Table 1 Lineage classification of previously undetected SARS-CoV-2 in NYC.
From: Molecular evidence of SARS-CoV-2 in New York before the first pandemic wave
Sample | Week ending | Ct values (ORF1ab, E) | Genome completeness (%) | NextStrain clade | Clade-defining mutations | PANGO lineage | Lineage detection prior to 1 March |
|---|---|---|---|---|---|---|---|
Pool-134 | 7-Mar-2020 | 18.62, 18.63 | 99.9 | 20C | S:D614G, ORF1b:P314L, OFR3a:Q57H, ORF1a:T265I | B.1 | Mainly Europe, linked to Italian outbreak, only a few North American (non-US) isolates |
Pool-41 | 7-Mar-2020 | 28.94, 29.36 | 99.7 | 20C | S:D614G, ORF1b:P314L, OFR3a:Q57H, ORF1a:T265I | B.1 | |
Pool-58 | 7-Mar-2020 | 31.66, 33.65 | 99.8 | 20C | S:D614G, ORF1b:P314L, OFR3a:Q57H, ORF1a:T265I | B.1 | |
Pool-53 | 7-Mar-2020 | 20.64, 21.07 | 99.8 | 20C | S:D614G, ORF1b:P314L, OFR3a:Q57H, ORF1a:T265I | B.1 | |
Pool-38 | 7-Mar-2020 | 28.91, 29.43 | 98.9 | 20A | S:D614G, ORF1b:P314L | B.1.5 | Europe/South America/Asia |
Pool-95 | 29-Feb-2020 | 20.80, 21.11 | 99.8 | 19A | T14408C | B.2.12 | Asia/Europe/Oceania |
Pool-56 | 7-Mar-2020 | 25.37, 25.65 | 99.7 | 19B | C8782T ORF8:L84S | A.2 | Europe |
