Volume 26, Number 8—August 2020
Synopsis
US CDC Real-Time Reverse Transcription PCR Panel for Detection of Severe Acute Respiratory Syndrome Coronavirus 2
Xiaoyan Lu, Lijuan Wang, Senthilkumar K. Sakthivel, Brett Whitaker, Janna Murray, Shifaq Kamili, Brian Lynch, Lakshmi Malapati, Stephen A. Burke, Jennifer Harcourt, Azaibi Tamin, Natalie J. Thornburg, Julie M. Villanueva, and Stephen Lindstrom
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.
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Page updated: July 17, 2020
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