Phylodynamics of major CRF01_AE epidemic clusters circulating in mainland of China

Wang, Xiaolin; He, Xiang; Zhong, Ping; Liu, Yongjian; Gui, Tao; Jia, Dijing; Li, Hanping; Wu, Jianjun; Jin, Yan; Kang, Dianmin; Han, Yang; Li, Taisheng; Yang, Rongge; Han, Xiaoxu; Chen, Lin; Zhao, Jin; Xing, Hui; Liang, Shu; He, Jianmei; Yan-sheng, Yan; Xue, Ying; Zhang, Jiafeng; Zhuang, Xun; Liang, Shujia; Bao, Zhenmin; Li, Tianyi; Zhuang, Daomin; Liu, Siyang; Han, Jingwan; Jia, Lei; Li, Jingyun; Li, Lin

doi:10.1038/s41598-017-06573-6

Cited by 36 publications

(28 citation statements)

References 45 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…A greater number of MSM were observed within clusters and linked with other high-risk populations [64]. Several other large-scale studies have also demonstrated multiple epidemic clusters responsible for 85% of the total CRF01_AE infections in China [65], among which two large clusters were found with high prevalence among MSM [57,58]. These findings all suggest that MSM are at higher risk than others in the population and highlight the importance of MSM-focused interventions for the control of HIV in China.…”

Section: Molecular Network Reconstruct the History Of Hiv Spreadmentioning

confidence: 99%

Molecular network-based intervention brings us closer to ending the HIV pandemic

Han

Zhao

et al. 2020

Front. Med.

Self Cite

View full text Add to dashboard Cite

Precise identification of HIV transmission among populations is a key step in public health responses. However, the HIV transmission network is usually difficult to determine. HIV molecular networks can be determined by phylogenetic approach, genetic distance-based approach, and a combination of both approaches. These approaches are increasingly used to identify transmission networks among populations, reconstruct the history of HIV spread, monitor the dynamics of HIV transmission, guide targeted intervention on key subpopulations, and assess the effects of interventions. Simulation and retrospective studies have demonstrated that these molecular network-based interventions are more cost-effective than random or traditional interventions. However, we still need to address several challenges to improve the practice of molecular network-guided targeting interventions to finally end the HIV epidemic. The data remain limited or difficult to obtain, and more automatic real-time tools are required. In addition, molecular and social networks must be combined, and technical parameters and ethnic issues warrant further studies.

show abstract

Section: Molecular Network Reconstruct the History Of Hiv Spreadmentioning

confidence: 99%

Molecular network-based intervention brings us closer to ending the HIV pandemic

Han

Zhao

et al. 2020

Front. Med.

Self Cite

View full text Add to dashboard Cite

show abstract

“…CRF01_AE, CRF_BC and Subtype B/B' are most prevalent in Mainland China (Su et al, 2014), and CRF01_AE has recently replaced subtype B as the dominant circulating subtype among Chinese MSM (Zhang et al, 2015). A number of detailed phylogenetic analyses revealed that several major transmission clusters of HIV-1 CRF01_AE existed and expanded after their multiple introductions into China (Abubakar et al, 2013;Feng et al, 2013;Peng et al, 2015;Zeng et al, 2016;Wang et al, 2017). Three of them were prevalent among heterosexuals and IDUs (CN.01AE.HST/IDU-1/2/3 clusters), and two were related to MSM transmission (CN.01AE.MSM-4/5 clusters) (Feng et al, 2013).…”

Section: Introductionmentioning

confidence: 99%

Cross-Continental Dispersal of Major HIV-1 CRF01_AE Clusters in China

Han

Zhao

et al. 2020

Front. Microbiol.

