Volume 26, Number 9—September 2020
Research
Isolation, Sequence, Infectivity, and Replication Kinetics of Severe Acute Respiratory Syndrome Coronavirus 2
, and Samira Mubareka
Table
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 |
1 |
1 |
| 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 |
98.6% |
98.2% |
| 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.
1These authors contributed equally to this article.