Complete nucleotide sequence of an Indian strain of Japanese Encephalitis Virus: sequence comparison with other strains and phylogenetic analysis

Abstract. The RNA genome of an Indian strain of Japanese encephalitis virus (JEV), GP78, was reverse transcribed and the cDNA fragments were cloned in bacterial plasmids. Nucleotide sequencing of the cDNA clones covering the entire genome of the virus established that the GP78 genome was 10,976 nucleotides long. An open reading frame of 10,296 bases, capable of coding for a 3,432 amino acid polyprotein, was flanked by 95- and 585base long 5�- and 3�-non-coding regions, respectively. When compared with the nucleotide sequence of the JaOArS982 strain, the JEV GP78 genome had a number of nucleotide substitutions that were scattered throughout the genome except for the 5�-noncoding region, the sequence of which was fully conserved. Comparison of the complete genome sequences of different JEV isolates showed a 1.3–4.1 % nucleotide sequence divergence among them, which resulted in 0.6–l.8 % amino acid sequence divergence. Analysis based on the complete genome sequences of different JEV isolates showed that the GP78 isolate from India was phylogenetically closer to the Chinese SA14 isolate. Japanese encephalitis virus (JEV) is a mosquito-borne virus that was first isolated from a human case in Japan in 1933. The virus has since become a major public healt

COVID-19 pandemic to endemic

The COVID-19 pandemic appeared in late 2019 and became a major health concern with rapid transmission and very high mortality rates across the globe. Although precautionary, preventive, protective and therapeutic measures have been adopted against COVID-19, still the disease has drastically affected people. In order to overcome the challenges of the pandemic, the understanding of the route of transmission, its fusion with receptors and invasion into the human body and hacking the immune system, the viral genome was sequenced. The viral genome keeps on mutating and altering its original form into its subtypes. Moreover, age and comorbid conditions had their impact on developing the disease differing from individual to individual due to interaction varying between the host genome and virus. Considering the pathogenesis of the virus, neutralizing antibodies reduced the viral impact and severity. This review is focused on highlighting the COVID-19 genome, host genetic factors, the pathogenesis of the disease and available therapeutic measures to overcome the pandemic

Isolation and Genomic Characterization of SARS-CoV-2 Omicron Variant Obtained from Human Clinical Specimens

Due to the failure of virus isolation of the Omicron variant in Vero CCL-81 from the clinical specimens of COVID-19 cases, an initial in vivo and subsequent in vitro approach was utilized for the isolation of the virus. A total of 74 oropharyngeal/nasopharyngeal specimens were collected from SARS-CoV-2 positive international travellers and a contact case at Delhi and Mumbai, India. All the specimens were sequenced using next-generation sequencing and simultaneously inoculated onto Vero CCL-81 cells for virus isolation. Subsequently, two omicron positive specimens were inoculated into Syrian hamsters for two passages. The initial passage of the positive hamster specimens was inoculated onto Vero CCL-81 cells. The clinical specimens, hamster specimens, and Vero CCL-81 passages were sequenced to assess the mutational changes in different host species. The replication of the Omicron variant in hamsters was confirmed with the presence of a high viral load in nasal turbinate and lung specimens of both passages. The successful isolation of the virus from hamster specimens with Vero CCL-81 was observed with cytopathic effect in infected cells and high viral load in the cell suspension. The genome analysis revealed the presence of L212C mutation, Tyrosine 69 deletion, and C25000T nucleotide change in spike gene of hamster passage sequences and an absence of V17I mutation in E gene in hamster passage sequences, unlike human clinical specimen and Vero CCL-81 passages. No change was observed in the furin cleavage site in any of the specimen sequences, suggesting intact pathogenicity of the virus isolate. Our data demonstrated successful isolation of the Omicron variant with the in vivo method first followed by in vitro method. The virus isolate could be used in the future to explore different aspects of the Omicron variant