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Volume 26, Number 9—September 2020

Isolation, Sequence, Infectivity, and Replication Kinetics of Severe Acute Respiratory Syndrome Coronavirus 2

Arinjay Banerjee, Jalees A. Nasir1, Patrick Budylowski1, Lily Yip, Patryk Aftanas, Natasha Christie, Ayoob Ghalami, Kaushal Baid, Amogelang R. Raphenya, Jeremy A. Hirota, Matthew S. Miller, Allison J. McGeer, Mario Ostrowski, Robert A. Kozak, Andrew G. McArthur, Karen MossmanComments to Author , and Samira Mubareka
Author affiliations: McMaster University, Hamilton, Ontario, Canada (A. Banerjee, J.A. Nasir, K. Baid, A.R. Raphenya, J.A. Hirota, M.S. Miller, A.G. McArthur, K. Mossman); University of Toronto, Toronto, Ontario, Canada (P. Budylowski, N. Christie, A. Ghalami, A.J. McGeer, M. Ostrowski, R.A. Kozak, S. Mubareka); Sunnybrook Research Institute, Toronto (L. Yip, P. Aftanas, R.A. Kozak, S. Mubareka); Mount Sinai Hospital, Toronto (A.J. McGeer)

Main Article


Sequencing read and genome assembly statistics used in study of isolation, sequence, infectivity, and replication kinetics of SARS-CoV-2*

Metric or mutation SARS-CoV-2/SB2 SARS-CoV-2/SB3_TYAGNC
Number of paired reads 730,137 bp 690,167 bp
Reads from SARS-CoV-2 94.0% 94.4%
Number of assembly contigs
Assembly N50 29,494 bp 29,369 bp
Average depth of coverage of reads 7940.0-fold 7550.1-fold
Total assembly length 29,494 bp 29,369 bp
SARS-CoV-2 assembly completeness
Unresolved 5′ sequence 262 bp 272 bp
Unresolved 3′ sequence
200 bp
205 bp
Pos. 884 (orf1ab polyprotein) R207C (CGT→TGT)
Pos. 1397 (orf1ab polyprotein) V378I (GTA→ATA) V378I (GTA→ATA)
Pos. 2832 (orf1ab polyprotein) K856R (AAG→AGG)
Pos. 3040 (orf1ab polyprotein) Y925Y (TAC→TAT)
Pos. 8327 (or1ab polyprotein) 18.1% of reads suggest L2688F (CTT→TTT)
Pos. 8653 (orf1ab polyprotein) M2796I (ATG→ATT)
Pos. 10353 (orf1ab polyprotein) 5.6% of reads suggest K3363T (AAG→ACG)
Pos. 11074 (orf1ab polyprotein) 10.2% of reads suggest +TTT and a deletion between positions 10809 and 13203
Pos. 11083 (orf1ab polyprotein)
L3606F (TTG→TTT)
L3606F (TTG→TTT)
Pos. 25413 (orf3a protein)

36.7% of reads suggest I7I (ATC→ATT)
Pos. 28688 (nucleocapsid phosphoprotein) L139L (TTG→CTG) L139L (TTG→CTG)

*Predicted mutations are relative to the MN908947.3 SARS-CoV-2 genome (29,903 bp). Mutations within codons are underlined. All mutations were predicted by 100% of sequencing reads mapping to that position, unless otherwise noted. None of the mutations with support from <100% of sequencing reads appeared in the final assembled genome consensus sequences. Substitutions in boldface have been observed in direct sequencing of patient isolates (S. Mubareka, A.G.McArthur, unpub. data). orf1ab, open reading frame 1ab; pos., position; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2.

Main Article

1These authors contributed equally to this article.

Page created: June 03, 2020
Page updated: August 18, 2020
Page reviewed: August 18, 2020
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