FDA announces availability of reference sequence data for SARS-CoV-2

April 2, 2020

The Food and Drug Administration—in collaboration with the Centers for Disease Control and Prevention (CDC), the Biodefense and Emerging Infections Research Resources Repository (BEI Resources), the Institute for Genome Sciences at the University of Maryland, and the National Center for Biotechnology Information (NCBI) at the National Institutes of Health (NIH)— have developed quality-controlled reference sequence data for the SARS-CoV-2 reference strain for the United States, the FDA announced. 

According to the FDA, the availability of traceable and quality-controlled data will help test developers and vaccine developers: 

•             Expedite development of medical countermeasures.

•             Identify new or more stable targets for future tests.

•             Enable in silico confirmation of targets.

•             Support development of synthetic reference material.

•             Enable viral population/quasi species analysis. 

Genomic RNA isolated from a clinical sample from the first confirmed case of COVID-19 (January 22, 2020) in the United States from Washington State yielded a subsequent SARS-CoV-2 reference material available from BEI Resources. This reference was passaged in total four times (Vero [3] at CDC followed by Vero E6 [1] at BEI resources). 

The genomic RNA and prepared Illumina libraries were quality controlled for (1) shotgun sequencing by using the Ovation RNA-Seq System V2 kit and (2) target-capture sequencing by using the New England Biolabs Ultra II direction RNA preparation kit and H/M/R Riboreduction prior to sequencing the SARS-CoV-2 reference strain. For target-capture sequencing, the library was target-enriched using Twist custom target enrichment for COVID-19. Raw data from both sequencing approaches was used to generate the FDA-ARGOS SARS-CoV-2 reference sequence. 

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