ◽  
Visa H. Mikkola ◽  
Andrey Shemshura ◽  
Sergey Saukhat ◽  
...  
Keyword(s):  
Low Frequency ◽  
Federal District ◽  
Epidemiological Data ◽  
Epidemiological Studies ◽  
Heterosexual Contact ◽  
Hiv Epidemiology ◽  
Subtype B ◽  
Accurate Knowledge ◽  
Systematic Identification ◽  
Hiv 1

Russia has one of the largest and fastest growing HIV epidemics. However, epidemiological data are scarce. Sub-subtype A6 is most prevalent in Russia but its identification is challenging. We analysed protease/reverse transcriptase-, integrase-sequences, and epidemiological data from 303 patients to develop a methodology for the systematisation of A6 identification and to describe the HIV epidemiology in the Russian Southern Federal District. Drug consumption (32.0%) and heterosexual contact (27.1%) were the major reported transmission risks. This study successfully established the settings for systematic identification of A6 samples. Low frequency of subtype B (3.3%) and large prevalence of sub-subtype A6 (69.6%) and subtype G (23.4%) were detected. Transmitted PI- (8.8%) and NRTI-resistance (6.4%) were detected in therapy-naive patients. In therapy-experienced patients, 17.3% of the isolates showed resistance to PIs, 50.0% to NRTI, 39.2% to NNRTIs, and 9.5% to INSTIs. Multiresistance was identified in 52 isolates, 40 corresponding to two-class resistance and seven to three-class resistance. Two resistance-associated-mutations significantly associated to sub-subtype A6 samples: A62VRT and G190SRT. This study establishes the conditions for a systematic annotation of sub-subtype A6 to normalise epidemiological studies. Accurate knowledge on South Russian epidemiology will allow for the development of efficient regional frameworks for HIV-1 infection management.

scholarly journals Number of HIV-1 founder variants is determined by the recency of the source partner infection

Science ◽  
2020 ◽  
Vol 369 (6499) ◽  
pp. 103-108 ◽  
Author(s):  
Ch. Julián Villabona-Arenas ◽  
Matthew Hall ◽  
Katrina A. Lythgoe ◽  
Stephen G. Gaffney ◽  
Roland R. Regoes ◽  
...  
Keyword(s):  
Early Stage ◽  
Control Strategies ◽  
Sexual Transmission ◽  
Low Frequency ◽  
Epidemiological Data ◽  
High Genetic Diversity ◽  
Partner Characteristics ◽  
Infection Stage ◽  
Hiv 1 ◽  
Founder Strain

During sexual transmission, the high genetic diversity of HIV-1 within an individual is frequently reduced to one founder variant that initiates infection. Understanding the drivers of this bottleneck is crucial to developing effective infection control strategies. Little is known about the importance of the source partner during this bottleneck. To test the hypothesis that the source partner affects the number of HIV founder variants, we developed a phylodynamic model calibrated using genetic and epidemiological data on all existing transmission pairs for whom the direction of transmission and the infection stage of the source partner are known. Our results suggest that acquiring infection from someone in the acute (early) stage of infection increases the risk of multiple–founder variant transmission compared with acquiring infection from someone in the chronic (later) stage of infection. This study provides the first direct test of source partner characteristics to explain the low frequency of multiple–founder strain infections.

scholarly journals Contribution of Epidemiological Predictors in Unraveling the Phylogeographic History of HIV-1 Subtype C in Brazil

2015 ◽  
Vol 89 (24) ◽  
pp. 12341-12348 ◽  
Author(s):  
Tiago Gräf ◽  
Bram Vrancken ◽  
Dennis Maletich Junqueira ◽  
Rúbia Marília de Medeiros ◽  
Marc A. Suchard ◽  
...  
Keyword(s):  
Epidemiological Data ◽  
Sampling Bias ◽  
Alternative View ◽  
Subtype C ◽  
Data Set ◽  
Federal States ◽  
Subtype B ◽  
Phylogeographic History ◽  
History Of ◽  
Hiv 1

