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

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 B Reveals Heterogeneous Transmission Risk: Implications for Intervention and Control

The Journal of Infectious Diseases ◽

10.1093/infdis/jiy044 ◽

2018 ◽

Vol 217 (10) ◽

pp. 1522-1529 ◽

Cited By ~ 19

Author(s):

Erik M Volz ◽

Stephane Le Vu ◽

Oliver Ratmann ◽

Anna Tostevin ◽

David Dunn ◽

...

Keyword(s):

Molecular Epidemiology ◽

Transmission Risk ◽

Subtype B ◽

And Control ◽

Heterogeneous Transmission ◽

Hiv 1

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Comprehensive Characterization of HIV-1 Molecular Epidemiology and Demographic History in the Brazilian Region Most Heavily Affected by AIDS

Journal of Virology ◽

10.1128/jvi.00363-16 ◽

2016 ◽

Vol 90 (18) ◽

pp. 8160-8168 ◽

Cited By ~ 9

Author(s):

Tiago Gräf ◽

Hegger Machado Fritsch ◽

Rúbia Marília de Medeiros ◽

Dennis Maletich Junqueira ◽

Sabrina Esteves de Matos Almeida ◽

...

Keyword(s):

Molecular Epidemiology ◽

Demographic History ◽

Phylogenetic Analyses ◽

Viral Population ◽

Subtype C ◽

Capital Cities ◽

Subtype B ◽

High Prevalence ◽

Hiv 1 ◽

South Brazil

ABSTRACTThe high incidence of AIDS cases and the dominance of HIV-1 subtype C infections are two features that distinguish the HIV-1 epidemic in the two southernmost Brazilian states (Rio Grande do Sul [RS] and Santa Catarina [SC]) from the epidemic in other parts of the country. Nevertheless, previous studies on HIV molecular epidemiology were conducted mainly in capital cities, and a more comprehensive understanding of factors driving this unique epidemic in Brazil is necessary. Blood samples were collected from individuals in 13 municipalities in the Brazilian southern region. HIV-1envandpolgenes were submitted to phylogenetic analyses for assignment of subtype, and viral population phylodynamics were reconstructed by applying Skygrid and logistic coalescent models in a Bayesian analysis. A high prevalence of subtype C was observed in all sampled locations; however, an increased frequency of recombinant strains was found in RS, with evidence for new circulating forms (CRFs). In the SC state, subtype B and C epidemics were associated with distinct exposure groups. Although logistic models estimated similar growth rates for HIV-1 subtype C (HIV-1C) and HIV-1B, a Skygrid plot reveals that the former epidemic has been expanding for a longer time. Our results highlight a consistent expansion of HIV-1C in south Brazil, and we also discuss how heterosexual and men who have sex with men (MSM) transmission chains might have impacted the current prevalence of HIV-1 subtypes in this region.IMPORTANCEThe AIDS epidemic in south Brazil is expanding rapidly, but the circumstances driving this condition are not well known. A high prevalence of HIV-1 subtype C was reported in the capital cities of this region, in contrast to the subtype B dominance in the rest of the country. This study sought to comparatively investigate the HIV-1 subtype B and C epidemics by sampling individuals from several cities in the two states with the highest AIDS incidences in Brazil. Our analyses showed distinct epidemic growth curves for the two epidemics, and we also found evidence suggesting that separate transmission chains may be impacting the viral phylodynamics and the emergence of new recombinant forms.

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Short Communication: HIV-1 Subtype B in the Dominican Republic: Evolution and Molecular Epidemiology

AIDS Research and Human Retroviruses ◽

10.1089/aid.2014.0304 ◽

2015 ◽

Vol 31 (7) ◽

pp. 679-684 ◽

Cited By ~ 3

Author(s):

Pablo López ◽

Vanessa Rivera-Amill ◽

Robert Paulino-Ramirez ◽

Yasuhiro Yamamura

Keyword(s):

Dominican Republic ◽

Molecular Epidemiology ◽

Short Communication ◽

Subtype B ◽

Hiv 1

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Molecular epidemiology of HIV-1 subtype B in the Basque Country (Spain)

Retrovirology ◽

10.1186/1742-4690-9-s1-p33 ◽

2012 ◽

Vol 9 (Suppl 1) ◽

pp. P33

Author(s):

Juan Patiño ◽

Miguel M Thomson ◽

Fernando González-Candelas

Keyword(s):

Molecular Epidemiology ◽

Basque Country ◽

Subtype B ◽

Hiv 1

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Molecular Epidemiology of HIV-1 in Brazil: High Prevalence of HIV-1 Subtype B and Identification of an HIV-1 Subtype D Infection in the City of Rio de Janeiro, Brazil

Journal of Acquired Immune Deficiency Syndromes & Human Retrovirology ◽

10.1097/00042560-199808150-00011 ◽

1998 ◽

Vol 18 (5) ◽

pp. 488-494 ◽

Cited By ~ 50

Author(s):

Mariza G. Morgado ◽

Monick L. Guimarães ◽

Carmen B. G. Gripp ◽

Catia I. Costa ◽

Ivan Neves ◽

...

Keyword(s):

Molecular Epidemiology ◽

Rio De Janeiro ◽

Subtype B ◽

High Prevalence ◽

The City ◽

Hiv 1

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Molecular Epidemiology of the HIV-1 Subtype B Sub-Epidemic in Bulgaria

Viruses ◽

10.3390/v12040441 ◽

2020 ◽

Vol 12 (4) ◽

pp. 441

Author(s):

Ivailo Alexiev ◽

Ellsworth M. Campbell ◽

Sergey Knyazev ◽

Yi Pan ◽

Lyubomira Grigorova ◽

...

Keyword(s):

Molecular Epidemiology ◽

Linkage To Care ◽

High Risk Behaviors ◽

Network Analyses ◽

Antiretroviral Drug Resistance ◽

Subtype B ◽

Recent Transmission ◽

Sex With Men ◽

Large Clusters ◽

Hiv 1

HIV-1 subtype B is the predominant strain in Bulgaria, yet little is known about the molecular epidemiology of these infections, including its origin and transmissibility. We used a phylodynamics approach by combining and analyzing 663 HIV-1 polymerase (pol) sequences collected from persons diagnosed with HIV/AIDS between 1988–2018 and associated epidemiologic data to better understand this sub-epidemic in Bulgaria. Using network analyses at a 1.5% genetic distance threshold (d) we found several large phylogenetic clusters composed mostly of men who have sex with men (MSM) and male heterosexuals (HET). However, at d = 0.5%, used to identify more recent transmission, the largest clusters dissociated to become smaller in size. The majority of female HET and persons with other transmission risks were singletons or pairs in the network. Phylogenetic analysis of the Bulgarian pol sequences with publicly available global sequences showed that subtype B was likely introduced into Bulgaria from multiple countries, including Israel and several European countries. Our findings indicate that subtype B was introduced into Bulgaria multiple times since 1988 and then infections rapidly spread among MSM and non-disclosed MSM. These high-risk behaviors continue to spread subtype B infection in Bulgaria as evidenced by the large clusters at d = 0.5%. Relatively low levels of antiretroviral drug resistance were observed in our study. Prevention strategies should continue to include increased testing and linkage to care and treatment, as well as expanded outreach to the MSM communities.

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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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