Sequences (COVID)

University of Washington has released (at GISAID) 25 SARS CoV2 sequences from Idaho (20 today and 5 on 4/12). All 25 are the Italian lineage.

NYU Langone released 40 sequences (at GISAID) from New York patient collections this month. All 40 are the Italian lineage.

Michigan DHHS has released (at GISAID) 9 sequences from Michigan. 7 of the 9 are the Italian lineage.

The CDC released 3 sequences (at GISAID) from North Carolina. Two were the Italian lineage. UNC Chapel Hill recently released 2 sequences from North Carolina and both were the Italian lineage.

CDC released 4 SARS CoV2 sequences from New Hampshire. All four were the Italian lineage.

CDC released 2 SARS CoV2 sequences (at GISAID) from New Jersey, and both were the Italian lineage. Mt Sinai also recently released a sequence from New Jersey, which was also the Italian lineage. NYU Langone recently released 4 sequences from New Jersey and 3 were the Italian lineage.

CDC released 7 SARS CoV2 sequences (at GISAID) from Iowa. All 7 are the Italian lineage.

CDC released 18 SARS CoV2 sequences (at GISAID) from Massachusetts. 17 were the Italian lineage.

The CDC has released (at GISAID) the first 6 SARS CoV2 sequences from Pennsylvania. All six are the Italian lineage.

The NY Times publication confirms the high frequency of European sequences (Italian strain) in New York COVID patients. Most New York Coronavirus Cases Came From Europe, Genomes Show Travelers seeded multiple cases starting as early as mid-February, genomes show. https://www.nytimes.com/2020/04/08/science/new-york-coronavirus-cases-europe-genomes.html

NYU has release (at GISAID) another set of sequences from Manhattan and Nassau New York COVID patients. All 11 of the 14 newly released sequences are closely related to each other and sequences from patients in Italy. The two recent sets, as well as the initial four sequences, are heavily dominated by matches with Italy (30/34).

NYU has release (at GISAID) a set of 16 sequences from Manhattan and Nassau New York COVID patients. All 16 sequences are closely related to each other and sequences from patients in Italy.

Mount Sinai released the sequence, hCoV-19/USA/NY2-PV08100/2020, of the New Rochelle index case (50sM) case (at GISAID). It is the orf8 lineage that has markers(T9477A, C14805T, C28863T), found in European isolates.

The CDC has released 18 full sequences (at GISAID) from COVID positive US passengers. The sequences, other than one with a fifteen nucleotide deletion, are closely related to the Wuhan index sequence, in contrast to sequences from Japan passengers, which had G11083T.

UCSF has released a sequence (at GISAID), hCoV-19/USA/CA-CDPH-UC1/2020 from a Solano Co case who was on the first trip of the Grand Princess cruise ship, that matches a series of sequences from King Co Washington, including the LTCF.

Two more sequences from King Co were released tonight at GISAID. One, BetaCoV/USA/WA-S2/2020, was released by the Seattle Flu study, and the other, BetaCoV/USA/WA6-UW3/2020, was release by the University of Washington. Like the sequence released earlier, BetaCoV/USA/WA4-UW2/2020, they match the two Snohomish sequences (from 35M and 17M) via the two polymorphism that define the lineage (C8782T and T28144C) and the rare polymorphism (C18060T). However, all three of the sequences released today also have two unique polymorphisms (C17747T and A17858G) indicating they are all from patients linked to the long term care facility (LTCF) in Kirkland, Washington and t…

https://www.cnbc.com/2020/03/04/coronavirus-chinese-scientists-identify-two-types-covid-19.html Chinese scientists identify two strains of the coronavirus, indicating it’s already mutated at least once The more aggressive type of virus was found to be prevalent in the early stages of the outbreak in Wuhan — the Chinese city where COVID-19 was first detected late last year. But the frequency of this type of virus has since decreased from early January, the scientists said. Researchers cautioned that data examined in the study was still “very limited.” https://academic.oup.com/nsr/advance-article/doi/10.1093/nsr/nwaa036/5775463

University of Washington has released a sequence at GISAID, BetaCoV/USA/WA4-UW2/2020, from a female which would be linked to the Long Term Care Facility In Kirkland. This sequence matches the two sequences from Snohomish County (35M from mid Jan and 17M from late Feb). The match indicates this lineage has been circulating in the Seattle area since mid January.

Sequence (BetaCoV/USA/WA-WA3_UW1/2020) of King Co WA ex-South Korea (58F) is a recombinant with polyphorphisms shared by LA2 (Orange County) and AZ (Phoenix)

Seattle Flu Study has released at GISAID full sequence, BetaCoV/USA/WA2/2020, from Snohomish Co community spread from high school student (17M) which matches original sequence, which was first US case, BetaCoV/USA/WA1/2020. That isolate has been cloned (BetaCoV/USA/WA1-A12/2020 and BetaCoV/USA/WA1-F6/2020), each of which have 3 polymorphisms (C8782T, C18060T, and T28144C) and WA2 has all three, which includes the orf8 mutation.

CDC has released full sequences of Solano Co case (46F) at GISAID (BetaCoV/USA/CA9/2020) collected on Feb 23,2020.

Thanks for the great Rense interview tonight, Dr. Niman. A few questions I hope you can find the time to comment on before too long: 1) Have any sequences of recently announced cases in Iran and Italy, especially been released? From the most recent sequences you have seen would you say that there are two strains or lineages now, the original one and the one with changes in the ORF8 gene? And is it known how their effects differ and how prevalent each is? 2) Why do you think the number of reported new cases in Chinese cities outside Hubei province has been markedly going down, rather than up? Do you think the Chinese government may be misreporting or purposely no…

Full sequence of a 2020 collection from a Guangdong Pangolin is 90% identical with human COVID sequences from patients in China and the United States

Beijing has released four full sequences from 2017 Guangxi Pangolins. Closest matches at Genbank are COVID-2019 sequences from human cases in Wuhan, China and United States

Three nCoV sequences from Australia (2 from Queensland - Gold Coast and 1 from New South Wales - Sydney) are the orf8 lineage with Queensland sequences have mixed signals.