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

Autor: Choga WT; Research Laboratory, Botswana Harvard AIDS Institute Partnership Gaborone, Gaborone, Botswana.; Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.; Faculty of Health Sciences, School of Allied Health Professionals, University of Botswana, Gaborone, Botswana., Letsholo SL; Botswana National Veterinary Laboratory, Gaborone, Botswana., Marobela-Raborokgwe C; Botswana National Veterinary Laboratory, Gaborone, Botswana., Gobe I; Faculty of Health Sciences, School of Allied Health Professionals, University of Botswana, Gaborone, Botswana., Mazwiduma M; VetPro Consultants, Gaborone, Botswana., Maruapula D; Research Laboratory, Botswana Harvard AIDS Institute Partnership Gaborone, Gaborone, Botswana.; Department of Biological Sciences, University of Botswana, Gaborone, Botswana., Rukwava J; Kweneng Veterinary Clinic, Gaborone, Botswana., Binta MG; Botswana National Veterinary Laboratory, Gaborone, Botswana., Zuze BJL; Research Laboratory, Botswana Harvard AIDS Institute Partnership Gaborone, Gaborone, Botswana., Koopile L; Research Laboratory, Botswana Harvard AIDS Institute Partnership Gaborone, Gaborone, Botswana., Seru K; Research Laboratory, Botswana Harvard AIDS Institute Partnership Gaborone, Gaborone, Botswana., Motshosi P; Research Laboratory, Botswana Harvard AIDS Institute Partnership Gaborone, Gaborone, Botswana., Bareng OT; Research Laboratory, Botswana Harvard AIDS Institute Partnership Gaborone, Gaborone, Botswana.; Faculty of Health Sciences, School of Allied Health Professionals, University of Botswana, Gaborone, Botswana., Radibe B; Research Laboratory, Botswana Harvard AIDS Institute Partnership Gaborone, Gaborone, Botswana., Smith-Lawrence P; Health Services Management, Ministry of Health and Wellness, Gaborone, Botswana., Macheke K; Health Services Management, Ministry of Health and Wellness, Gaborone, Botswana., Kuate-Lere L; Health Services Management, Ministry of Health and Wellness, Gaborone, Botswana., Motswaledi MS; Faculty of Health Sciences, School of Allied Health Professionals, University of Botswana, Gaborone, Botswana.; Presidential COVID-19 Taskforce, Gaborone, Botswana., Mbulawa MB; Health Services Management, National Health Laboratory, Gaborone, Botswana., Matshaba M; Presidential COVID-19 Taskforce, Gaborone, Botswana.; Botswana-Baylor Children's Clinic Centre of Excellence, Gaborone, Botswana., Masupu KV; Presidential COVID-19 Taskforce, Gaborone, Botswana., Lockman S; Research Laboratory, Botswana Harvard AIDS Institute Partnership Gaborone, Gaborone, Botswana.; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts., Shapiro R; Research Laboratory, Botswana Harvard AIDS Institute Partnership Gaborone, Gaborone, Botswana.; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts., Makhema J; Research Laboratory, Botswana Harvard AIDS Institute Partnership Gaborone, Gaborone, Botswana.; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts., Mosepele M; Research Laboratory, Botswana Harvard AIDS Institute Partnership Gaborone, Gaborone, Botswana.; Presidential COVID-19 Taskforce, Gaborone, Botswana.; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts.; Faculty of Medicine, Department of Internal Medicine, University of Botswana, Gaborone, Botswana., Gaseitsiwe S; Research Laboratory, Botswana Harvard AIDS Institute Partnership Gaborone, Gaborone, Botswana.; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts., Moyo S; Research Laboratory, Botswana Harvard AIDS Institute Partnership Gaborone, Gaborone, Botswana.; Faculty of Health Sciences, School of Allied Health Professionals, University of Botswana, Gaborone, Botswana.; Presidential COVID-19 Taskforce, Gaborone, Botswana.; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts.
Jazyk: angličtina
Zdroj: Veterinary medicine and science [Vet Med Sci] 2023 Jul; Vol. 9 (4), pp. 1465-1472. Date of Electronic Publication: 2023 Apr 29.
DOI: 10.1002/vms3.1152
Abstrakt: 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 from Gaborone, Botswana that presented overt clinical signs (flu-like symptoms, dry hacking cough and mild dyspnoea). It was only sampled a posteriori, because three adult owners were diagnosed with SARS-CoV-2 infection. Next-generation sequencing based on Oxford Nanopore Technology (ONT) 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 real cycle threshold (qCt) value of 36 based on the Nucleocapsid (N) gene. Descriptive comparisons to known sequences in Botswana and internationally were made using mutation profiling analysis and phylogenetic inferences. Human samples 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 sublineage 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 Spike (S) region mutation profiling, we performed phylogenetic analysis including 30 Delta sequences publicly available reference also isolated from dogs. In addition, we performed another exploratory analysis to investigate the phylogenetic relatedness of sequence isolated from dog with those from humans in Botswana (n = 1303) as of 31 March 2022 and of same sublineage. Expectedly, the sequence formed a cluster with Delta sublineages - AY.43, AY.116 and B.1.617.2 - circulating in 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.
(© 2023 The Authors. Veterinary Medicine and Science published by John Wiley & Sons Ltd.)
Databáze: MEDLINE
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