Phylogenetics applied to the human immunodeficiency virus type 1 (HIV-1): from the cross-species transmissions to the contact network inferences

Gräf, Tiago; Delatorre, Edson; Bello, Gonzalo

doi:10.1590/0074-02760190461

Cited by 5 publications

(6 citation statements)

References 30 publications

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“…It is well known that phylogenetic analyses have elucidated the origin and spread of the pandemic human immunodeficiency virus type (HIV-1) group M virus, both during the pre-epidemic period and the epidemic phase of spread among humans 4 . Additionally, it is also applied to evaluate small transmission chains between infected individuals, such as some forensic studies 5 – 7 , and to track the founder events that resulted in the spread of HIV-1 strains across vast geographic areas, specific countries, and within geographically restricted communities 8 .…”

Section: Introductionmentioning

confidence: 99%

HIV-1 subtype diversity and transmission strain source among men who have sex with men in Guangxi, China

Chen

Shen

Feng

et al. 2021

Sci Rep

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With the rapid increase in HIV prevalence of men who have sex with men (MSM) in recent years and common human migration and travelling across different provinces in China, MSM are now finding it easier to meet each other, which might contribute to local HIV epidemics as well as fueling cross-province transmission. We performed a cross-sectional survey in 2018–2019 to investigate the current HIV subtype diversity and inferred HIV strain transmission origin among MSM in Guangxi province, China based on a phylogenetic analysis. Based on 238 samples, we found that the HIV-1 subtype diversity was more complicated than before, except for three major HIV subtypes/circulating recombinant forms (CRFs): CRF07_BC, CRF01_AE, CRF55_01B, five other subtypes/CRFs (CRF59_01B, B, CRF08_BC, CRF67_01B, CRF68_01B) and five unique recombinant forms (URFs) were detected. In total, 76.8% (169/220) of samples were infected with HIV from local circulating strains, while others originated from other provinces, predominantly Guangdong and Shanghai. The high diversity of HIV recombinants and complicated HIV transmission sources in Guangxi MSM indicates that there has been an active sexual network between HIV positive MSM both within and outside Guangxi without any effective prevention. Inter-province collaboration must be enforced to provide tailored HIV prevention and control services to MSM in China.

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Section: Introductionmentioning

confidence: 99%

HIV-1 subtype diversity and transmission strain source among men who have sex with men in Guangxi, China

Chen

Shen

Feng

et al. 2021

Sci Rep

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“…Sequences were submitted to the REGA Subtyping Tool v3.0 program [27] and COMET [28]. Due to possibly recombinants or sequences with conflicting results, the classification was confirmed by molecular phylogeny by the Neighbor-Joining method [29] using MEGA 7.0 software [23]. Subtype reference sequences were obtained from Los Alamos HIV Sequence Database (http://www.hiv.lanl.gov/ (accessed on 25 March 2021)).…”

Section: Sequence Analysismentioning

confidence: 99%

“…One way to investigate the existence of HIV transmission networks is to use phylogenetic analysis. Phylogenetic and phylodynamic approaches are broadly used to update HIV epidemiology, infer changing trends in the local and regional spread of HIV-1, and guide prevention measures and public health interventions [21][22][23]. This study aimed to verify potential HIV transmission networks among prisoners by investigating HIV polymerase nucleotide sequences isolated from HIV-infected prisoners and those obtained from other populations in MS, available in sequence databases.…”

Section: Introductionmentioning

confidence: 99%

Molecular Epidemiology of HIV-1 among Prisoners in Central Brazil and Evidence of Transmission Clusters

Tanaka

Cesar

Rezende

et al. 2022

Viruses

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Higher rates of human immunodeficiency virus (HIV) infection have been detected in prisoners when compared with the general population, but research into HIV molecular epidemiology and its transmission network has been lacking among them. Thus, this study aimed to verify potential HIV molecular transmission networks among prisoners. In addition, we aimed to describe the mutations related to antiretroviral resistance in these isolates. Thus, we conducted a cross-sectional survey from 2013 to 2018 in prisons in Central-Western Brazil, and the final sampling composed of 84 prisoners. Proviral DNA was extracted from each whole blood sample followed by amplification of the partial polymerase gene and sequencing. Forty-nine sequences (58.3%) were classified as subtype B, followed by C (14.3%), D, and F1 (2.4% each). A complex and dynamic HIV-1 epidemic is observed in the prisons, as 25% of the sequences were recombinant forms. We detected 15 HIV transmission clusters composed of at least two sequences, that included not only prisoners but also individuals from the general population from the same State with a variety of risk behaviors. Thirty-two percent (32.0%) of treatment-experienced prisoners had at least one drug resistance mutation (DRM), while transmitted DRMs were found in 5.9% of the prisoners. We highlight the urgent need for routine surveillance of HIV-1 infection including resistance genotypic tests considering the high disease burden, risky behaviors inside prisons, and the dynamic relationship of prisoners with the outside community.

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“…The high mutation rate of HIV-1 due to the absence of viral reverse transcriptase proofreading [6], combined with the fact that the virus causes a chronic infection, creates a unique viral population in each individual that changes during the course of the infection. This viral population descends from some genetically very similar founder viruses, which were selected shortly after the transmission event and harbor genetic signatures from the viral population of the "donor" individual, allowing the reconstruction of viral transmission networks from the genetic data [7]. In summary, when groups of HIV sequences isolated from different patients have a high degree of genetic similarity, they are connected by a common source, a direct or a short chain of transmissions [8].…”

Section: Introductionmentioning

confidence: 99%

Characterization of HIV-1 Transmission Clusters Inferred from the Brazilian Nationwide Genotyping Service Database

Andrade

Arantes

Tanuri

et al. 2022

Viruses

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The study of HIV-1 transmission networks inferred from viral genetic data can be used to clarify important factors about the dynamics of HIV-1 transmission, such as network growth rate and demographic composition. In Brazil, HIV transmission has been stable since the early 2000s and the study of transmission clusters can provide valuable data to understand the drivers of virus spread. In this work, we analyzed a nation-wide database of approximately 53,000 HIV-1 nucleotide pol sequences sampled from genotyped patients from 2008–2017. Phylogenetic trees were reconstructed for the HIV-1 subtypes B, C and F1 in Brazil and transmission clusters were inferred by applying genetic distances thresholds of 1.5%, 3.0% and 4.5%, as well as high (>0.9) cluster statistical support. An odds ratio test revealed that young men (15–24 years) and individuals with more years of education presented higher odds to cluster. The assortativity coefficient revealed that individuals with similar demographic features tended to cluster together, with emphasis on features, such as place of residence and age. We also observed that assortativity weakens as the genetic distance threshold increases. Our results indicate that the phylogenetic clusters identified here are likely representative of the contact networks that shape HIV transmission, and this is a valuable tool even in sites with low sampling density, such as Brazil.

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Phylogenetics applied to the human immunodeficiency virus type 1 (HIV-1): from the cross-species transmissions to the contact network inferences

Cited by 5 publications

References 30 publications

HIV-1 subtype diversity and transmission strain source among men who have sex with men in Guangxi, China

HIV-1 subtype diversity and transmission strain source among men who have sex with men in Guangxi, China

Molecular Epidemiology of HIV-1 among Prisoners in Central Brazil and Evidence of Transmission Clusters

Characterization of HIV-1 Transmission Clusters Inferred from the Brazilian Nationwide Genotyping Service Database

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