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. 2020 Dec;31(4):554-559.
doi: 10.1007/s13337-020-00621-y. Epub 2020 Aug 13.

Detection and molecular characterization of rotavirus of pigs in Kerala, India

G Logeshwaran  1 , Chintu Ravishankar  1 , D Nandhakumar  1 , Stephy Rose Sebastian  1 , R Rajasekhar  1 , K Sumod  1 , Binu K Mani  1 , E D Benjamin  2 , T R Jayakrishnan  3 , Koshy John  1 , M Mini  4
Affiliations

Detection and molecular characterization of rotavirus of pigs in Kerala, India

G Logeshwaran et al. Virusdisease. 2020 Dec.

Abstract

Group A rotaviruses (GAR) are an important cause of diarrhoea in infants and newborn animals especially pigs. In this paper, we report the detection, G and P typing and phylogenetic analysis of GAR of pigs in Kerala. A total of 100 fecal samples from diarrhoeic piglets were collected from organized farms in Wayanad, Ernakulam, Thrissur, and Palakkad districts of Kerala. The samples were tested for the presence of GAR employing reverse transcriptase polymerase chain reaction (RT-PCR) targeting VP6 gene. Positive samples were tested by G and P genotyping primers and representative amplicons were sequenced. Of the 100 samples, 12 were positive for GAR. The G and P types detected were G2, G4, G5, G6, G9, P[6] and P[19]. An untypable P type (P21-5 like) was also detected. In some of the samples more than one G type was detected. The nucleotide sequences of G2, G4 and G5 types were similar to those seen in pigs and that of G6 was similar to bovine sequences. G9, P[6] and P[19] sequences showed similarity to human rotavirus sequences. The findings of this study provide the first information on the G and P genotypes of GAR of pigs in Kerala.

Keywords: Nucleic acid sequencing; Phylogeny; RT-PCR; Rotavirus; VP4 gene; VP6 gene; VP7 gene.

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Figures

Fig. 1
Fig. 1
Maximum likelihood tree constructed using nucleotide sequences of part of VP7 gene of Group A rotaviruses from Kerala. Filled triangle: isolate obtained during this study. Boot strap replicates = 1000. Evolutionary distances between sequences were calculated by Tamura-Nei method. Branch length are given as 20 substitutions per position according to scale bar underneath the tree
Fig. 2
Fig. 2
Maximum likelihood tree constructed using nucleotide sequences of part of VP4 gene of Group A rotaviruses from Kerala. Filled triangle: isolate obtained during this study. Boot strap replicates = 1000. Evolutionary distances between sequences were calculated by Hasegawa-Kishino-Yano method. Branch length are given as 0.50 substitutions per position according to scale bar underneath the tree
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