Volume 26, Number 8—August 2020
Synopsis
US CDC Real-Time Reverse Transcription PCR Panel for Detection of Severe Acute Respiratory Syndrome Coronavirus 2
Table 6
Nucleotide mismatches among 7,158 SARS-CoV-2 genome sequences found in the primer and probe regions included in the US CDC rRT-PCR panel for detection of SARS-CoV-2*
Primer/probe | N1 probe | N1 reverse |
N2 forward | N3 forward |
N3 probe |
N3 reverse | |||
---|---|---|---|---|---|---|---|---|---|
Location, 5′→3′ | 3 | 15 | 21 | 4 | 8 | 10 | 5 | 17 | 14 |
Mismatch nucleotide | C>T | G>T | T>C | C>T | T>C | G>T | C>T | C>T | C>A |
No. sequences | 39 | 22 | 33 | 7 | 111 | 7 | 7 | 9 | 22 |
Mismatch frequency, %† | 0.54 | 0.31 | 0.46 | 0.10 | 1.55 | 0.10 | 0.10 | 0.13 | 0.31 |
*CDC, Centers for Disease Control and Prevention; N, nucleocapsid protein gene; rRT-PCR, real-time reverse transcription PCR; SARS-CoV-2, severe acute respiratory coronavirus 2.
†Only mismatches with frequency >0.10% are shown.