Surveillance and molecular characterization of SARS-CoV-2 infection in
non-human hosts in Gujarat, India.
Abstract
Since December 2019, severe acute respiratory syndrome coronavirus-2
(SARS-CoV-2) has been spreading worldwide, triggering one of the most
challenging pandemics in human population. In the light of reporting of
this virus in domestic and wild animals from several parts of world, a
systematic surveillance study was conceptualized to detect the
SARS-CoV-2 among species of Veterinary importance. Nasal and/or rectal
samples of 413 animals (Dog=195, cattle=64, horse=42, goat=41,
buffalo=39, sheep=19, cat=6, camel=6 and monkey=1) were collected from
different places of Gujarat state of India. RNA was extracted from
samples and subjected to RT-qPCR based amplification of target sequences
in viral nucleoprotein (N), spike (S) and ORF1ab genes. A total of 95
(23.79 %) animals were found positive, comprised of 67 (34.35 %) dogs,
15(23.43 %) cattle and 13(33.33 %) buffaloes. Overall, nasal samples
(N=80/412, 19.41 %) gave more positive results than rectal samples
(N=70/407, 17.19 %) in RT-qPCR. The whole SRAS-CoV-2 genome sequencing
was done on one sample (ID-A4N; from dog) where 32 mutations, including
29 single nucleotide variation (SNV) and two deletions, were detected.
Among them, 9 mutations were located in the receptor binding domain of
the spike (S) protein. The consequent changes in amino acid sequence
revealed that T19R, G142D, E156-, F157-, A222V, L452R, T478K, D614G,
P681R mutation in S protein and D63G, R203M and D377Y in N protein. The
lineage assigned to this SARS-CoV-1 sequence is B.1.617.2. Thus, the
present study highlights the importance of SARS-CoV-2 surveillance in
non-human host.