ABSTRACTThe phylogeographic history of the Brazilian HIV-1 subtype C (HIV-1C) epidemic is still unclear. Previous studies have mainly focused on the capital cities of Brazilian federal states, and the fact that HIV-1C infections increase at a higher rate than subtype B infections in Brazil calls for a better understanding of the process of spatial spread. A comprehensive sequence data set sampled across 22 Brazilian locations was assembled and analyzed. A Bayesian phylogeographic generalized linear model approach was used to reconstruct the spatiotemporal history of HIV-1C in Brazil, considering several potential explanatory predictors of the viral diffusion process. Analyses were performed on several subsampled data sets in order to mitigate potential sample biases. We reveal a central role for the city of Porto Alegre, the capital of the southernmost state, in the Brazilian HIV-1C epidemic (HIV-1C_BR), and the northward expansion of HIV-1C_BR could be linked to source populations with higher HIV-1 burdens and larger proportions of HIV-1C infections. The results presented here bring new insights to the continuing discussion about the HIV-1C epidemic in Brazil and raise an alternative hypothesis for its spatiotemporal history. The current work also highlights how sampling bias can confound phylogeographic analyses and demonstrates the importance of incorporating external information to protect against this.IMPORTANCESubtype C is responsible for the largest HIV infection burden worldwide, but our understanding of its transmission dynamics remains incomplete. Brazil witnessed a relatively recent introduction of HIV-1C compared to HIV-1B, but it swiftly spread throughout the south, where it now circulates as the dominant variant. The northward spread has been comparatively slow, and HIV-1B still prevails in that region. While epidemiological data and viral genetic analyses have both independently shed light on the dynamics of spread in isolation, their combination has not yet been explored. Here, we complement publically available sequences and new genetic data from 13 cities with epidemiological data to reconstruct the history of HIV-1C spread in Brazil. The combined approach results in more robust reconstructions and can protect against sampling bias. We found evidence for an alternative view of the HIV-1C spatiotemporal history in Brazil that, contrary to previous explanations, integrates seamlessly with other observational data.

The epidemiology of multiple sclerosis in Latin America and the Caribbean: a systematic review

2012 ◽  
Vol 19 (7) ◽  
pp. 844-854 ◽  
Author(s):  
E Cristiano ◽  
JI Rojas ◽  
M Romano ◽  
N Frider ◽  
G Machnicki ◽  
...  
Keyword(s):  
Multiple Sclerosis ◽  
Systematic Review ◽  
Latin America ◽  
Low Frequency ◽  
Epidemiological Data ◽  
Developed Countries ◽  
Epidemiological Studies ◽  
Incidence Data ◽  
Full Text Review ◽  
The Caribbean

The incidence and prevalence of multiple sclerosis (MS) varies geographically as shown through extensive epidemiological studies performed mainly in developed countries. Nonetheless, scant data is available in Latin America and the Caribbean (LAC). The objective of this review is to assess epidemiological data of MS in LAC. We conducted a systematic review of published articles and gray literature from January 1995 to May 2011. Twenty-two studies met the inclusion criteria after full-text review. Incidence data were found in only three studies and ranged from 0.3 to 1.9 annual cases per 100,000 person-years. Prevalence was reported in 10 studies and ranged from 0.83 to 21.5 cases per 100,000 inhabitants. The most prevalent subtype of MS was the relapsing–remitting form (48% to 91% of the series). No data about mortality were found. This study showed low frequency for MS in LAC compared with North American and European countries. The role of environmental and genetic factors should be well studied, providing new insights about its etiology.

scholarly journals HIV-1 founder variant multiplicity is determined by the infection stage of the source partner

