| Literature DB >> 33102246 |
Keqiang Huang1, Yong Zhang1,2, Zhenzhi Han1, Xiaofang Zhou3, Yang Song1, Dongyan Wang1, Shuangli Zhu1, Dongmei Yan1, Wen Xu3, Wenbo Xu1,2.
Abstract
The subgenotype B5 of EV-A71 is a widely circulating subgenotype that frequently spreads across the globe. Several outbreaks have occurred in nations, such as Malaysia, Thailand, Vietnam, and Japan. Appearing first in Taiwan, China, the subgenotype has been frequently reported in mainland of China even though no outbreaks have been reported so far. The current study reconstructed the migration of the B5 subgenotype of EV-A71 in China via phylogeographical analysis. Furthermore, we investigated its population dynamics in order to draw more credible inferences. Following a dataset cleanup of B5 subgenotype of EV-A71, we detected earlier B5 subgenotypes of EV-A71 sequences that had been circulating in Malaysia and Singapore since the year 2000, which was before the 2003 outbreak that occurred in Sarawak. The Bayesian inference indicated that the most recent common ancestor of B5 subgenotype EV-A71 appeared in September, 1994 (1994.75). With respect to the overall prevalence, geographical reconstruction revealed that the B5 subgenotype EV-A71 originated singly from single-source cluster and subsequently developed several active lineages. Based on a large amount of data that was accumulated, we conclude that the appearance of the B5 subgenotype of EV-A71 in mainland of China was mainly due to multiple migrations from different origins.Entities:
Keywords: B5 subgenotype; enterovirus A71; migration; molecular evolution; phylogeographical analysis
Mesh:
Year: 2020 PMID: 33102246 PMCID: PMC7546772 DOI: 10.3389/fcimb.2020.00475
Source DB: PubMed Journal: Front Cell Infect Microbiol ISSN: 2235-2988 Impact factor: 5.293
Figure 1The prevalence of the B5 subgenotype of EV-A71 is divided into two stages. The root-to-tip diagnostic tool using heuristic residual mean square methods suggested that data redundancy and discrete nodes existed in the total dataset (A) and the compact dataset (B); the phylogenetic tree indicated the recent epidemics (after 2012) were mostly found in the end of a branch of the evolutionary tree (C).
Figure 2Estimation of TMRCA and population dynamics for the B5 subgenotype of EV-A71. (A) The results of the mismatching distribution showing that the simulated curves were in good agreement with the measured ones. (B) The Bayesian skyride plot indicates that more expansions occurred.
The TMRCA of the B5 subgenotypes of EV-A71 in different countries and regions.
| Mean rate | 5.65 × 10−3 | 95%HPD | (4.83 × 10−3, 6.44 × 10−3) |
| Location | TMRCA | 95%HPD | |
| France | 2013.24 | (2012.90, 2013.49) | |
| Malaysia | 1994.79 | (1988.66, 1998.98) | |
| Taiwan, China | 1996.27 | (1991.19, 2000.39) | |
| Vietnam | 1999.1 | (1994.61, 2004.52) | |
| Brunei | 2003.58 | (2000.15, 2005.74) | |
| Cambodia | 1998.33 | (1993.44, 2001.11) | |
| Mainland of China | 1997.49 | (1992.87, 2000.53) | |
| Indonesia | 2006.47 | (2005.49, 2007.36) | |
| Japan | 1995.62 | (1990.16, 1998.72) | |
| Singapore | 1994.77 | (1988.66, 1998.96) | |
| Thailand | 1997.39 | (1992.4, 2000.63) |
Figure 3Analyis of recombination events of B5 sub-genotype of EV-A71. (A) A maximum likelihood tree (1,000 bootstrap replicates) was constructed, and seven Yunnan B5 sub-genotype of EV-A71 genomes were separated into two groups; (B,C) no significant inter-serotypes or inter-species recombination events were found.
Figure 4The time-scaled MCC tree constructed based on the entire VP1 region. The time-scaled MCC tree reveals that all the B5 subgenotypes of EV-A71 were from a geographical mono-originated cluster. Posterior probability, an indicator of phylogeography, shows that continuous processes with particular reference to the connections between Malaysia and other countries, such as Japan, Thailand, and Vietnam.
Figure 5Estimation of the geographical origin and spread of the B5 subgenotype of EV-A71. (A) Spatial spread links of B5 sub-genotype of EV-A71 among sampling locations were identified. The lines connecting different locations are colored according to the heat map. (B) The heat map shows Bayes factor (BF) values estimated between two geographic locations. The maps are based on satellite pictures made available in Google Earth (http://earth.google.com).