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Repository for suggesting new lineages that should be added to the current scheme
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New lineage proposal Sub-lineage of: B.1.1.7 that is exclusive to USA, with spike protein D178H and membrane protein V70L mutations #92

Closed ShenLishuang closed 3 years ago

ShenLishuang commented 3 years ago

New lineage proposal by Lishuang Shen, and Xiaowu Gai Description Sub-lineage of: B.1.1.7 that is exclusive to the USA

Earliest sequence: 2021-02-04 (hCoV-19/USA/CA-SEARCH-13556/2021, USA/CA-SEARCH-13588/2021 )

Most recent sequence: 2021-05-12: hCoV-19/USA/KS-KHEL-1686/2021, EPI_ISL_2101377, 2021-05-12, North America / USA / Kansas hCoV-19/USA/CA-CDC-FG-033558/2021, EPI_ISL_2160799, 2021-05-11, North America / USA / California hCoV-19/USA/CA-CDC-FG-033504/2021, EPI_ISL_2160801, 2021-05-11, North America / USA / California hCoV-19/USA/CA-CDC-FG-033398/2021, , EPI_ISL_2160802, 2021-05-11, North America / USA / California

Countries circulating: USA exclusive as of May 12, 2021 (2016 of 2016 genomes)

We identify a distinct cluster of B.1.1.7 infections where the virus genome carries both Spike S:D178H and M:V70L mutations, and it appeared to be 100% USA-exclusive as of May 12, 2021 (2016 of 2016 genomes) . This sub-lineage was first detected in California, USA, on February 4, 2021, and as of data freeze on May 1st, this sub-lineage appeared to be U.S.-specific with reported cases in 31 states, including Hawaii. In April 2021, it constituted 36.8% of all B.1.1.7 isolates in Washington. The percentage of B.1.1.7 isolates in the U.S. that belong to this sub-lineage increased from 0.15% in February 2021 to 1.8% in April 2021. Given the rapidly increased prevalence of this sub-lineage in Washington State, the exclusive presence in USA, and the fact that the prevalence within the B.1.1.7 lineage increased from 0.15% in February to 1.8% in April, we believe it is a distinct sub-lineage that needs a designated name.

Our preprint: https://www.medrxiv.org/content/10.1101/2021.05.14.21257247v1

It was reported by: The Global Virus Network: https://gvn.org/covid-19/u-k-variant/ ,

The CDC PHGKB COVID-19 Genomics and Precision Public Health Weekly Update, May 20, 2021 Issue: https://phgkb.cdc.gov/PHGKB/coVInfoClip.action?action=archive&date=05/20/2021

News-Medical Life Sciences: https://www.news-medical.net/news/20210521/Study-shows-distinctive-mutation-in-rapidly-emerging-SARS-CoV-2-B117-sublineage.aspx

Genomes (2016)

B.1.1.7_USA_M_V70L_and_S_D178H.txt

Proposed lineage name B.1.1.7/USA

Evidence:

B 1 1 7_USA_M_V70L_and_S_D178H B 1 1 7_USA_M_V70L_and_S_D178H_transmission

B 1 1 7_USA_M_V70L_and_S_D178H_Lineeage_and_genotypes

chrisruis commented 3 years ago

Thanks @ShenLishuang. We've added this as Q.3 in v1.2.52 with 5357 sequence designations. We've taken the root of the lineage back slightly to correspond to the introduction of the lineage into the USA - G20962A occurred on the branch leading to the Q.3 common ancestor

ShenLishuang commented 3 years ago

Thanks @ShenLishuang. We've added this as Q.3 in v1.2.52 with 5357 sequence designations. We've taken the root of the lineage back slightly to correspond to the introduction of the lineage into the USA - G20962A occurred on the branch leading to the Q.3 common ancestor

Chris: Thank you for your diligent effort. Thank you for addressing this ticket.

Lishuang Shen Sr. Bioinformatics Scientist Center for Personalized Medicine Children's Hospital Los Angeles

ShenLishuang commented 3 years ago

Dear Chris:

Thank you and the pangolin team for your diligent effort. Thank you for addressing this ticket.

Lishuang Shen Sr. Bioinformatics Scientist Center for Personalized Medicine Children's Hospital Los Angeles Email: @., @.

Suite 300 2100 W 3rd St Los Angeles, CA 90057

On Tue, Aug 3, 2021 at 3:39 AM Chris Ruis @.***> wrote:

Thanks @ShenLishuang https://github.com/ShenLishuang. We've added this as Q.3 in v1.2.52 https://github.com/cov-lineages/pango-designation/releases/tag/v1.2.52 with 5357 sequence designations. We've taken the root of the lineage back slightly to correspond to the introduction of the lineage into the USA - G20962A occurred on the branch leading to the Q.3 common ancestor

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