Molecular Epidemiology of HIV-1 Subtype B Reveals Heterogeneous Transmission Risk: Implications for Intervention and Control

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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Update on diversity and distribution of HIV-1 subtypes in Yunnan province

Epidemiology and Infection ◽

10.1017/s0950268812002713 ◽

2013 ◽

Vol 141 (11) ◽

pp. 2418-2427 ◽

Cited By ~ 10

Author(s):

Y.-Z. SU ◽

Y.-L. MA ◽

M.-H. JIA ◽

X. HE ◽

L. YANG ◽

...

Keyword(s):

Yunnan Province ◽

Sequence Data ◽

Distribution Data ◽

Subtype C ◽

Subtype B ◽

Tree Construction ◽

Complex Population ◽

And Control ◽

Hiv 1 ◽

Hiv Subtypes

SUMMARYThe aim of this study was to characterize updated HIV subtypes in Yunnan to determine their origins and distribution within the population. RT–PCR of both thegagandenvgenes were sequenced from Yunnan province inhabitants newly diagnosed with HIV-1. Sequence data from 290 samples were used for statistical analysis of subtype distribution and phylogenetic tree construction. Distribution data were adjusted to account for different geographical distributions of HIV-1 subtypes in the population. Phylogenetic analysis revealed six HIV-1 subtypes in Yunnan, including eight types of unique recombination forms (URFs). The most prevalent subtypes in this province, CRF07_BC (18·9%), CRF08_BC (39·1%), CRF01_AE (22·4%), and URFs (subtype C, 5·9% and subtype B, 4·5%), were all recombinants. We found significant differences in the distribution of these HIV-1 subtypes not only geographically, but also between various ethnic groups and with respect to transmission routes. Our findings indicate a complex population of HIV-1 subtypes, URFs, and recombinant subtypes in Yunnan province. This diversity could make the prevention and control of HIV infection in Yunnan more difficult due to the possibility of virus recombination or infection by multiple subtypes.

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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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Impact of HIV-1 CRF55_01B infection on the evolution of CD4 count and plasma HIV RNA load in men who have sex with men prior to antiretroviral therapy

10.21203/rs.3.rs-390294/v1 ◽

2021 ◽

Author(s):

Lan Wei ◽

Hao Li ◽

Xing Lv ◽

Chenli Zheng ◽

Guilian Li ◽

...

Keyword(s):

Viral Load ◽

Antiretroviral Therapy ◽

Cd4 Count ◽

Transmission Risk ◽

Mixed Effect ◽

Cd4 Cell Count ◽

Hiv Rna ◽

Subtype B ◽

The Impact ◽

Hiv 1

Abstract Background CRF55_01B is a newly identified HIV-1 circulating recombinant form originated from MSM in China. However, its impact on the disease progression and transmission risk has not been investigated. This study aimed to determine the impact of CRF55_01B infection on viral dynamics and immunological status, so as to provide implications for future prevention, treatment, or target interventions. Linear mixed effect models were applied to evaluate CD4 cell count decline and viral load increase by subtype.Results Of the 3418 blood samples, 1446 (42.3%) were CRF07_BC, 1169 (34.2%) CRF01_AE, 467 (13.7%) CRF55_01B, 249 (7.3%) type B, and 87 (2.5%) other subtypes (CRF_08BC, CRF_01B, C). CRF55_01B had replaced subtype B as the third predominant strain since 2012 in Shenzhen, China. CRF55_01B-infected MSM showed lower median of CD4 count than CRF07_BC-infected MSM (349.5 [IQR, 250.2~474.8] vs 370.0 [IQR, 278.0~501.0], P<0.05). CRF55_01B infection was associated with slower loss of CD4 count than CRF01_AE (13.6 vs 23.3 [cells/μL]¹/²/year, P<0.05)among MSM with initial CD4 count of 200~350 cells/μL. On the other hand, those infected with CRF55_01B showed higher median plasma HIV RNA load (5.4 [IQR, 5.0~5.9]) than both CRF01_AE (5.3 [IQR, 4.8~5.7], P<0.05) and CRF07_BC (5.0 log10 [IQR, 4.5~5.5], P<0.001) at the initiation of antiretroviral therapy. Furthermore, the annual increasing rate of viral load for CRF55_01B infection was significantly higher than that of CRF07_BC (2.0 vs 0.7 log10 copies/ml/year, P<0.01).Conclusions The relatively lower CD4 count and faster increase of plasma HIV RNA load of CRF55_01B-infected MSM without antiretroviral therapy suggest that CRF55_01B may lead to longer asymptomatic phase and higher risk of HIV transmission. Strengthened surveillance, tailored prevention strategies and interventions, and in-depth research focusing on CRF55_01B are urgently needed to forestall potential epidemic.

