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Li F, Feng Y, Wang G, Zhang W, Fu S, Wang Z, Yin Q, Nie K, Yan J, Deng X, He Y, Liang L, Xu S, Wang Z, Liang G, Wang H. Tracing the spatiotemporal phylodynamics of Japanese encephalitis virus genotype I throughout Asia and the western Pacific. PLoS Negl Trop Dis 2023; 17:e0011192. [PMID: 37053286 PMCID: PMC10128984 DOI: 10.1371/journal.pntd.0011192] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 04/25/2023] [Accepted: 02/24/2023] [Indexed: 04/15/2023] Open
Abstract
BACKGROUND Japanese encephalitis virus (JEV; Flaviridae: Flavivirus) causes Japanese encephalitis (JE), which is the most important arboviral disease in Asia and the western Pacific. Among the five JEV genotypes (GI-IV), GI has dominated traditional epidemic regions in the past 20 years. We investigated the transmission dynamics of JEV GI through genetic analyses. METHODS We generated 18 JEV GI near full length sequences by using multiple sequencing approaches from mosquitoes collected in natural settings or from viral isolates obtained through cell culture. We performed phylogenetic and molecular clock analyses to reconstruct the evolutionary history by integrating our data with 113 publicly available JEV GI sequences. RESULTS We identified two subtypes of JEV GI (GIa and GIb), with a rate of 5.94 × 10-4 substitutions per site per year (s/s/y). At present, GIa still circulates within a limited region, exhibited no significant growth, the newest strain was discovered in China (Yunnan) in 2017, whereas most JEV strains circulating belong to the GIb clade. During the past 30 years, two large GIb clades have triggered epidemics in eastern Asia: one epidemic occurred in 1992 [95% highest posterior density (HPD) = 1989-1995] and the causative strain circulates mainly in southern China (Yunnan, Shanghai, Guangdong, and Taiwan) (Clade 1); the other epidemic occurred in 1997 (95% HPD = 1994-1999) and the causative strain has increased in circulation in northern and southern China during the past 5 years (Clade 2). An emerging variant of Clade 2 contains two new amino acid markers (NS2a-151V, NS4-169K) that emerged around 2005; this variant has demonstrated exponential growth in northern China. CONCLUSION JEV GI stain circulating in Asia have shifted during the past 30 years, spatiotemporal differences were observed among JEV GI subclade. GIa is still circulating within a limited range, exhibite no significant growth. Two large GIb clades have triggered epidemics in eastern Asia, all JEV sequences identified in northern China during the past 5 years were of the new emerging variant of G1b-clade 2.
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Affiliation(s)
- Fan Li
- Department of Arboviruses, NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, State Key Laboratory for Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, Beijing, PR China
| | - Yun Feng
- Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Yunnan Institute of Endemic Disease Control and Prevention, Dali, PR China
| | - Guowei Wang
- Ningxia Medical University, Yinchuan, PR China
| | - Weijia Zhang
- Department of Arboviruses, NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, State Key Laboratory for Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, Beijing, PR China
| | - Shihong Fu
- Department of Arboviruses, NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, State Key Laboratory for Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, Beijing, PR China
| | - Zuosu Wang
- Liaoning Center for Disease Control and Prevention, Shenyang, PR China
| | - Qikai Yin
- Department of Arboviruses, NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, State Key Laboratory for Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, Beijing, PR China
| | - Kai Nie
- Department of Arboviruses, NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, State Key Laboratory for Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, Beijing, PR China
| | - Juying Yan
- Zhejiang Center for Disease Control and Prevention, Hangzhou, PR China
| | - Xuan Deng
- Zhejiang Center for Disease Control and Prevention, Hangzhou, PR China
| | - Ying He
- Department of Arboviruses, NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, State Key Laboratory for Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, Beijing, PR China
| | - Liang Liang
- Guangxi Zhuang Autonomous Region Center for Disease Control and Prevention, Nanning, PR China
| | - Songtao Xu
- Department of Arboviruses, NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, State Key Laboratory for Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, Beijing, PR China
| | - Zhenhai Wang