Self Cite

View full text Add to dashboard Cite

Since the 1990s, several distinct clusters of human immunodeficiency virus-type 1 (HIV-1) CRF01_AE related to a large epidemic in China have been identified, but it is yet poorly understood whether its transmission has dispersed globally. We aimed to characterize and quantify the genetic relationship of HIV-1 CRF01_AEs circulating in China and other countries. Using representative sequences of Chinese clusters as queries, all relevant CRF01_AE pol sequences in two large databases (the Los Alamos HIV sequence database and the UK HIV Drug Resistance Database) were selected with the online basic local alignment search (BLAST) tool. Phylogenetic and phylogeographic analyses were then carried out to characterize possible linkage of CRF01_AE strains between China and the rest of the world. We identified that 269 strains isolated in other parts of the world were associated with five major Chinese CRF01_AE clusters. 80.7% were located within CN.01AE.HST/IDU-2, most of which were born in Southeast Asia. 17.8% were clustered with CN.01AE.MSM-4 and -5. Two distinct sub-clusters associated with Chinese men who have sex with men (MSM) emerged in HK-United Kingdom and Japan after 2000. Our analysis suggests that HIV-1 CRF01_AE strains related to viral transmission in China were initially brought to the United Kingdom or other countries during the 1990s by Asian immigrants or returning international tourists from Southeast Asia, and then after having circulated among MSM in China for several years, these Chinese strains dispersed outside again, possibly through MSM network. This study provided evidence of regional and global dispersal of Chinese CRF01_AE strains. It would also help understand the global landscape of HIV epidemic associated with CRF01_AE transmission and highlight the need for further international collaborative study in this field.

show abstract

“…CRF01_AE accounts for about 80% of CRFs in southeast and east Asia, and it increased consistently in east Asia between 2010 to 2015 [7]. In China, CRF01_ AE is one of the main epidemic strains of HIV-1, accounting for 42.5% of the reported HIV-1 infection cases in China according to a systematic review [15], and multiple lineages of CRF01_AE have been reported to be transmitted in China [16,17].…”

Section: Introductionmentioning

confidence: 99%

Natural polymorphisms in HIV-1 CRF01_AE strain and profile of acquired drug resistance mutations in a long-term combination treatment cohort in northeastern China

et al. 2020

Self Cite

View full text Add to dashboard Cite

Background: The impacts of genetic polymorphisms on drug resistance mutations (DRMs) among various HIV-1 subtypes have long been debated. In this study, we aimed to analyze the natural polymorphisms and acquired DRM profile in HIV-1 CRF01_AE-infected patients in a large first-line antiretroviral therapy (ART) cohort in northeastern China. Methods: The natural polymorphisms of CRF01_AE were analyzed in 2034 patients from a long-term ART cohort in northeastern China. The polymorphisms in 105 treatment failure (TF) patients were compared with those in 1148 treatment success (TS) patients. The acquired DRM profile of 42 patients who experienced TF with tenofovir/ lamivudine/efavirenz (TDF/3TC/EFV) treatment was analyzed by comparing the mutations at TF time point to those at baseline. The Stanford HIVdb algorithm was used to interpret the DRMs. Binomial distribution, McNemar test, Wilcoxon test and CorMut package were used to analyze the mutation rates and co-variation. Deep sequencing was used to analyze the evolutionary dynamics of co-variation. Results: Before ART, there were significantly more natural polymorphisms of 31 sites on reverse transcriptase (RT) in CRF01_AE than subtype B HIV-1 (|Z value| ≥ 3), including five known drug resistance-associated sites (238, 118, 179, 103, and 40). However, only the polymorphism at site 75 was associated with TF (|Z value| ≥ 3). The mutation rate at 14 sites increased significantly at TF time point compared to baseline, with the most common DRMs comprising G190S/C, K65R, K101E/N/Q, M184 V/I, and V179D/I/A/T/E, ranging from 66.7 to 45.2%. Moreover, two unknown mutations (V75 L and L228R) increased by 19.0 and 11.9% respectively, and they were under positive selection (Ka/ Ks > 1, log odds ratio [LOD] > 2) and were associated with several other DRMs (cKa/Ks > 1, LOD > 2). Deep sequencing of longitudinal plasma samples showed that L228R occurred simultaneously or followed the appearance of Y181C.

show abstract

Phylodynamics of major CRF01_AE epidemic clusters circulating in mainland of China

Cited by 36 publications

References 45 publications

Molecular network-based intervention brings us closer to ending the HIV pandemic

Molecular network-based intervention brings us closer to ending the HIV pandemic

Cross-Continental Dispersal of Major HIV-1 CRF01_AE Clusters in China

Natural polymorphisms in HIV-1 CRF01_AE strain and profile of acquired drug resistance mutations in a long-term combination treatment cohort in northeastern China

Contact Info

Product

Resources

About