Genotyping and sequence characterization of the NSP4 gene of human group A rotavirus strains in Northern Iran

Rotavirus is known to be responsible for remarkable numbers of severe diarrheal episodes and even death in infants and young children. In this study, we aimed to survey genetic diversity and variation analysis of viroporin, which is encoded by the rotavirus NSP4 segment. Thirty‐five rotavirus‐positi...

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Published in:Journal of medical virology 2021-08, Vol.93 (8), p.4824-4830
Main Authors: Khalkhali, Parinaz, Khavandegar, Armin, Mozhgani, Sayed‐Hamidreza, Teimoori, Ali, Moradi, Abdolvahhab, Ajorloo, Mehdi, Lorestani, Nazanin, Kaveh, Kimia, Akbar, Soroush, Razavi Nikoo, Hadi
Format: Article
Language:English
Subjects:
Amino acids
Binding sites
Children
Diarrhea
DNA-directed RNA polymerase
Genetic analysis
Genetic diversity
Genotypes
Genotyping
NSP4
NSP4 gene
phylogenetic analyses
Polymerase chain reaction
Rotavirus
Virology
viroporin
Viruses
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Summary:Rotavirus is known to be responsible for remarkable numbers of severe diarrheal episodes and even death in infants and young children. In this study, we aimed to survey genetic diversity and variation analysis of viroporin, which is encoded by the rotavirus NSP4 segment. Thirty‐five rotavirus‐positive specimens were obtained, and RNA extraction and polymerase chain reaction amplification were performed. After the sequencing process, four specimens were excluded, and the final 31 samples remained for genetic diversity and variation analysis. The predominant single G/P combination was G1P[8] (~78%), followed by G2P[8] (~13%), and equal percentages (3%) of G2P[4], G3P[8], and G‐non‐typeable‐P[8]. Further analyses revealed that variations could be found in the three regions of NSP4, including VP4 binding site (aa 112–146), double‐layered particle binding site (aa 161–175), and finally, in the predicted amphipathic alpha‐helix. Phylogenic tree analysis demonstrated that the mentioned samples clustered with genotype E1 and E2 reference sequences. As previously reported in the literature, in this study, it was revealed that no apparent correlation exists in the deduced amino acid sequences corresponding to this region between the rotaviruses collected from patients with and without diarrhea.
ISSN:0146-6615
1096-9071
DOI:10.1002/jmv.26998