The epidemic origin and molecular properties of B′: a founder strain of the HIV-1 transmission in Asia

Deng, Xiang; Liu, Haizhou; Shao, Yiming; Rayner, Simon; Yang, Rongge

doi:10.1097/qad.0b013e32830f4c62

Cited by 51 publications

(48 citation statements)

References 54 publications

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“…Our evolutionary analysis of HIV-1B¢ agrees with other studies in the timing of its introduction into China. [12][13][14] Perhaps the number of HIV-1 sequences recovered from early victims of AIDS was too small; in the BSP analysis, we did not observe an increase in the period of the B subtype on the whole, as others reported. Demographic reconstruction of the entire B subtype showed an exponential decrease in the median number of effective infections from 1994 to 2009, followed by an asymptotic phase afterward.…”

supporting

confidence: 42%

“…Discoveries made independently by three groups have provided similar answers recently to its temporal and geographic distribution patterns, including its origin and dissemination. [12][13][14] However, the spatial diffusion of the epidemic from the perspective of Pan-B has not previously been traced. In this study, we used phylogenetic analyses and a Bayesian coalescent-based approach to investigate the temporal and spatial dynamics of HIV-1 subtype B transmission including B¢ and Pan-B together in order to provide a greater understanding of the epidemic growth model of the HIV-1B virus.…”

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: 42%

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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“…These analytical frameworks have identified genes under selection, characterized population structure and migration routes, characterized population dynamic and evolutionary processes, and identified mutations leading to epidemics and pandemics in pathogens (Grenfell et al 2004;Deng et al 2008;Holmes and Grenfell 2009; Humphrey et al 2010;Hofinger et al 2011;CastroNallar et al 2012). However, precision of estimates from conventional population genetic methods are limited by the amount of available sequence data.…”

Section: Discussionmentioning

confidence: 99%

Selective Whole Genome Amplification for Resequencing Target Microbial Species from Complex Natural Samples

Leichty¹,

Brisson

2014

Genetics

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Population genomic analyses have demonstrated power to address major questions in evolutionary and molecular microbiology. Collecting populations of genomes is hindered in many microbial species by the absence of a cost effective and practical method to collect ample quantities of sufficiently pure genomic DNA for next-generation sequencing. Here we present a simple method to amplify genomes of a target microbial species present in a complex, natural sample. The selective whole genome amplification (SWGA) technique amplifies target genomes using nucleotide sequence motifs that are common in the target microbe genome, but rare in the background genomes, to prime the highly processive phi29 polymerase. SWGA thus selectively amplifies the target genome from samples in which it originally represented a minor fraction of the total DNA. The post-SWGA samples are enriched in target genomic DNA, which are ideal for population resequencing. We demonstrate the efficacy of SWGA using both laboratoryprepared mixtures of cultured microbes as well as a natural host-microbe association. Targeted amplification of Borrelia burgdorferi mixed with Escherichia coli at genome ratios of 1:2000 resulted in .10 5 -fold amplification of the target genomes with ,6.7-fold amplification of the background. SWGA-treated genomic extracts from Wolbachia pipientis-infected Drosophila melanogaster resulted in up to 70% of high-throughput resequencing reads mapping to the W. pipientis genome. By contrast, 2-9% of sequencing reads were derived from W. pipientis without prior amplification. The SWGA technique results in high sequencing coverage at a fraction of the sequencing effort, thus allowing population genomic studies at affordable costs. C LASSICAL population genetics, coupled with advances in coalescent modeling, has been foundational to studies of the evolutionary histories and ecological forces that shape natural populations (Rosenberg and Nordborg 2002;Hume et al. 2003;Wakeley 2004). However, detecting fine scale processes using population genetics and coalescent analyses is limited by the amount of available sequence data per sample. Datasets with substantially greater genetic information per sample, such as genomic data from population-level sampling, would be optimal to study biological processes at all relevant scales. The promise of population genomics for many microbial species is tempered, however, by the difficulty of isolating and preparing microbial genomes for nextgeneration sequencing. Currently, sequencing microbial genomes requires laboratory culture to isolate them from other organisms with which they are naturally associated to obtain the appropriate samples for sequencing-sufficient numbers of the target genome with limited contaminating DNA (Mardis 2008).Methodological issues in obtaining populations of genomes from microbial species occur both because the target microbial genomes often constitutes only a miniscule fraction of the DNA in complex, field-derived samples and because many important microbial specie...

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“…Therefore, the relaxed clock model with a BSP prior was used to investigate the evolutionary rate and the TMRCA of the five Central American HIV1-B clades. Several studies, on the basis of different methods, estimated HIV-1 group M TMRCA in 1921 to 1931 using env sequences (40,42) and in 1902 to 1939 (median, 1920) using pol sequences (43), while the origin of subtype B has been placed around the early 1960s (44). These estimates were used as internal controls to verify the robustness of the Bayesian inference.…”

Section: Hiv-1 Subtype Classificationmentioning

confidence: 99%

A Single Early Introduction of HIV-1 Subtype B into Central America Accounts for Most Current Cases

Murillo

Véras

Prosperi

et al. 2013

J Virol

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The epidemic origin and molecular properties of B′: a founder strain of the HIV-1 transmission in Asia

Abstract: Our research is the first large-scale investigation on HIV-1 B' at a global level and provides a deep insight into one of the founder strains of HIV-1 epidemic in Asia. Our results provide an important reference for HIV scientists, public health officials and HIV vaccine designers.

Cited by 51 publications

References 54 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

Selective Whole Genome Amplification for Resequencing Target Microbial Species from Complex Natural Samples

A Single Early Introduction of HIV-1 Subtype B into Central America Accounts for Most Current Cases

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