niman

LOCUS MW422255 29763 bp RNA linear VRL 30-DEC-2020 DEFINITION Severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/human/USA/SEARCH-5574-SAN/2020, complete genome. ACCESSION MW422255 VERSION MW422255.1 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. REFERENCE 1 (bases 1 to 29763) AUTHORS SEARCH Alliance,S.D. TITLE Direct Submission JOURNAL Submitted (30-DEC-2020) Department of Immunology, The Scripps Research Institute, 10550 N Torrey Pines Rd, San Diego, CA 92122, USA COMMENT ##Assembly-Data-START## Assembly Method :: artic-ncov2019 v. 1.0 Sequencing Technology :: Nanopore ##Assembly-Data-END## FEATURES Location/Qualifiers source 1..29763 /organism="Severe acute respiratory syndrome coronavirus 2" /mol_type="genomic RNA" /isolate="SARS-CoV-2/human/USA/SEARCH-5574-SAN/2020" /isolation_source="nasopharyngeal swab" /host="Homo sapiens" /db_xref="taxon:2697049" /country="USA: San Diego, California" /collection_date="2020-12-29" https://www.ncbi.nlm.nih.gov/nucleotide/MW422255.1?report=genbank&log$=nucltop&blast_rank=1&RID=ZEP33G4G016

Middlesex County 662 New Confirmed Cases 1,515 Confirmed Deaths 86 New Probable Cases 48,222 Total Confirmed Cases 220 Probable Deaths 3,142 Total Probable Cases Hudson County 601 New Confirmed Cases 1,571 Confirmed Deaths 105 New Probable Cases 46,886 Total Confirmed Cases 169 Probable Deaths 3,600 Total Probable Cases Monmouth County 577 New Confirmed Cases 985 Confirmed Deaths 123 New Probable Cases 34,771 Total Confirmed Cases 102 Probable Deaths 3,044 Total Probable Cases Bergen County 571 New Confirmed Cases 2,095 Confirmed Deaths 195 New Probable Cases 49,974 Total Confirmed Cases 266 Probable Deaths 5,122 Total Probable Cases Essex County 542 New Confirmed Cases 2,167 Confirmed Deaths 106 New Probable Cases 49,865 Total Confirmed Cases 255 Probable Deaths 3,978 Total Probable Cases Ocean County 431 New Confirmed Cases 1,351 Confirmed Deaths 124 New Probable Cases 35,174 Total Confirmed Cases 83 Probable Deaths 3,724 Total Probable Cases Camden County 400 New Confirmed Cases 801 Confirmed Deaths 34 New Probable Cases 30,639 Total Confirmed Cases 66 Probable Deaths 2,721 Total Probable Cases Passaic County 400 New Confirmed Cases 1,337 Confirmed Deaths 98 New Probable Cases 41,659 Total Confirmed Cases 159 Probable Deaths 3,172 Total Probable Cases Union County 335 New Confirmed Cases 1,401 Confirmed Deaths 151 New Probable Cases 38,180 Total Confirmed Cases 183 Probable Deaths 5,204 Total Probable Cases Morris County 284 New Confirmed Cases 800 Confirmed Deaths 95 New Probable Cases 21,711 Total Confirmed Cases 187 Probable Deaths 3,465 Total Probable Cases Burlington County 277 New Confirmed Cases 592 Confirmed Deaths 75 New Probable Cases 23,063 Total Confirmed Cases 51 Probable Deaths 2,208 Total Probable Cases Gloucester County 226 New Confirmed Cases 400 Confirmed Deaths 39 New Probable Cases 15,395 Total Confirmed Cases 20 Probable Deaths 1,932 Total Probable Cases Mercer County 190 New Confirmed Cases 708 Confirmed Deaths 23 New Probable Cases 19,897 Total Confirmed Cases 39 Probable Deaths 982 Total Probable Cases Atlantic County 161 New Confirmed Cases 369 Confirmed Deaths 82 New Probable Cases 13,238 Total Confirmed Cases 17 Probable Deaths 3,205 Total Probable Cases Somerset County 136 New Confirmed Cases 596 Confirmed Deaths 79 New Probable Cases 13,440 Total Confirmed Cases 93 Probable Deaths 2,782 Total Probable Cases Sussex County 96 New Confirmed Cases 178 Confirmed Deaths 22 New Probable Cases 4,978 Total Confirmed Cases 46 Probable Deaths 622 Total Probable Cases Cumberland County 90 New Confirmed Cases 232 Confirmed Deaths 43 New Probable Cases 8,494 Total Confirmed Cases 10 Probable Deaths 1,511 Total Probable Cases Warren County 66 New Confirmed Cases 171 Confirmed Deaths 18 New Probable Cases 4,263 Total Confirmed Cases 13 Probable Deaths 421 Total Probable Cases Hunterdon County 62 New Confirmed Cases 86 Confirmed Deaths 11 New Probable Cases 4,084 Total Confirmed Cases 54 Probable Deaths 396 Total Probable Cases Salem County 60 New Confirmed Cases 108 Confirmed Deaths 5 New Probable Cases 3,082 Total Confirmed Cases 7 Probable Deaths 337 Total Probable Cases Cape May County 44 New Confirmed Cases 124 Confirmed Deaths 40 New Probable Cases 2,579 Total Confirmed Cases 19 Probable Deaths 2,343 Total Probable Cases https://www.nj.gov/health/cd/topics/covid2019_dashboard.shtml

