On March 11, 2020, the World Health Organization declared COVID-19 a pandemic. The President of the United States declared a national emergency on March 13, 2020, in response to the COVID-19 outbreak in the United States. This public health emergency has led to an unprecedented number of Emergency Use Authorizations (EUAs) for COVID-19 diagnostic tests.
In response to the COVID-19 pandemic, the FDA—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—developed quality-controlled reference sequence data for the SARS-CoV-2 reference strain for the United States.
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 4 times (Vero  at CDC followed by Vero E6  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.
The FDA-ARGOS SARS-CoV-2 reference sequences (FDAARGOS_983, MT233526.1 [shotgun], MT246667.1 [target-capture]) had 100% identity to the 2019-nCoV/USA-WA1/2020 strain (GenBank accession no. MN985325.1). FDA-ARGOS SARS-CoV-2 reference sequence metadata, genome assemblies, raw data, and protocols are publicly available at the links provided below.
SARS-CoV-2 Reference Sequence Data:
- Reference sequence from shotgun data under GenBank accession MT233526.1
- Reference sequence from target-capture data under GenBank accession MT246667.1
- Metadata under BioSample accession SAMN143844141 and here.
- Raw data and protocol from shotgun sequencing under SRA accession SRX7972536
- Raw data and protocol from target-capture sequencing under SRA accession SRX7988130
- Reference material from BEI Resources catalog NR-52281 (lot 70033135)