2019 ◽  
Author(s):  
Ch. Julián Villabona-Arenas ◽  
Matthew Hall ◽  
Katrina A. Lythgoe ◽  
Stephen G. Gaffney ◽  
Roland R. Regoes ◽  
...  
Keyword(s):  
Early Stage ◽  
Control Strategies ◽  
Sexual Transmission ◽  
Low Frequency ◽  
Clinical Intervention ◽  
Epidemiological Data ◽  
Genetic Characteristics ◽  
Partner Characteristics ◽  
Infection Stage ◽  
Hiv 1

AbstractDuring sexual transmission, the large genetic diversity of HIV-1 within an individual is frequently reduced to one founder variant that initiates infection 1. Understanding the drivers of this bottleneck is crucial to develop effective infection control strategies 2. Genetic characteristics of the potential founder viruses and events in the recipient partner are both known to contribute to this bottleneck, but little is understood about the importance of the source partner 3. To test the hypothesis that the source partner affects the multiplicity of HIV founder variants, we developed a phylodynamic model calibrated using genetic and epidemiological data on all existing transmission pairs for whom the direction of transmission and the infection stage of the source partner are known. Our results demonstrate the importance of infection stage of the source partner, and not exposure route, in determining founder variant multiplicity. Specifically, acquiring infection from someone in the acute (early) stage of infection increases the risk of multiple variant transmission when compared with someone in the chronic (later) stage of infection. This study provides the first direct test of source partner characteristics to explain the low frequency of multiple founder strain infections and can inform clinical intervention study design and interpretation.

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 Genetic Profile of HIV-1 in the Vologda Region: Domination of CRF03_AB and Rapid Distribution of URFs

2020 ◽  
Vol 12 (2) ◽  
pp. 79-88
Author(s):  
E. N. Ozhmegova ◽  
A. A. Antonova ◽  
A. V. Lebedev ◽  
T. N. Melnikova ◽  
Т. V. Krylova ◽  
...  
Keyword(s):  
Mononuclear Cells ◽  
Federal District ◽  
Risk Groups ◽  
Genetic Profile ◽  
Peripheral Blood Mononuclear ◽  
Epidemiological Analysis ◽  
Vologda Oblast ◽  
North West ◽  
Subtype B ◽  
Hiv 1

The work was carried out molecular-epidemiological analysis of HIV-1 in the cities of the North-West Federal District — Vologda and Cherepovets. The study used a collection of peripheral blood mononuclear cells (PBMC) obtained from 80 HIVinfected patients: 52 samples were obtained from patients living in Cherepovets, and 28 samples — from Vologda. The distribution of the HIV-1 genetic variants in the studied cities was as follows: sub-subtype A6 — 51,25%; subtype B — 6,25%; the recombinant form of CRF_03AB — 32,5%; unique recombinant forms (URFs) — 6,25%, and 3,75% were represented by other subtypes: G and CRF63_02A1. A phylogenetic analysis confirmed the relationship of the sub-subtype A6 viruses with the A6 (IDU-A) variant predominating in Ukraine, Russia and other former Soviet Union (FSU) countries; the sequences of subtype B formed a common branch on the phylogram with reference strains characteristic of men who have sex with men; 32,5% of the nucleotide sequences formed a single cluster with the reference strain CRF03_AB. In addition to these subtypes, the presence of unique recombinant forms of HIV-1 containing segments of the sub-subtype A6 and IDU-B viruses were also found. The results of the molecular epidemiological analysis in the Vologda Oblast also showed significant differences in the genetic profile of HIV-1 in two nearby cities — Vologda and Cherepovets. Thus, the evolution of HIV-1 in the Vologda Oblast continues, with the main source of variability being the mutual penetration of viruses between risk groups and recombination processes.

scholarly journals Low Frequency of CXCR4-Using Viruses in Patients at the Time of Primary Non-Subtype-B HIV-1 Infection

