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Genotyping and sequence characterization of the NSP4 gene of human group A rotavirus strains in Northern Iran
Author(s) -
Khalkhali Parinaz,
Khavandegar Armin,
Mozhgani SayedHamidreza,
Teimoori Ali,
Moradi Abdolvahhab,
Ajorloo Mehdi,
Lorestani Nazanin,
Kaveh Kimia,
Akbar Soroush,
Razavi Nikoo Hadi
Publication year - 2021
Publication title -
journal of medical virology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.782
H-Index - 121
eISSN - 1096-9071
pISSN - 0146-6615
DOI - 10.1002/jmv.26998
Subject(s) - rotavirus , genotyping , genotype , biology , virology , polymerase chain reaction , sequence analysis , genetic diversity , genetic variation , gene , diarrhea , peptide sequence , genetics , microbiology and biotechnology , virus , population , medicine , environmental health
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.