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Volume 26, Number 8—August 2020

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 LindstromComments to Author 
Author affiliations: Centers for Disease Control and Prevention, Atlanta, Georgia, USA (X. Lu, B. Whitaker, S.A. Burke, J. Harcourt, A. Tamin, N.J. Thornburg, J.M. Villanueva, S. Lindstrom); Synergy America, Inc., Atlanta (L. Wang, S. Kamili); Eagle Contracting, Atlanta (S.K. Sakthivel, J. Murray, B. Lynch); Leidos, Atlanta (L. Malapati); Battelle, Atlanta (S.A. Burke)

Main Article

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.

Main Article

Page created: May 14, 2020
Page updated: July 17, 2020
Page reviewed: July 17, 2020
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