The ongoing pandemic caused by a novel coronavirus, SARS‐CoV‐2, affects thousands of people every day worldwide. Hence, drugs and vaccines effective against all variants of SARS‐CoV‐2 are crucial today. Viral genome mutations are commonly existent which may impact the encoded proteins, possibly resulting to varied effectivity of detection tools and disease treatment. Thus, this study surveyed the SARS‐CoV‐2 genome and proteome and evaluated its mutation characteristics. Phylogenetic analyses of SARS‐CoV‐2 genes and proteins show three major clades and one minor clade (P6810S; ORF1ab). The overall frequency and densities of mutations in the genes and proteins of SARS‐CoV‐2 were observed Nucleocapsid exhibited the highest mutation density among the structural proteins while the Spike D614G was the most common, occurring mostly in genomes outside China and USA. ORF8 protein had the highest mutation density across all geographical areas. Moreover, mutation hotspots neighboring and at the catalytic site of RNA‐dependent‐RNA‐polymerase were found that might challenge the binding and effectivity of remdesivir. Mutation coldspots may present as conserved diagnostic and therapeutic targets were found in ORF7b, ORF9b and ORF14. These findings suggest that the virion's genotype and phenotype in a specific population should be considered in developing diagnostic tools, and treatment options. This article is protected by copyright. All rights reserved.

Flaviviruses include virus species that are major public health threats worldwide. To determine the immunity landscape of these viruses, seroprevalence studies are often performed using IgG ELISA, which is a simple and rapid alternative to the virus neutralization test. In this review, we aim to describe the trends in flavivirus IgG ELISA-based serosurveys. A systematic literature review using six databases was performed to collate cohort and cross-sectional studies performed on the general population. A total of 204 studies were included in this review. The results show that most studies were performed on dengue virus (DENV), whereas Japanese Encephalitis Virus (JEV) was the least studied. For geographic distribution, serosurveys followed known disease prevalence. Temporally, the number of serosurveys increased after outbreaks and epidemics except for JEV, for which studies were performed to demonstrate the effectiveness of vaccination campaigns. Commercial kits were more commonly used than in-house assays for DENV, West Nile Virus (WNV), and Zika virus (ZIKV). Overall, most studies employed an indirect ELISA format, and the choice of antigens varied per virus. This review shows that flavivirus epidemiology is related to the regional and temporal distribution of serosurveys. It also highlights that endemicity, cross-reactivities, and kit availabilities affect assay choice in serosurveys.

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