Near-complete genome of SARS-CoV-2 Delta variant of concern identified
in a symptomatic dog (Canis lupus familiaris) in Botswana
Abstract
We sought to investigate whether SARS-CoV-2 was present, and to perform
full-length genomic sequencing, in a 5-year-old male crossbreed dog that
presented with flu-like symptoms (including a dry hacking cough and mild
dyspnea) and resided in a household with 3 adults that were diagnosed
with SARS CoV-2 infection. Next generation sequencing based on MinION
technology was performed on amplicons that were generated using a
reverse transcriptase real-time polymerase chain reaction (RT-qPCR) of
confirmed positive SARS-CoV-2 nasopharyngeal and buccal swabs, as well
as a bronchoalveolar lavage with mean qCt value of 36 based on the
Nucleocapsid gene. Descriptive comparisons to known sequences in
Botswana and internationally were made using mutation profiling analysis
and phylogenetic inferences based on maximum likelihood. Samples from
the dog’s owners were not available. A near-full length SARS-CoV-2
genome (~90% coverage) was successfully genotyped and
classified under clade 20 O and Pango-Lineage AY.43 (Pango v.4.0.6
PLEARN-v1.3; 2022-04-21), which is a sub-lineage of the Delta variant of
concern (VOC) (formerly called B.1.617.2, first detected in India). We
did not identify novel mutations that may be used to distinguish
SARS-CoV-2 isolates from the dog and humans. In addition to S region
mutation profiling, we performed phylogenetic analysis using Delta
sequences from Botswana (n=1303); expectedly, the sequence isolated from
the dog was closely related to the Delta sequences, particularly the
AY.43, AY.116, and B.1.617.2 sub-lineages that were reported in Botswana
within the same time frame. This is the first documented report of
human-associated SARS-CoV-2 infection in a dog in Botswana. Although the
direction of transmission remains unknown, this study further affirms
the need for monitoring pets during different COVID-19 waves for
possible clinically relevant SARS-CoV-2 transmissions between species.