2010 ◽  
Vol 48 (10) ◽  
pp. 3487-3491 ◽  
Author(s):  
P. Frange ◽  
M.-L. Chaix ◽  
S. Raymond ◽  
J. Galimand ◽  
C. Deveau ◽  
...  
Keyword(s):  
Low Frequency ◽  
Subtype B ◽  
Hiv 1

scholarly journals Characterizing HIV-1 Splicing by Using Next-Generation Sequencing

2017 ◽  
Vol 91 (6) ◽  
Author(s):  
Ann Emery ◽  
Shuntai Zhou ◽  
Elizabeth Pollom ◽  
Ronald Swanstrom
Keyword(s):  
Deep Sequencing ◽  
Splice Variants ◽  
Low Frequency ◽  
Subtype C ◽  
Subtype B ◽  
Deep Sequencing Technology ◽  
Immunodeficiency Virus ◽  
High Level ◽  
Splicing Patterns ◽  
Hiv 1

ABSTRACT Full-length human immunodeficiency virus type 1 (HIV-1) RNA serves as the genome or as an mRNA, or this RNA undergoes splicing using four donors and 10 acceptors to create over 50 physiologically relevant transcripts in two size classes (1.8 kb and 4 kb). We developed an assay using Primer ID-tagged deep sequencing to quantify HIV-1 splicing. Using the lab strain NL4-3, we found that A5 (env/nef) is the most commonly used acceptor (about 50%) and A3 (tat) the least used (about 3%). Two small exons are made when a splice to acceptor A1 or A2 is followed by activation of donor D2 or D3, and the high-level use of D2 and D3 dramatically reduces the amount of vif and vpr transcripts. We observed distinct patterns of temperature sensitivity of splicing to acceptors A1 and A2. In addition, disruption of a conserved structure proximal to A1 caused a 10-fold reduction in all transcripts that utilized A1. Analysis of a panel of subtype B transmitted/founder viruses showed that splicing patterns are conserved, but with surprising variability of usage. A subtype C isolate was similar, while a simian immunodeficiency virus (SIV) isolate showed significant differences. We also observed transsplicing from a downstream donor on one transcript to an upstream acceptor on a different transcript, which we detected in 0.3% of 1.8-kb RNA reads. There were several examples of splicing suppression when the env intron was retained in the 4-kb size class. These results demonstrate the utility of this assay and identify new examples of HIV-1 splicing regulation. IMPORTANCE During HIV-1 replication, over 50 conserved spliced RNA variants are generated. The splicing assay described here uses new developments in deep-sequencing technology combined with Primer ID-tagged cDNA primers to efficiently quantify HIV-1 splicing at a depth that allows even low-frequency splice variants to be monitored. We have used this assay to examine several features of HIV-1 splicing and to identify new examples of different mechanisms of regulation of these splicing patterns. This splicing assay can be used to explore in detail how HIV-1 splicing is regulated and, with moderate throughput, could be used to screen for structural elements, small molecules, and host factors that alter these relatively conserved splicing patterns.

scholarly journals Basic clinicolaboratory and genetic characteristic of patients with mucoviscidosis living in Perm krai, other regions of Privolzhsky federal district and Central federal district of Russia

2020 ◽  
Vol 37 (1) ◽  
pp. 48-62
Author(s):  
V. V. Shadrina ◽  
E. I. Kondratieva ◽  
E. G. Furman ◽  
E. L. Amelina ◽  
M. A. Starinova ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Federal District ◽  
Epidemiological Data ◽  
Epidemiological Studies ◽  
Central Federal District ◽  
Perm Krai ◽  
Federal Districts ◽  
Chuvash Republic ◽  
And Migration ◽  
Epidemiological Characteristics