- Department of Neurology, General Hospital of Ningxia Medical University, Engineering Research Center for Diagnosis and Treatment of Ningxia Nervous System Diseases, Yinchuan, PR China
| | - Guodong Liang
- Department of Arboviruses, NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, State Key Laboratory for Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, Beijing, PR China
| | - Huanyu Wang
- Department of Arboviruses, NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, State Key Laboratory for Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, Beijing, PR China
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Leiva S, Bugnon Valdano M, Gardiol D. Unravelling the epidemiological diversity of Zika virus by analyzing key protein variations. Arch Virol 2023; 168:115. [PMID: 36943525 DOI: 10.1007/s00705-023-05726-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 01/19/2023] [Indexed: 03/23/2023]
Abstract
The consequences of Zika virus (ZIKV) infections were limited to sporadic mild diseases until almost a decade ago, when epidemic outbreaks took place, with quick spread into the Americas. Simultaneously, novel severe neurological manifestations of ZIKV infections were identified, including congenital microcephaly. However, why the epidemic strains behave differently is not yet completely understood, and many questions remain about the actual significance of genetic variations in the epidemiology and biology of ZIKV. In this study, we analysed a large number of viral sequences to identify genes with different levels of variability and patterns of genomic variations that could be associated with ZIKV diversity. We compared numerous epidemic strains with pre-epidemic strains, using the BWA-mem algorithm, and we also examined specific variations among the epidemic ZIKV strains derived from microcephaly cases. We identified several viral genes with dissimilar mutation rates among the ZIKV strain groups and novel protein variation profiles that might be associated with epidemiological particularities. Finally, we assessed the impact of the detected changes on the structure and stability of the NS1, NS5, and E proteins using the I-TASSER, trRosetta, and RaptorX modelling algorithms, and we found some interesting variations that might help to explain the heterogeneous features of the diverse ZIKA strains. This work contributes to the identification of genetic differences in the ZIKV genome that might have a phenotypic impact, providing a basis for future experimental analysis to elucidate the genetic causes of the recent ZIKV emergency.
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Affiliation(s)
- Santiago Leiva
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Biología Molecular y Celular de Rosario-CONICET, Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina
| | - Marina Bugnon Valdano
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Biología Molecular y Celular de Rosario-CONICET, Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina.
| | - Daniela Gardiol
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Biología Molecular y Celular de Rosario-CONICET, Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina.
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Bernardo-Menezes LC, Agrelli A, Oliveira ASLED, Moura RRD, Crovella S, Brandão LAC. An overview of Zika virus genotypes and their infectivity. Rev Soc Bras Med Trop 2022; 55:e02632022. [PMID: 36197380 PMCID: PMC9536801 DOI: 10.1590/0037-8682-0263-2022] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 08/31/2022] [Indexed: 11/22/2022] Open
Abstract
Zika virus (ZIKV) is an enveloped, single-stranded RNA arbovirus belonging to the
genus Flavivirus. It was first isolated from a sentinel monkey
in Uganda in 1947. More recently, ZIKV has undergone rapid geographic expansion
and has been responsible for outbreaks in Southeast Asia, the Pacific Islands,
and America. In this review, we have highlighted the influence of viral genetic
variants on ZIKV pathogenesis. Two major ZIKV genotypes (African and Asian) have
been identified. The Asian genotype is subdivided into Southwest Asia, Pacific
Island, and American strains, and is responsible for most outbreaks.
Non-synonymous mutations in ZIKV proteins C, prM, E, NS1, NS2A, NS2B, NS3, and
NS4B were found to have a higher prevalence and association with virulent
strains of the Asian genotype. Consequently, the Asian genotype appears to have
acquired higher cellular permissiveness, tissue persistence, and viral tropism
in human neural cells. Therefore, mutations in specific coding regions of the
Asian genotype may enhance ZIKV infectivity. Considering that mutations in the
genomes of emerging viruses may lead to new virulent variants in humans, there
is a potential for the re-emergence of new ZIKV cases in the future.
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