niman

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USA/MD-CDC-LC1054598/2023 Maryland Collected 8/25/23 59F Spike ins16MPLF, V483del NSP3 K1155R BA.2.86.1 NSP2 Y441C NSP14 N408K T27134C (M)

isolate SARS-CoV-2/Human/USA/MD-CDC-LC1054598/2023 collected by Laboratory Corporation of America collection date 2023-08-25 isolation source Nasal Swabs geographic location USA: Maryland 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_gene_name_1 N1 gene diagnostic_pcr_protocol_1 Labcorp LDT diagnostic_pcr_Ct_value_1 Unknown diagnostic_gene_name_2 N2 gene diagnostic_pcr_protocol_2 Labcorp LDT diagnostic_pcr_Ct_value_2 Unknown diagnostic_gene_name_3 RP gene diagnostic_pcr_protocol_3 Labcorp LDT diagnostic_pcr_Ct_value_3 Unknown lineage/clade name BA.2.86 BioProject PRJNA716984 Severe acute respiratory syndrome coronavirus 2 Retrieve all samples from this project Submission Centers for Disease Control and Prevention; 2023-09-12 Accession: SAMN37364111 ID: 37364111 SRA Nucleotide https://www.ncbi.nlm.nih.gov/biosample/37364111

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USA/NY-CDC-VSX-A336671/2023 New York 9/16/23 collection 51M Spike ins16MPLF, V483del NSP3 K1155R BA.2.86.1 NSP2 Y441C NSP3 V1932I NSP14 S221A NSP14 N408K NSP15 V69M T26229C (ORF3a) T27134C (M)

isolate SARS-CoV-2/Human/USA/NY-CDC-VSX-A336671/2023 collected by Helix collection date 2023-09-16 isolation source PrimeStore MTM - Nasal Swab geographic location USA: New York host Homo sapiens host disease COVID-19 host sex male host age 51 collection device PrimeStore MTM - Nasal Swab collection method PrimeStore MTM - Nasal Swab purpose of sequencing baseline surveillance (random sampling) host_race White diagnostic_gene_name_1 N diagnostic_pcr_protocol_1 Helix COVID-19 and Flu Test diagnostic_pcr_Ct_value_1 Unknown diagnostic_gene_name_2 ORF1ab diagnostic_pcr_protocol_2 Helix COVID-19 and Flu Test diagnostic_pcr_Ct_value_2 Unknown diagnostic_gene_name_3 S diagnostic_pcr_protocol_3 Helix COVID-19 and Flu Test diagnostic_pcr_Ct_value_3 Unknown lineage/clade name BA.2.86 BioProject PRJNA720050 Severe acute respiratory syndrome coronavirus 2 Retrieve all samples from this project Submission CDC-OAMD; 2023-10-01 https://www.ncbi.nlm.nih.gov/biosample/37631168

LOCUS OR645919 29737 bp RNA linear VRL 06-OCT-2023 DEFINITION Severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/human/USA/NY-PRL-230929_83C07/2023 ORF1ab polyprotein (ORF1ab), ORF1a polyprotein (ORF1ab), surface glycoprotein (S), ORF3a protein (ORF3a), envelope protein (E), membrane glycoprotein (M), ORF6 protein (ORF6), ORF7a protein (ORF7a), ORF7b (ORF7b), ORF8 protein (ORF8), nucleocapsid phosphoprotein (N), and ORF10 protein (ORF10) genes, complete cds. ACCESSION OR645919 VERSION OR645919.1 KEYWORDS . SOURCE Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ORGANISM Severe acute respiratory syndrome coronavirus 2 Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Nidovirales; Cornidovirineae; Coronaviridae; Orthocoronavirinae; Betacoronavirus; Sarbecovirus; Severe acute respiratory syndrome-related coronavirus. REFERENCE 1 (bases 1 to 29737) AUTHORS Opentrons,P. TITLE Direct Submission JOURNAL Submitted (06-OCT-2023) Bureau of the Public Health Laboratory, NYC DOHMH, 455 First Ave, New York, NY 10016, USA COMMENT ##Assembly-Data-START## Assembly Method :: bwa v. 0.7.17-r1188 Sequencing Technology :: Illumina ##Assembly-Data-END## FEATURES Location/Qualifiers source 1..29737 /organism="Severe acute respiratory syndrome coronavirus 2" /mol_type="genomic RNA" /isolate="SARS-CoV-2/human/USA/NY-PRL-230929_83C07/2023" /isolation_source="nasopharyngeal swab" /host="Homo sapiens" /db_xref="taxon:2697049" /country="USA: New York" /collection_date="2023-09-25"

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USA/NY-PRL-230929_83C07/2023 New York City 9/25/23 collection not at GISAID NSP3 K1155R BA.2.86.1

LOCUS OR645779 29736 bp RNA linear VRL 06-OCT-2023 DEFINITION Severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/human/USA/NY-PRL-230929_81C04/2023 ORF1ab polyprotein (ORF1ab), ORF1a polyprotein (ORF1ab), surface glycoprotein (S), ORF3a protein (ORF3a), envelope protein (E), membrane glycoprotein (M), ORF6 protein (ORF6), ORF7a protein (ORF7a), ORF7b (ORF7b), ORF8 protein (ORF8), nucleocapsid phosphoprotein (N), and ORF10 protein (ORF10) genes, complete cds. ACCESSION OR645779 VERSION OR645779.1 KEYWORDS . SOURCE Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ORGANISM Severe acute respiratory syndrome coronavirus 2 Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Nidovirales; Cornidovirineae; Coronaviridae; Orthocoronavirinae; Betacoronavirus; Sarbecovirus; Severe acute respiratory syndrome-related coronavirus. REFERENCE 1 (bases 1 to 29736) AUTHORS Opentrons,P. TITLE Direct Submission JOURNAL Submitted (06-OCT-2023) Bureau of the Public Health Laboratory, NYC DOHMH, 455 First Ave, New York, NY 10016, USA COMMENT ##Assembly-Data-START## Assembly Method :: bwa v. 0.7.17-r1188 Sequencing Technology :: Illumina ##Assembly-Data-END## FEATURES Location/Qualifiers source 1..29736 /organism="Severe acute respiratory syndrome coronavirus 2" /mol_type="genomic RNA" /isolate="SARS-CoV-2/human/USA/NY-PRL-230929_81C04/2023" /isolation_source="nasopharyngeal swab" /host="Homo sapiens" /db_xref="taxon:2697049" /country="USA: New York" /collection_date="2023-09-21"

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USA/NY-PRL-230929_81C04/2023 New York City 9/23/23 collection not at GISAID NSP3 K1155R BA.2.86.1

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England/CLIMB-CM7YRGBE/2023 England 10/4/23 collected https://ukcovid.xyz/ba_2_86_daily.php

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England/CLIMB-CM7YK1CW/2023 England 10/2/23 collection https://ukcovid.xyz/ba_2_86_daily.php

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England/CLIMB-CM7YGDNC/2023 England 9/30/23 collection https://ukcovid.xyz/ba_2_86_daily.php

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England/CLIMB-CM7YFSS6/2023 England 10/1/23 collection https://ukcovid.xyz/ba_2_86_daily.php

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England/CLIMB-CM7Y8TRA/2023 England 9/29/23 https://ukcovid.xyz/ba_2_86_daily.php

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England/CLIMB-CM7YGTQR/2023 England 9/29/23 collection https://ukcovid.xyz/ba_2_86_daily.php

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