Intra-host genetic evolution of HIV-1 pol gene and estimation of infection time for five infections
XIN Ruolei*, LI Jia, SUN Lijun, LIU An, ZHANG Qin, SUN Weidong, LI Jie, LU Hongyan, BAI Lishi
*Institute of AIDS/STD Prevention and Treatment, Beijing Municipal Center for Disease Prevention and Control( Beijing Research Center for Preventive Medicine ), Beijing 100013, China
Abstract：Objective To explore the intra-host genetic evolution of HIV-1 pol gene via follow-up for treatment-naïve HIV infections, and estimate the infection time with Bayesian coalescent theory, so as to support the evaluation of HIV epidemic. Methods Five cases were recruited and followed up. The pol gene fragments were amplified for the characteristics of transmitted drug resistance ( TDR ) by RT-PCR. Bayesian coalescent theory was utilized to construct maximum clade credibility ( MCC ) tree for genetic evolution and calculate the time to the most recent common ancestor ( tMRCA ). Results The five cases were all male, and aged from 27 to 50 years old.Five to nine sampling times were obtained from each case, and the pol gene sequences from each case formed a unique subcluster (posterior probability: 100% ), with different evolution characteristics, in the MCC tree. The three cases in primary HIV-1 infection were estimated to be infected one to five months before the first positive reaction of HIV screening, whereas the two HIV-1 diagnosed cases at first screening were extrapolated to get infected fourteen months and seven months before diagnosis, respectively. One case with acute HIV-1 infection carried TDR mutation ( M46I ) , expressing fast disease progress and quasispecies variation. Conclusions The general infection time can be estimated by analyzing the characteristics of intra-host genetic evolution of HIV-1 pol gene with Bayesian coalescent theory, and this method can help to estimate the HIV epidemic.
辛若雷, 李佳, 孙丽君, 刘安, 张琴, 孙伟东, 李洁, 卢红艳, 白立石. 5例HIV-1感染者pol基因进化和感染时间推断研究[J]. 预防医学, 2021, 33(6): 545-550.
XIN Ruolei, LI Jia, SUN Lijun, LIU An, ZHANG Qin, SUN Weidong, LI Jie, LU Hongyan, BAI Lishi. Intra-host genetic evolution of HIV-1 pol gene and estimation of infection time for five infections. Preventive Medicine, 2021, 33(6): 545-550.
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