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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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Heterosexual Transmission as a CRF01_AE HIV-1 Spread Factor in Mimika Papua

Journal of Health Science and Prevention ◽

10.29080/jhsp.v2i2.127 ◽

2018 ◽

Vol 2 (2) ◽

pp. 108-113

Author(s):

Mirna Widiyanti ◽

Reynold Ubra ◽

Evi Iriani

Keyword(s):

Transmission Rate ◽

Sexual Transmission ◽

Transmission Risk ◽

Heterosexual Transmission ◽

Cross Sectional ◽

Genetic Characteristics ◽

Subtype B ◽

Hiv Epidemic ◽

Spread Factor ◽

Hiv 1

The HIV epidemic has particular characteristic on each region. The genetic diversity of HIV-1 would affect variability of HIV virus that could potentially most virulent, pathogenic and high transmission rate. Thus it triggers the disease progresivity more rapidly and caused a new pandemic of HIV infection. The aim of the study is determine the genetic characteristics of HIV-1 on patient with heterosexual transmission based on gene fragment encoding the glycoprotein-41 (gp41) of HIV envelope. Descriptive analytic method and cross sectional design were attended on VCT clinic Mitra Masyarakat Mimika in March-May 2015. Samples of blood plasma from patient with HIV-1 sexual transmission wer amplified using RT-PCR and nested PCR. Genetic characteristics were analyzed with DNA Sequencing using software Bioedit and Mega 5. Identification using sequence analysis showed two subtypes of HIV patient in Mimika, which were CRF01_AE and B subtypes. There were 40 patients (87%) identified as having genetic characteristics CRF01_AE. Subtypes B was also identified in 6 heterosexual patients. This study suggest that CRF01_AE have heterosexual transmission risk higher than subtype B. Predominance of CRF01_AE contribute to the rapid spread of the HIV epidemic in Mimika

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High prevalence and association of HIV-1 non-B subtype with specific sexual transmission risk among antiretroviral naïve patients in Porto Alegre, RS, Brazil

Revista do Instituto de Medicina Tropical de São Paulo ◽

10.1590/s0036-46652009000400003 ◽

2009 ◽

Vol 51 (4) ◽

pp. 191-196 ◽

Cited By ~ 20

Author(s):

Cláudia Fontoura Dias ◽

Cynara Carvalho Nunes ◽

Isabela Osório Freitas ◽

Isabel Saraiva Lamego ◽

Ilda Maria Rodrigues de Oliveira ◽

...

Keyword(s):

Sexual Transmission ◽

Outpatient Service ◽

Transmission Risk ◽

Laboratory Evaluation ◽

Molecular Characteristics ◽

Porto Alegre ◽

Epidemiologic Surveillance ◽

Subtype B ◽

The Impact ◽

Hiv 1

In South Brazil the circulation of two HIV-1 subtypes with different characteristics represents an important scenario for the study of the impact of HIV-1 diversity on the evolution of the HIV-1 epidemic and AIDS disease. HIV-1 B, the predominant variant in industrialized countries and HIV-1 C, the most prevalent subtype in areas with rapid epidemic growth, are implicated in most infections. We evaluated blood samples from 128 antiretroviral (ARV) naïve patients recruited at entry to the largest HIV outpatient service in Porto Alegre. Based on partial pol region sequencing, HIV-1 C was observed in 29%, HIV-1 B in 22.6% and, the recently identified CRF31_BC, in 23.4% of 128 volunteers. Other variants were HIV-1 F in 10% and other mosaics in 5.5%. In order to evaluate the association of socio-behavioral characteristics and HIV-1 subtypes, interviews and laboratory evaluation were performed at entry. Our data suggest an established epidemic of the three major variants, without any evidence of partitioning in either of the subgroups analyzed. However, anal sex practices were associated with subtype B, which could indicate a greater transmissibility of non-B variants by vaginal intercourse. This study provides baseline information for epidemiologic surveillance of the changes of the molecular characteristics of HIV-1 epidemics in this region.

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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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