Sequences (COVID)

Danish Covid-19 Genome Consortium deposited 3 sequences from Nordjylland (at GISAID - collected Nov 30) that matched the UK variant.

Danish Covid-19 Genome Consortium submitted 3 COVID sequences from Hovedstaden area in Denmark, which matched the UK variant. The samples were collected on Nov 23, 2020.

Danish Covid-19 Genome Consortium submitted 3 COVID sequences from Hovedstaden area in Denmark, which matched the UK variant. The samples were collected on Nov 9, 2020.

Hong Kong DoH has release sequences (at GISAID) from two students, hCoV-19/Hong Kong/CM20000461/2020 (17M collected 12/13) and hCoV-19/Hong Kong/CM20000424/2020 (14M collected 12/7). Both sequences match the consensus UK variant (with 3 Spike AAs deleted along with 3 NSP6 AAs).

Israel MoH National labs released the sequence (at GISAID), hCoV-19/Israel/CVL-7075/2020, of UK variant with 3 Spike deletions and 3 NSB6 deletions (collected Dec 16).

Recent reports of a variant from South Africa suggests it transmits more easily than the UK variant. Both usually have 3 amino acids deleted from the Spike protein as well as RBD mutation N501Y and G clade mutation D614G. The Spike deletion in South Africa (L242 A243 L244) is also in a recently deposited (at GISAID and Genbank) isolate collected on July 3 in Florida, USA/FL-BPHL-2075. This isolate only has one additional Spike non-synonymous change, D614G

The recently released variant sequence from Singapore (collected Dec 12) was missing the NSB 6 deletion (but had 2 nonsynonymous changes in two of the 3 deleted amino acids). A recently released sequence from Scotland (hCoV-19/Scotland/CVR6050/2020) is also missing the deletion, but does not have the two nonsynonymous changes. These differences highlight rapid evolution of the UK variant.

Recently release sequences (at GISAID) provide compelling evidence that the UK variant is rapidly evolving via recombination. An isolate from Scotland (hCoV-19/Scotland/CVR6032/2020) has 8 of the 10 Spike mutations - it is missing the 6 BP deletion that encodes H69 and V70. Moreover, it is missing the 9 BP deletion in NSB 6. The presence and absence of these well established deletions in the UK variants is most easily explained by rapid recombination.

UK COVID variants have significant heterogeneity. A recent (collected Dec 7) isolate from London, hCoV-19/England/LOND-12F102B/2020, has the two Spike deletions (at positions 69 and 70) as well as most of the nonsynonymous Spike changes and other mutations, including the 3 amino acid deletion in NSB 6, but does not have the Spike deletion at position 145 (Y145del), strongly suggesting rapid recombination.

Two UK variant sequences from The Netherlands released today (/Netherlands/NH-RIVM-20432/2020 & Netherlands/NH-RIVM-20227/2020 Virus name Passage details/history Accession ID Collection date Submission Date Length …

While posting the 281 variant COVID sequences released at GISAID today, 100's more were release (although these included some earlier sequences)

281 Variant UK COVID sequences were released today at GISAID. Most were collected on Dec 10, with additional collections on Dec 11 & Dec 12.

I don't know why nobody but Jeff Rense is interviewing you, Dr. Niman, when you're always so far ahead of the pack! https://www.washingtonpost.com/health/2020/09/23/houston-coronavirus-mutations/ Massive genetic study shows coronavirus mutating and potentially evolving amid rapid U.S. spread

Any thoughts on this paper, Dr. Niman? https://zenodo.org/record/4028830#.X2KwouhKiMr Unusual Features of the SARS-CoV-2 Genome Suggesting Sophisticated Laboratory Modification Rather Than Natural Evolution and Delineation of Its Probable Synthetic Route

Hong Kong patient (33M) has been infected by two distinct lineages (deposited at GISAID). The first infection, HKU-200823-001 (clade V collected March 26, 2020) with a 58 aa truncation in orf8, was easily distinguished from HKU-200823-002, clade G (infected during travel to UK/Spain with collection date August 17, 2020)

Just as Dr. Niman has been saying: Coronavirus: recovered Chinese patients may be defenceless against foreign mutation, study says Antibodies found in blood of people who have fought disease failed to stop D614G, Chinese scientists say Mutant form identified in genetic data of samples collected at Xinfadi food market in Beijing where latest outbreak began https://www.scmp.com/coronavirus/greater-china/article/3089983/coronavirus-recovered-chinese-patients-may-be-defenceless

China CDC has released (at GISAID) 3 full SARS CoV2 sequences (two from cases and one environmental) collected on June 11, 2020 at the Xinfadi Wholesale Market in Beijing . All three are the Italian linage (clade GR).

Microbial Genomic Epidemiological Laboratory has released (at GISAID) 59 recent (largely April collections) SARS CoV2 sequences from Pittsburgh patients at UPMC, 55 were the Italian lineage (largely GISAID clade GH).

UPMC has released (at GISAID) 39 SARS CoV2 sequences from Pittsburgh patients. 37 were the Italian (clade G) lineage. For Pennsylvania, there are now 48 SARS CoV sequences, with 46 being the Italian lineage.

Michigan DHHS has released (at GISAID) 100 March (collected between 3/10-3/28) SARS CoV2 sequences. 88 are the Italian lineage (clade G).

Kabara Cancer Research Institute in La Crosse WI has recently released (at GISAID) 27 SARS CoV2 sequences (collection dates 3/25-4/26) from regional counties in WI, MN, IA. All were the Italian lineage (Clade G). 8 sequences were from Wisconsin counties (La Crosse, Jackson, Monroe, Adams).

Kabara Cancer Research Institute in La Crosse WI has recently released (at GISAID) 27 SARS CoV2 sequences (collection dates 3/25-4/26) from regional counties in WI, MN, IA. All were the Italian lineage (clade G). 4 of the sequences were from Winona Co MN.

Kabara Cancer Research Institute in La Crosse WI has recently released (at GISAID) 27 SARS CoV2 sequences (collection dates 3/25-4/26) from regional counties in WI, MN, IA. All were the Italian lineage (Clade G). 15 sequences were from patients in northeast Iowa (Allamakee and Winneshiek Cos)

Utah Public Health has released (at GISAID) 42 SARS CoV2 collected since March 27. All are the Italian lineage (clade G).

National Institute for Biomedical Research has recently released (at GISAID) 33 SARS CoV2 sequences from patients in Kinshasa, Democratic Republic of Congo. All are the Italian lineage (clade G).