Phylogenetic transmission clusters among newly diagnosed antiretroviral drug-naïve patients with human immunodeficiency virus-1 in Korea: A study from 1999 to 2012

Chung, Youngjin; Choi, Ju-Yeon; Yoo, Myoung-Su; Seong, Jae Hyun; Choi, Byeong‐Sun; Kang, Chun

doi:10.1371/journal.pone.0217817

Cited by 6 publications

(13 citation statements)

References 46 publications

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“…When possible, sequences of the appropriate length belonging to transmission events previously identified in the literature were included in the phylogenetic analysis to verify the correct Bayesian inference [37,38].…”

Section: Phylogenetic Analyses and Transmission Clustersmentioning

confidence: 99%

Prevalence of Non-B HIV-1 Subtypes in North Italy and Analysis of Transmission Clusters Based on Sequence Data Analysis

et al. 2019

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HIV-1 diversity is increasing in European countries due to immigration flows, as well as travels and human mobility, leading to the circulation of both new viral subtypes and new recombinant forms, with important implications for public health. We analyzed 710 HIV-1 sequences comprising protease and reverse-transcriptase (PR/RT) coding regions, sampled from 2011 to 2017, from naive patients in Spedali Civili Hospital, Brescia, Italy. Subtyping was performed by using a combination of different tools; the phylogenetic analysis with a structured coalescence model and Makarov Chain Monte Carlo was used on the datasets, to determine clusters and evolution. We detected 304 (43%) patients infected with HIV-1 non-B variants, of which only 293 sequences were available, with four pure subtypes and five recombinant forms; subtype F1 (17%) and CRF02_AG (51.1%) were most common. Twenty-five transmission clusters were identified, three of which included >10 patients, belonging to subtype CRF02_AG and subtype F. Most cases of alleged transmission were between heterosexual couples. Probably due to strong migratory flows, we have identified different subtypes with particular patterns of recombination or, as in the case of the subtype G (18/293, 6.1%), to a complete lack of relationship between the sequenced strains, revealing that they are all singletons. Continued HIV molecular surveillance is most important to analyze the dynamics of the boost of transmission clusters in order to implement public health interventions aimed at controlling the HIV epidemic.

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Section: Phylogenetic Analyses and Transmission Clustersmentioning

confidence: 99%

Prevalence of Non-B HIV-1 Subtypes in North Italy and Analysis of Transmission Clusters Based on Sequence Data Analysis

et al. 2019

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“…Among the 876 infected individuals reported from 1985 to 1998, OSs accounted for 18.4% 1 . Previous studies have shown that 80% of patients in these groups and their partners were infected with non-B subtype viruses 5 , 6 .…”

Section: Introductionmentioning

confidence: 97%

“…The proportion of MSM was higher in younger age groups, 71.5% in 18–29 years and 92.9% in 18–19 years, respectively 3 . Currently, more than 80% of the HIV epidemic in Korea is attributed to subtype B 6 , 10 . A recent nationwide study demonstrated that subtype B was identified in 93.1% of 927 samples collected between 1999 and 2012 6 .…”

Section: Introductionmentioning

confidence: 99%

Epidemiological and phylogenetic analysis for non-B subtypes of human immunodeficiency virus type 1 in Busan, Korea

Lee

et al. 2021

Sci Rep

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Recent data on non-B subtypes’ epidemiology among patients infected with human immunodeficiency virus-1 (HIV-1) in Korea are lacking. We aimed to assess the changing trends in the epidemiology of non-B subtypes of HIV-1 in Korea using phyloepidemiological analyses. We analyzed the demographic records and sequencing data obtained from genotypic drug resistance tests between 2005 and 2019 from 517 patients infected with HIV attending a tertiary care hospital in Busan, Korea. Subtyping and phylogenetic analyses with reference sequences were performed. Additionally, transmission clusters were identified via maximum-likelihood trees. Non-B subtypes accounted for 21.3% of the 517 sequences. CRF01_AE (52.7%) was the most common non-B subtype, followed by CRF02_AG (16.4%), A1 (11.8%), and C (5.5%). The prevalence of non-B subtypes decreased from 36.4 to 13.4% by 2009, while it increased to 27.4% between 2015 and 2019. Among patients with non-B subtypes, the proportion of overseas sailors decreased from 66.7 to 7.5%; contrarily, the proportion of men-who-have-sex-with-men (MSM) increased from 0 to 46.9% over the study period. We identified 8 transmission clusters involving non-B subtypes, with sizes ranging from 2 to 4 patients, including 3 clusters containing MSM. Our results highlight the changes in the epidemiological trends of non-B subtypes of HIV-1 in Korea.

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“…In Korea, many epidemiological studies have been conducted using partial genome sequence, such as gag , pol , or env genes, and the proportion of Korean B was reported (87.3%) 7 , 24 , 25 . Several studies consistently reported this unique Korean clade B (Korean B), by analyzing various genes such as nef 24 , env 26 , vif 27 , and pol 28 , 29 .…”

Section: Discussionmentioning

confidence: 99%

Characterization of HIV-1 recombinant and subtype B near full-length genome among men who have sex with men in South Korea

Ryou

Yoo

Kim

et al. 2021

Sci Rep

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In Korea, subtype B is the predominant variant of HIV-1, but full genome sequencing and analysis of its viral variants are lacking. We performed near full-length genome (NFLG) sequencing and phylogenetic and recombination analyses of fifty plasma samples from HIV-positive men who have sex with men (MSM) from a Korea HIV/AIDS cohort study. Viral genomes were amplified and the near-full-length sequences were determined using next-generation sequencing (NGS) and Sanger sequencing. We focused on the HIV-1 subtype classification and identification of HIV recombinants. Twelve HIV-1 NFLGs were determined: ten were subtyped as pure HIV-1 subtype B and two recombinant strains as a common subtype CRF07_BC, and a novel subtype CRF43_02G recombined with CRF02_AG again, or a new CRF02_AG and subtype G recombinant. For the ten NFLGs determined by NGS, “the novel recombinant emerged at approximately 2003 and the other nine subtype B about 2004 or 2005”. This is the first report analyzing HIV-1 NFLG, including recombinants and clinical characteristics, by subtype among MSM in Korea. Our results provide novel insights for understanding the recombinants in the HIV-1 epidemic in Korea.

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Phylogenetic transmission clusters among newly diagnosed antiretroviral drug-naïve patients with human immunodeficiency virus-1 in Korea: A study from 1999 to 2012

Cited by 6 publications

References 46 publications

Prevalence of Non-B HIV-1 Subtypes in North Italy and Analysis of Transmission Clusters Based on Sequence Data Analysis

Prevalence of Non-B HIV-1 Subtypes in North Italy and Analysis of Transmission Clusters Based on Sequence Data Analysis

Epidemiological and phylogenetic analysis for non-B subtypes of human immunodeficiency virus type 1 in Busan, Korea

Characterization of HIV-1 recombinant and subtype B near full-length genome among men who have sex with men in South Korea

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