Phylogenomics reveals viral sources, transmission, and potential superinfection in early-stage COVID-19 patients in Ontario, Canada.

Affiliation

Sjaarda CP(1)(2), Rustom N(3)(4), Evans GA(5)(6)(7), Huang D(8), Perez-Patrigeon S(5), Hudson ML(9)(3), Wong H(10), Sun Z(8), Guan TH(11), Ayub M(3)(4), Soares CN(9)(3), Colautti RI(#)(8), Sheth PM(#)(6)(7)(10)(12).
Author information:
(1)Queen's Genomics Lab At Ongwanada
(QGLO), Ongwanada Resource Center, Kingston, ON, K7M8A6, Canada. [Email]
(2)Department of Psychiatry, Queen's University, Kingston, ON, K7L3N6, Canada. [Email]
(3)Department of Psychiatry, Queen's University, Kingston, ON, K7L3N6, Canada.
(4)Centre for Neuroscience Studies, Queen's University, Kingston, ON, K7L3N6, Canada.
(5)Division of Infectious Diseases, Department of Medicine, Queen's University, Kingston, ON, Canada.
(6)Department of Pathology and Molecular Medicine, Queen's University, Kingston, ON, Canada.
(7)Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada.
(8)Biology Department, Queen's University, Kingston, ON, Canada.
(9)Queen's Genomics Lab At Ongwanada
(QGLO), Ongwanada Resource Center, Kingston, ON, K7M8A6, Canada.
(10)Division of Microbiology, Kingston Health Sciences Center, Kingston, ON, Canada.
(11)Department of Family Medicine, Queen's University, Kingston, ON, Canada.
(12)Gastrointestinal Disease Research Unit, Kingston Health Sciences Center, Kingston, ON, Canada.
(#)Contributed equally

Abstract

The emergence and rapid global spread of SARS-CoV-2 demonstrates the importance of infectious disease surveillance, particularly during the early stages. Viral genomes can provide key insights into transmission chains and pathogenicity. Nasopharyngeal swabs were obtained from thirty-two of the first SARS-CoV-2 positive cases (March 18-30) in Kingston Ontario, Canada. Viral genomes were sequenced using Ion Torrent (n = 24) and MinION (n = 27) sequencing platforms. SARS-CoV-2 genomes carried forty-six polymorphic sites including two missense and three synonymous variants in the spike protein gene. The D614G point mutation was the predominate viral strain in our cohort (92.6%). A heterozygous variant (C9994A) was detected by both sequencing platforms but filtered by the ARTIC network bioinformatic pipeline suggesting that heterozygous variants may be underreported in the SARS-CoV-2 literature. Phylogenetic analysis with 87,738 genomes in the GISAID database identified global origins and transmission events including multiple, international introductions as well as community spread. Reported travel history validated viral introduction and transmission inferred by phylogenetic analysis. Molecular epidemiology and evolutionary phylogenetics may complement contact tracing and help reconstruct transmission chains of emerging diseases. Earlier detection and screening in this way could improve the effectiveness of regional public health interventions to limit future pandemics.