Sequences (COVID)

The University of Washington has released sequences at GISAID from two isolates (BetaCoV/USA/WA1-F6/2020 and BetaCoV/USA/WA1-A12/2020) from the first confirmed nCoV case (35M) from Snohomish County,WA. They match the original sequence which has the orf8 mutation and is the same lineage as sequences from Shenzhen, Chicago, Yorkshire clusters,and other US sequences (from CA and AZ) and other sequences from China (Shenzhen and Wohan) and the first sequence from South Korea.

The first nCoV sequence (released at GISAID) from South Korea, BetaCoV/Korea/KCDC03/2020, has the orf8 mutation and is the same lineage as the Shenzhen, Chicago, and Yorkshire clusters, as well as US cases from WA, CA, AZ and additional sequences from China (Wohan and Shenzhen).

Sequence from Maricopa County, Arizona released at GISAID. It also matches recently released sequences from the cluster in Shenzhen, Guangdong (described in Lancet) and three of the four sequences from the United States (Snohomish County, WA; Cook County,IL : Los Angeles County CA) are in the same lineage defined by C8782T (in orf 1ab) and T28114C (in orf 8),

Sequences from England BetaCoV/England/01/2020 (50F) and BetaCoV/England/02/2020 (23M) closely related to each other and same lineage as US (WA, IL, CA, AZ) and Shenzhen cluster with orf 8 mutation

The sequences from three members of a large familial cluster in Shenzhen share three mutations,including one in orf8,the gene with the 29 nt deletion in the SARS expansion from the Metropole Hotel. The US sequence shares two of those three muations, including orf8.

Pasteur Institute has deposited full sequences from patients in Paris. The two sequences do not match the Shenzhen cluster,but do match each other - 32M matches 31F

Full sequence, BetaCoV/Australia/VIC01/2020 from Victoria, Australia 50M pateient at GISAID

Full sequence, BetaCoV/Munich/BavPat1/2020, from Bavaria cluster patient 1 deposited at GISAID

Full sequences for all five confirmed cases in the United States have been released and all except for Orange Co in California have the orf 8 mutation present in Shenzhen cluster described in Lancet. The orf 8 gene acquired in 29 nt deletion and was present in the physician at the Metropole Hotel who was the index case for the international expansion of SARS in 2003.

Guangdong CDC has submitted 8 full sequences at GISAID from Guangdong Province, including 3 from Foshan. None of these sequences are in the lineage found in Shenzhen and 4 US States (WA,IL, CA, AZ)

Recently released sequences at GISAID from the cluster in Shenzhen, Guangdong (described in Lancet) and three of the four sequences from the United States (Snohomish County, WA; Cook County,IL : Los Angeles County CA) are in the same lineage defined by C8782T (in orf 1ab) and T28114C (in orf 8),

CDC has placed full nCoV sequences from the two cases from California at GISAID.

The sequences from Shenzhen cluster available at GISAID and GenBank

Sequences from Shezhen cluster described in Lancet at Genbank

Complete nCoV sequence from WA and IL cases at Genbank

CDC has already released the full sequence of the first nCoV case (at Genbank). Such sequences will be posted here.

Partial sequences from orf1ab from Thailand patients released at Genbank.

BetaCoV/USA/IL1/2020|EPI_ISL_404253 full sequence at GISAID

The first novel coronavirus has been released (WH-Human_1`|China|2019-Dec). This thread will analyze additional sequences. Initial genome release of novel coronavirus Novel 2019 coronavirus arambautARTIC Network 2 2h …

Wuhan scientists describe SARS-like bat coronovirus which have extensive recombination and ACE2 receptor binding.