niman

collection date 2023-09-03 geographic location United Kingdom host common name not provided host health state not provided host Homo sapiens host sex not provided host subject id not provided isolate not provided sample capture status active surveillance in response to outbreak sample name COG-UK/CLIMB-CM7YJ4ZU ENA-CHECKLIST ERC000033 INSDC center name Respiratory Virus Unit, Microbiology Services Colindale, Public Health England Submitter Id COG-UK/CLIMB-CM7YJ4ZU broker name COVID-19 Genomics UK Consortium collecting institution Respiratory Virus Unit, Microbiology Services Colindale, Public Health England collector name not provided definition for seropositive sample not provided geographic location (region and locality) England receipt date 2023-09-05 scientific_name Severe acute respiratory syndrome coronavirus 2 serotype (required for a seropositive sample) not provided virus identifier not provided

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Scotland/CLIMB-CM7YKEH5/2023 Scotland MRC-University of Glasgow Centre for Virus Research collected 8/19/23 Spike V483del NSP3 K1155R, BA.2.86.1 C13971T (nsp12)

collection date 2023-08-19 geographic location United Kingdom host common name not provided host health state not provided host Homo sapiens host sex not provided host subject id not provided isolate not provided sample capture status active surveillance in response to outbreak sample name COG-UK/CLIMB-CM7YKEH5 ENA-CHECKLIST ERC000033 INSDC center name West of Scotland Specialist Virology Centre, NHSGGC / MRC-University of Glasgow Centre for Virus Research Submitter Id COG-UK/CLIMB-CM7YKEH5 broker name COVID-19 Genomics UK Consortium collecting institution West of Scotland Specialist Virology Centre, NHSGGC / MRC-University of Glasgow Centre for Virus Research collector name not provided definition for seropositive sample not provided geographic location (region and locality) Scotland scientific_name Severe acute respiratory syndrome coronavirus 2 serotype (required for a seropositive sample) not provided virus identifier not provided BioProject PRJEB37886 COVID-19 Genomics UK (COG-UK) consortium https://www.ncbi.nlm.nih.gov/biosample/SAMEA114337676

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Scotland/CLIMB-CM7YM15Q/2023 Scotland MRC-University of Glasgow Centre for Virus Research collected 8/16/23 Spike V483del NSP3 K1155R BA.2.86.1 C13971T (nsp12)

collection date 2023-08-16 geographic location United Kingdom host common name not provided host health state not provided host Homo sapiens host sex not provided host subject id not provided isolate not provided sample capture status active surveillance in response to outbreak sample name COG-UK/CLIMB-CM7YM15Q ENA-CHECKLIST ERC000033 INSDC center name West of Scotland Specialist Virology Centre, NHSGGC / MRC-University of Glasgow Centre for Virus Research Submitter Id COG-UK/CLIMB-CM7YM15Q broker name COVID-19 Genomics UK Consortium collecting institution West of Scotland Specialist Virology Centre, NHSGGC / MRC-University of Glasgow Centre for Virus Research collector name not provided definition for seropositive sample not provided geographic location (region and locality) Scotland scientific_name Severe acute respiratory syndrome coronavirus 2 serotype (required for a seropositive sample) not provided virus identifier not provided BioProject PRJEB37886 COVID-19 Genomics UK (COG-UK) consortium

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Scotland/CLIMB-CM7YFCYP/2023 Scotland MRC-University of Glasgow Centre for Virus Research 2023-08-26 collection S V483del NSP3 K1155R BA.2.86.1 C13971T (nsp12)

collection date 2023-08-26 geographic location United Kingdom host common name not provided host health state not provided host Homo sapiens host sex not provided host subject id not provided isolate not provided sample capture status active surveillance in response to outbreak sample name COG-UK/CLIMB-CM7YFCYP ENA-CHECKLIST ERC000033 INSDC center name West of Scotland Specialist Virology Centre, NHSGGC / MRC-University of Glasgow Centre for Virus Research Submitter Id COG-UK/CLIMB-CM7YFCYP broker name COVID-19 Genomics UK Consortium collecting institution West of Scotland Specialist Virology Centre, NHSGGC / MRC-University of Glasgow Centre for Virus Research collector name not provided definition for seropositive sample not provided geographic location (region and locality) Scotland scientific_name Severe acute respiratory syndrome coronavirus 2 serotype (required for a seropositive sample) not provided virus identifier not provided BioProject PRJEB37886 COVID-19 Genomics UK (COG-UK) consortium https://www.ncbi.nlm.nih.gov/biosample/SAMEA114346566

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Scotland/CLIMB-CM7YF1YM/2023 Scotland MRC-University of Glasgow Centre for Virus Research collected 8/25/23 NSP3 K1155R BA.2.86.1 C13971T (nsp12)