On Friday, November 20, 2020 All 11 Regions of the Illinois COVID Regions entered in Tier 3 Mitigations Regional Metrics can be found here. Mitigations can be found here Total Cases 1,008,045 Confirmed Deaths 17,272 Probable Deaths 1,669 Total Tests Performed* 13,803,946 Recovery Rate** 98% *Total molecular and antigen tests performed and reported electronically for testing of COVID-19 at IDPH, commercial or hospital laboratories. All numbers displayed are provisional and will change. ** Recovered cases are defined as persons with initial positive specimen collection date > 42 days who have not expired. Recovery rate is calculated as the recovered cases divided by the sum of recovered cases and deceased cases. Information regarding the number of persons under investigation updated on 1/7/2021. Information to be updated daily.

https://covid19.ncdhhs.gov/dashboard/cases

New Tests Administered 56,708 08/25/2020 ... 01/06/2021 16,609 New Individuals Tested New Positive Cases 7,344 12/15/2020 ... 01/06/2021 Positivity - All Tests 16.4 %7-Day Rate 12/25/2020 ... 12/31/2020 10.8 % cumulative rate New Deaths 81 10/07/2020 ... 01/06/2021 Total Confirmed COVID-19 Counts Total Tests Administered 5,950,922 02/26/2020 ... 01/06/2021 2,710,638 Individuals Tested Total Positive Cases 546,499 03/06/2020 ... 01/06/2021 Positivity - Unique Individuals 27.8 %7-Day Rate 12/25/2020 ... 12/31/2020 20.2 % cumulative rate Total Deaths 8,452 03/15/2020 ... 01/06/2021 https://www.coronavirus.in.gov/

https://www.azdhs.gov/preparedness/epidemiology-disease-control/infectious-disease-epidemiology/covid-19/dashboards/index.php

https://www.vdh.virginia.gov/coronavirus/covid-19-in-virginia/

https://coronavirus.iowa.gov/#CurrentStatus

https://www.health.pa.gov/topics/disease/coronavirus/Pages/Cases.aspx#

Sweden/20-13052/2020 12/30 38F matched UK variant with 3 AAs deleted in Spike protein, 3 AAs deleted in NSP6 and Q27 stop codon in NS8. map update https://www.google.com/maps/d/u/1/edit?mid=1aQDSL2LwQFbuoCAg_nIOPK8D-LIJ5MYd&ll=59.26592795114904%2C17.982052505964912&z=7

The Public Health Agency of Sweden has released (at GISAID) a UK Variant B.1.1.7 SARS CoV2 sequence (Sweden/20-13052/2020 12/30) from Stockholm Sweden collected Dec 30.