Aim. The project National Register of Patients with Mucoviscidosis (MV), introduced in Russia, opened the widest perspectives for comparative analysis and summarizing of clinico-epidemiological data all over Russia, federal districts, regions and separate territories. The register data permit to generalize the experience of observation and management of MV patients in centers. Comparative analysis of the clinico-epidemiological characteristics of MV and volume of therapy in patients living in Perm Krai (PK) with the other regions of Privolzhsky Federal District (PFD) and Central Federal District (CFD) of Russia was carried out. Materials and methods. According to the Register of MV Patients in the Russian Federation for 2017, the data of 1576 patients with MV were analyzed: 930 (59.0 %) patients were observed in CFD, 600 (38.1 %) in PFD, 46 (2.9) in PK. Results. Among MV patients in PFD and PK, there was noted a great variety of variants of the gene CFTR, associated with both the presence of autochthonic and relatively closed ethnic groups and migration of the population. A high allele frequency of the variant E92K was revealed in patients of Chuvash Republic (55.3 %). A group of patients from PK, registered in 2017, had a low mean age, the lowest age of making a diagnosis. Conclusions. Clinico-epidemiological studies, according to the data of MV patients register, permitted to detect some peculiar features that can be significant for practical healthcare. Further studies on MV patients register should be continued.

scholarly journals THE PREVALENCE OF HIV RECOMBINANT FORMS IN RUSSIA AND COUNTRIES OF THE CIS: SYSTEMATIC REVIEW AND METAANALYSIS

2018 ◽  
Vol 8 (2) ◽  
pp. 127-138 ◽  
Author(s):  
O. A. Pasechnik ◽  
A. I. Blokh
Keyword(s):  
Meta Analysis ◽  
Federal District ◽  
Significant Heterogeneity ◽  
Russian Science ◽  
Cross Sectional ◽  
Subtype B ◽  
Russian Science Citation Index ◽  
Meta Regression ◽  
Cis Countries ◽  
Hiv 1

This review was to aimed to access the prevalence of HIV recombinant forms in Russia and countries of the CIS, which have  close social and economic ties. We conducted a search in Russian  Science Citation Index and PubMed for a depth of 8 years. We  included 22 articles, which contained the results of 35 independent  cross-sectional studies, in our review. Meta-analysis of HIV  recombinant forms prevalence was conducted in Open Meta-analyst  with the use of Der Simonian & Laird method, arcsin transformation  and correction factor for zero values. Subgroup analysis was used  along with meta-regression (by date of collection). Pooled prevalence of HIV recombinant forms was 21.3% (95% CI 16.2–26.5) and was  highly heterogeneous. Blood samples from 3,494 HIV patients living  in various regions of the Russian Federation and CIS countries —  Belarus, Kazakhstan, Kyrgyzstan, Uzbekistan, Tajikistan, Armenia,  Georgia — were examined. Among subtypes of HIV-1, the main  share was occupied by subtype A — 75.6% (n = 2643), subtype B —  5.5% (n = 193), C — 0.8% (n = 31), G — 0.2% (n = 7), F —  0.14% (n = 5). Among the recombinant forms (n = 616), the  fraction of CRF02_ AG was 39.6% (n = 244), CRF02_AG/A was  32.9% (n = 203), CRF63_02A1 was 15.9% (n = 98), CRF03_AB —  5.2% (n = 32), CRF06_cpx — 2.1% (n = 13). Unique recombinant  forms were 2.7% (n = 17), including URF63_A1 (2.5%). In Russia, the highest prevalence of recombinant forms of HIV-1 was  registered in the Siberian Federal District (33.2% (95% CI 12.2– 54.1), the lowest in the Northwest Federal District — 1.6% (95% CI  0.9–2.3). In the CIS countries, the highest prevalence of  recombinant forms of HIV-1 is found in a subgroup of the Central  Asian republics — Uzbekistan, Tajikistan, Kyrgyzstan, Kazakhstan —  51.7% (95% CI 38.5–64.9). The significant upward trend was shown with a meta-regression. Our review is the first such research in  Russia and thus is of significant interest, but the result should be  applied with caution due to high risk of publication bias as well as significant heterogeneity of our results.

Sign in / Sign up

Export Citation Format

Share Document