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Switzerland/VD-CHUV-GEN17627/2023 Vaud Lausanne University Hospital active surveillance not initiated by an outbreak collected 9/7/23 Spike V483del NSP3 K1155R BA.2.86.1

collection date 2023-09-07 geographic location Switzerland host common name Human host health state restricted access host Homo sapiens host sex restricted access host subject id restricted access isolate hCoV-19/Switzerland/VD-CHUV-GEN17627/2023 sample capture status active surveillance not initiated by an outbreak sample name SPSP10205404 ENA-CHECKLIST ERC000033 GISAID Accession ID EPI_ISL_18262719 INSDC center name Laboratory of genomics and metagenomics, Institute of Microbiology, University Hospital Centre and University of Lausanne, Switzerland Submitter Id SPSP10205404 broker name SIB collecting institution CHUV, CH-1011 Lausanne, Switzerland collector name Trestan Pillonel, Damien Jacot, Sébastien Aeby, Gilbert Greub, Claire Bertelli geographic location (region and locality) VD scientific_name Severe acute respiratory syndrome coronavirus 2 https://www.ncbi.nlm.nih.gov/biosample/SAMEA114389007

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Scotland/CLIMB-CM7YF1YM/2023 Scotland MRC-University of Glasgow Centre for Virus Research collected 8/25/23 NSP3 K1155R BA.2.86.1

collection date 2023-08-25 geographic location United Kingdom host common name not provided host health state not provided host Homo sapiens host sex not provided host subject id not provided isolate not provided sample capture status active surveillance in response to outbreak sample name COG-UK/CLIMB-CM7YF1YM ENA-CHECKLIST ERC000033 INSDC center name West of Scotland Specialist Virology Centre, NHSGGC / MRC-University of Glasgow Centre for Virus Research Submitter Id COG-UK/CLIMB-CM7YF1YM broker name COVID-19 Genomics UK Consortium collecting institution West of Scotland Specialist Virology Centre, NHSGGC / MRC-University of Glasgow Centre for Virus Research collector name not provided definition for seropositive sample not provided geographic location (region and locality) Scotland scientific_name Severe acute respiratory syndrome coronavirus 2 serotype (required for a seropositive sample) not provided virus identifier not provided BioProject https://www.ncbi.nlm.nih.gov/biosample/SAMEA114346501 PRJEB37886 COVID-19 Genomics UK (COG-UK) consortium

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USA/NY-CDC-QDX84783137/2023 New York 9/5/23 collection 59F Spike ins16MPLF, V483del NSP3 K1155R BA.2.86.1 NSP3 T1269I C1420T (nsp2)

isolate SARS-CoV-2/Human/USA/NY-CDC-QDX84783137/2023 collected by Quest Diagnostics Incorporated collection date 2023-09-05 isolation source Nasal Swabs geographic location USA: New York host Homo sapiens host disease COVID-19 host sex female host age 59 collection device Nasal Swabs collection method Nasal Swabs purpose of sequencing baseline surveillance (random sampling) host_race Unknown diagnostic_pcr_protocol_1 Roche diagnostic_pcr_Ct_value_1 Unknown lineage/clade name BA.2.86 https://www.ncbi.nlm.nih.gov/biosample/SAMN37536568

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USA/NY-CDC-LC1055462/2023 New York collected 8/23/23 43F Spike ins16MPLF, V483del NSP3 K1155R BA.2.86.1 NSP3 T1269I C1420T (nsp2)

isolate SARS-CoV-2/Human/USA/NY-CDC-LC1055462/2023 collected by Laboratory Corporation of America collection date 2023-08-23 isolation source Nasal Swabs geographic location USA: New York host Homo sapiens host disease COVID-19 host sex female host age 43 collection device Nasal Swabs collection method Nasal Swabs purpose of sequencing baseline surveillance (random sampling) host_race Unknown diagnostic_gene_name_1 N1 gene diagnostic_pcr_protocol_1 Labcorp LDT diagnostic_pcr_Ct_value_1 20.377 diagnostic_gene_name_2 N2 gene diagnostic_pcr_protocol_2 Labcorp LDT diagnostic_pcr_Ct_value_2 17.732 diagnostic_gene_name_3 RP gene diagnostic_pcr_protocol_3 Labcorp LDT diagnostic_pcr_Ct_value_3 33.897 lineage/clade name BA.2.86 https://www.ncbi.nlm.nih.gov/biosample/SAMN37363732

map update https://www.google.com/maps/d/u/1/edit?mid=1OCfYIWOx61CCNsWu-FDaiTeSYn066gY&ll=45.33348212929379%2C-123.02937750050495&z=8