Near-complete genome of SARS-CoV-2 Delta variant of concern identified in a symptomatic dog (Canis lupus familiaris) in Botswana

We investigated SARS-CoV-2 presence and performed near full-length genomic sequencing from a 5-year-old male crossbreed dog in Gaborone, Botswana that presented flu-like symptoms, dry hacking cough, and mild dyspnoea. Sampling occurred a posteriori after three adult owners were diagnosed with SARS-CoV-2. Next-generation sequencing (Oxford Nanopore Technology) was performed on RT-qPCR–confirmed positive nasopharyngeal and buccal swabs and a bronchoalveolar lavage with mean Ct ~36 (N gene). Comparative mutation profiling and phylogenetic analyses were conducted against Botswana and international sequences (no human samples from owners available). A near-full-length SARS-CoV-2 genome (~90% coverage) was obtained and classified within clade 20O and Delta variant sublineage (AY.43/AY.94 depending on Pango version). No novel mutations distinguishing canine from human isolates were identified. The sequence clustered with contemporaneous Delta sublineages circulating locally. This is the first documented report of human-associated SARS-CoV-2 infection in a dog in Botswana, underscoring the need to monitor pets for potential interspecies transmission.

Wonderful T Choga, Samantha L Letsholo, Chandapiwa Marobela-Raborokgwe, Irene Gobe, Mbatshi Mazwiduma, Dorcas Maruapula, John Rukwava, Mary Gorettie Binta, Boitumelo J L Zuze, Legodile Koopile, Kedumetse Seru, Patience Motshosi, Ontlametse Thato Bareng, Botshelo Radibe, Pamela Smith-Lawrence, Kutlo Macheke, Lesego Kuate-Lere, Modisa S Motswaledi, Mpaphi B Mbulawa, Mogomotsi Matshaba, Kereng V Masupu, Shahin Lockman, Roger Shapiro, Joseph Makhema, Mosepele Mosepele, Simani Gaseitsiwe, Sikhulile Moyo