Timing and evolution of the most recent common ancestor of the Korean clade HIV subtype B based on Nef and Vif sequences

Kim, Mi-Suk; Jang, Soyoung; Park, Chan-Seung; Lee, Keon Myung; Lee, Dong Hun; Lee, Chanhee

doi:10.1007/s12275-008-0240-x

Cited by 7 publications

(6 citation statements)

References 28 publications

(32 reference statements)

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“…The Taiwan clusters can be described as ''local epidemic'' strains, which transmitted in specific locations but did not spread nationwide in the manner of the ''national epidemic'' B¢. Local epidemic B strains have previously been noted in Korea, 20 and our results indicate that local epidemic subtypes also exist in Taiwan.…”

supporting

confidence: 59%

“…A phylogenetic tree (3) was reconstructed using the NJ method with 469 pol sequences, consisting of 409 sequences from China and 60 B reference sequences isolated in the United States/Europe (20), Thailand (20), and other countries (20). The tree demonstrated 13 out of 409 sequences from China (3.2%), which were scattered among the other sequences, while the other 386 sequences were segregated into four major distinct clusters with bootstrap values above 70% and more than 20 members (Fig.…”

mentioning

confidence: 99%

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Phylogenetic and Temporal Dynamics of Human Immunodeficiency Virus Type 1B in China: Four Types of B Strains Circulate in China

et al. 2014

AIDS Research and Human Retroviruses

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To investigate the origin and evolutionary history of the spread of HIV-1 subtype B in China, a total of 409 sequences of pol gene sampled from 1994 to 2012 in 29 provinces across China was subjected to phylogenetic and Bayesian molecular clock analyses. The study reveals that subtype B strains in China are genetically diverse and can be classified into four distinct subgroups, namely B¢ (Thai-B), BJ-B (Beijing-B), Pan-B (Pandemic-B), and TW-B (Taiwan-B), according to the origin of the sequences. The BJ-B and TW-B are reported for the first time. Phylogeographic analysis reveals that B¢ exhibits a nationwide, transprovincial distribution, and is found in 21 provinces in China in this study, whereas the Pan-B, BJ-B, and TW-B lineages are restricted to particular regions. From the same common ancestor of B¢, there arise two subclusters in which sequences from Yunnan occupy the basal position. The times of the most recent common ancestors (tMRCAs) of B¢ and BJ-B are estimated to be 1983.6 (1975.9-1990.3) and 1995.3 (1989.6-2000.3), respectively. The skyline plot profile reveals an exponential decrease in median number of effective infections of subtype B in China from 1994 to 2009. The existence of four types of B clades also indicates distinct transmission networks of subtype B, originating from different introduction events at different time points. The data presented here offer a new perspective on the epidemic of HIV-1 subtype B in China.

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supporting

confidence: 59%

mentioning

confidence: 99%

Phylogenetic and Temporal Dynamics of Human Immunodeficiency Virus Type 1B in China: Four Types of B Strains Circulate in China

et al. 2014

AIDS Research and Human Retroviruses

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“…KSB is presumed to have originated from strains in the USA through the founder effect [6,7], and the most recent common ancestor is estimated to have been active around 1984 [8]. The earliest case KSB HIV-1, was diagnosed in 1988 [2,3,4,5].…”

Section: Introductionmentioning

confidence: 99%

Genetic Analysis of the Full-Length gag Gene from the Earliest Korean Subclade B of HIV-1: An Outbreak among Korean Hemophiliacs

Cho

Kim

Foley

2019

Viruses

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We determined the earliest full-length HIV-1 gag gene sequences in 110 patients with HIV-1, including 20 hemophiliacs (HPs) and 90 local controls (LCs). The gag gene from stored sera was amplified using RT-PCR, and was subjected to direct sequencing. Phylogenetic analysis indicated that 94 and 16 sequences belonged to the Korean subclade of HIV-1 subtype B (KSB) and subtype B, respectively. A total of 12 signature pattern amino acids were found within the KSB, distinct from the worldwide consensus of subtype B. Within the KSB, the gag gene sequences from donors O and P and those from the 20 HPs comprised two subclusters. In particular, sequences from donor O strongly clustered with those of eight HPs. Moreover, signature pattern analysis indicated that 14 signature nucleotides were shared between the HPs and LCs within KSB (p < 0.01). Among the 14 nucleotides, positions 9 and 5 belonged to clusters O and P, respectively. In conclusion, signature pattern analysis for the gag gene revealed 12 signature pattern residues within the KSB and also confirmed the previous conclusion that the 20 HPs were infected with viruses due to incompletely inactivated clotting factor IX. This study is the first genetic analysis of the HIV-1 gag gene in Korea.

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“…KSB is a distinct, monophyletic clade within HIV-1 subtype B, and presumed to have originated from strains in the USA through a founder effect [8,[10][11][12][13]. The most recent common ancestor is estimated to have been active around 1984 [14]; however, the earliest case was diagnosed in 1988 [2][3][4][5][6].…”

Section: Introductionmentioning

confidence: 99%

Sequence Length of HIV-1 Subtype B Increases Over Time: Analyzing a Cohort of Patients with Hemophilia Over 30 Years

Cho

Kim

Foley

2021

Preprint

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The objective of this study is to investigate whether the sequence length of HIV-1 increases over time. A longitudinal analysis of full-length coding region sequences (FLs) in an outbreak of HIV-1 infection among patients with hemophilia and local controls identified as infected with the Korean subclade B of HIV-1 (KSB). Genes amplified by overlapping RT-PCR or nested PCR were subjected to direct sequencing. In total, 141 FLs were sequentially determined over 30 years in 62 KSB-infected patients. Non-KSB sequences were retrieved from the Los Alamos National Laboratory HIV Database. Phylogenetic analysis indicated that within KSB, 2 FLs from plasma donors O and P comprised two clusters together with 8 and 12 patients with hemophilia, respectively. Signature pattern analysis for the KSB of HIV-1 revealed signature nucleotide residues at 1.05%, compared with local controls. Additionally, in-depth FLs sequence analysis over 30 years in KSB indicates that the KSB FL significantly increases over time before combined antiretroviral therapy (cART) and decreases on cART. Furthermore, the increase in FLs over time significantly occurred in the subtypes B, C and G, but, there was no increase in the subtypes D, A, and F1. Consequently, subtypes F1 and D had the shortest sequence length. Our analysis was extended to compare HIV-1 with HIV-2 and SIVs. Essentially, the longer the sequence length (SIVsm > HIV-2 > SIVcpz > HIV-1), the longer the survival period. The increase in the length of the HIV-1 sequence over time suggests that it might be an evolutionary direction toward attenuated pathogenicity.

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Timing and evolution of the most recent common ancestor of the Korean clade HIV subtype B based on Nef and Vif sequences

Cited by 7 publications

References 28 publications

Phylogenetic and Temporal Dynamics of Human Immunodeficiency Virus Type 1B in China: Four Types of B Strains Circulate in China

Phylogenetic and Temporal Dynamics of Human Immunodeficiency Virus Type 1B in China: Four Types of B Strains Circulate in China

Genetic Analysis of the Full-Length gag Gene from the Earliest Korean Subclade B of HIV-1: An Outbreak among Korean Hemophiliacs

Sequence Length of HIV-1 Subtype B Increases Over Time: Analyzing a Cohort of Patients with Hemophilia Over 30 Years

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