Norway/7116/2020 12/22 Vestland matched UK variant with 2 AAs deleted in Spike protein, 3 AAs deleted in NSP6 and Q27 stop codon in NS8. map update https://www.google.com/maps/d/u/1/edit?mid=1aQDSL2LwQFbuoCAg_nIOPK8D-LIJ5MYd&ll=59.93877765222561%2C10.704297075781275&z=10

Norway/7110/2020 12/22 Vestland matched UK variant with 2 AAs deleted in Spike protein, 3 AAs deleted in NSP6 and Q27 stop codon in NS8. map update https://www.google.com/maps/d/u/1/edit?mid=1aQDSL2LwQFbuoCAg_nIOPK8D-LIJ5MYd&ll=59.93877765222561%2C10.704297075781275&z=10

Norwegian Institute of Public Health has released (at GISAID) two UK Variant B.1.1.7 SARS CoV2 sequences (Norway/7110/2020 12/22 & Norway/7116/2020 12/22 collected Dec 22.

Norway/7136/2020 12/15 Rogaland matched UK variant with 3 AAs deleted in Spike protein, 3 AAs deleted in NSP6 and Q27 stop codon in NS8. map update https://www.google.com/maps/d/u/1/edit?mid=1aQDSL2LwQFbuoCAg_nIOPK8D-LIJ5MYd&ll=58.91216777330577%2C5.416664932019435&z=9

Norwegian Institute of Public Health has released (at GISAID) a UK Variant B.1.1.7 SARS CoV2 sequences (Norway/7136/2020 12/15) collected Dec 15.

Australia/NSW3876/2021 33F matched 501.v2 with 3 AAs deleted in Spike protein, 3 AAs deleted in NSP6 map update https://www.google.com/maps/d/u/1/edit?mid=1aQDSL2LwQFbuoCAg_nIOPK8D-LIJ5MYd&ll=-33.925094919532555%2C151.1737176767578&z=11

Australia/NSW3872/2021 1M matched 501.v2 with 3 AAs deleted in Spike protein, 3 AAs deleted in NSP6 map update https://www.google.com/maps/d/u/1/edit?mid=1aQDSL2LwQFbuoCAg_nIOPK8D-LIJ5MYd&ll=-33.925094919532555%2C151.1737176767578&z=11

Prince of Wales Hospital has released (at GISAID) three501.v2 SARS-CoV2 COVID Sequences (Australia/NSW3872/2021, Australia/NSW3876/2021) collected between Jan 1.

Australia/SAP605/2021 1/4 matched UK variant with 3 AAs deleted in Spike protein, 3 AAs deleted in NSP6 and Q27 stop codon in NS8. map update https://www.google.com/maps/d/u/1/edit?mid=1aQDSL2LwQFbuoCAg_nIOPK8D-LIJ5MYd&ll=-34.78343981394609%2C136.9741969480385&z=7

Australia/SAP602/2020 12/31 matched UK variant with 3 AAs deleted in Spike protein, 3 AAs deleted in NSP6 and Q27 stop codon in NS8. map update https://www.google.com/maps/d/u/1/edit?mid=1aQDSL2LwQFbuoCAg_nIOPK8D-LIJ5MYd&ll=-34.78343981394609%2C136.9741969480385&z=7

SA Pathology has released (at GISAID) two UK Variant B.1.1.7 SARS CoV2 sequences (Australia/SAP602/2020, Australia/SAP605/2021) collected between Dec 31 - Jan 4.

Luxembourg/LNS7581211/2020 45F 12/29 matched UK variant with 3 AAs deleted in Spike protein, 3 AAs deleted in NSP6 and Q27 stop codon in NS8. map update https://www.google.com/maps/d/u/1/edit?mid=1aQDSL2LwQFbuoCAg_nIOPK8D-LIJ5MYd&ll=49.47238038673145%2C5.659342729949843&z=9

Luxembourg/LNS4604656/2020 52F 12/28 matched UK variant with 3 AAs deleted in Spike protein, 3 AAs deleted in NSP6 and Q27 stop codon in NS8. map update https://www.google.com/maps/d/u/1/edit?mid=1aQDSL2LwQFbuoCAg_nIOPK8D-LIJ5MYd&ll=49.47238038673145%2C5.659342729949843&z=9

Microbial Genomics Platform has released (at GISAID) two UK Variant B.1.1.7 SARS CoV2 sequences (Luxembourg/LNS7581211/2020, 6/2020) collected between Dec 28-29.