Reliable estimates of Japanese encephalitis virus evolutionary rate supported by a formal test of temporal signal

Abstract

AbstractJapanese encephalitis virus (JEV) is a positive-strand RNA virus, that causing encephalitis in humans, which is highly spread in East and Southeast Asia, Western Pacific countries and Australia. The main vector of JEV isCulexspp. (mainlyC. tritaeniorhynchus). The intraspecies structure of JEV comprises five genotypes (GI-GV). In the previous studies, the substitution rate and the age of the JEV most recent common ancestor (MRCA) based on complete open reading frame (ORF) / whole genome sequences were reported, however, the estimates are significantly different between some of the studies. Most importantly, the temporal signal in nucleotide data as the key aspect of the molecular clock application was evaluated by neither formal nor informal tests. In February 2023, we found 325 non-recombinant nucleotide sequences of ORF with known collection dates. The purpose of our study is the evaluation of temporal signal in the JEV ORF nucleotide data set using the Bayesian approach with the subsequent re-estimation of substitution rate and the age of the JEV common clade (GI-GV) and two JEV genotypes (GI and GIII) characterized by the number of sequences enough for reliable estimates. Results showed the presence of temporal signal in all analyzed data set. The substitution rate of the JEV GI-GV was 2.41×10−4(95% highest posterior density (HPD) interval, 1.67×10−4–3.14×10−4) or approximately 2.5 nucleotide substitutions per ORF (10,296 nucleotides) per year that is one the lowest substitution rate among the species closely related to JEV and other well-studied members of mosquito-borne flaviviruses. The substitution rate of GI and GIII evaluated as 4.13×10−4(95% HPD interval, 3.45×10−4– 4.82×10−4) and 6.17×10−5(95% HPD interval 3.84×10−5–8.62×10−5), accordingly, with the ages of clades of 153 (95% HPD, 87–237) and 216 (95% HPD, 139–317), respectively. The root height of JEV is 1234 years (95% HPD, 407–2333). To the best of our knowledge, this study provides the first reliable substitution rate assessment of the global clade of JEV embracing all five genotypes.