Typing tool
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Typing tool
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Complete norovirus genomes
| MH260493 | GII.2 | |
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| GII.P16 |
ORF1: 1..5099
ORF2: 5080..6708
ORF3: 6708..7487
LOCUS MH260493 7513 bp RNA linear VRL 16-JUN-2018
DEFINITION Norovirus GII isolate ST251 nonstructural polyprotein (ORF1) gene,
partial cds; and VP1 (ORF2) and VP2 (ORF3) genes, complete cds.
ACCESSION MH260493
VERSION MH260493.1
DBLINK BioProject: PRJNA338014
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7513)
AUTHORS Casto,A.M., Adler,A., Huang,M.-L., Makhsous,N., Xie,H., Zerr,D. and
Greninger,A.
TITLE The limits of epidemiology: Real-time metagenomic sequencing during
norovirus outbreak reveals discrete transmission clusters and
elucidates long-term sequelae of hospital acquired infections
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 7513)
AUTHORS Casto,A.M., Adler,A., Huang,M.-L., Makhsous,N., Xie,H., Zerr,D. and
Greninger,A.
TITLE Direct Submission
JOURNAL Submitted (25-APR-2018) Department of Laboratory Medicine,
University of Washington, 1100 Fairview Ave. N, E5-110, PO Box
19024, Seattle, WA 98109, USA
FEATURES Location/Qualifiers
source 1..7513
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="ST251"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="USA"
/collection_date="2017"
/note="genotype: GII"
gene <1..5099
/gene="ORF1"
CDS <1..5099
/gene="ORF1"
/codon_start=3
/product="nonstructural polyprotein"
/protein_id="AWT08335.1"
/translation="KMASNDATVAVACNNNNDKEKSSGEGLFTNMSSTLKKALGARPK
QPAPRDKPQKPPRPPTPELVKRIPPPPPNGEEEEEPVIRYEIKSGVSGLPELTTVPQP
DVANTAFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAAV
SMARVELTPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLND
SWLSRRMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLVG
KIKPLNILNILATCDWTFAGIVESLILIAELFGVFWTPPDVSAMIAPLLGDYELQGPE
DLAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEIFKLVMKWFF
PKKEEANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRLS
TKSASPDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLARE
VARKVASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELADT
CPLTLNCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVE
KAKRDFPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIAR
ASGLLHERMDEFELQGPTITTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVKT
MEELKQAIRNVTIKKCRIIYGGSTYDLESDGKGKVLVEKVKNTSVQTNNELAGALHHL
KHARIRYYVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEEA
PKSEDDEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGK
YSIEEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLVT
GSEIRKRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSPS
LFITSTHVIPAGITEAFGVPIKQIQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEGT
VATVLIKRPTGELMPLAARMGTHATMRIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDC
GCPYIYKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILGP
GGAPKLSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPR
GKPPRPSVLEAAKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGHPYHVRKNEFWN
GETFTGKLADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDLS
TMIRCARSFGGLMDEMKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWDS
TQQRAVLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCTS
QWNSIAHWLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLKE
YGLKPTRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGPN
HEDPNETMIPHSQRPIQLMALLGEASLHGPSFYSKISKLVITELKEGGMDFYVPRQEP
MFRWMRFSDLSTWEGDRNLAPNFVNEDGVE"
gene 5080..6708
/gene="ORF2"
CDS 5080..6708
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="AWT08333.1"
/translation="MKMASNDAAPSTDGAAGLVPESNNEVMALEPVAGAALAAPVTGQ
TNIIDPWIRANFVQAPNGEFTVSPRNAPGEVLLSLELGPELNPYLAHLARMYNGYAGG
MEVQVMLAGNAFTAGKLVFAAVPPHFPVENLSPQQITMFPHVIIDVRTLEPVLLPLPD
VRNNFFHYNQKDDPKMRIVAMLYTPLRSNGSGDDVFTVSCRVLTRPSPDFDFTYLVPP
TVESKTKPFTLPILTLGELSNSRFPVSIDQMYTSPNEVISVQCQNGRCTLDGELQGTT
QLQVSGICAFKGEVTAHLHDNDHLYNVTITNLNGSPFDPSEDIPAPLGVPDFQGRVFG
IISQRDKHNSPGHNEPANRGHDAVVPTYTAQYTPKLGQIQIGTWQTDDLAVNQPAKFT
PVGLNDTEHFNQWVVPRYAGALNLNTNLAPSVAPVFPGERLLFFRSYIPLKGGYGNPA
IDCLLPQEWVQHFYQEAAPSMSEVALVRYINPDTGRALFEAKLHRAGFMTVSSNTSAP
VVVPANGYFRFDSWVNQFYSLAPMGTGNGRRRVQ"
gene 6708..7487
/gene="ORF3"
CDS 6708..7487
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="AWT08334.1"
/translation="MAGAFVAGLAGDVLSNGLSSLINAGANAINQRAEFDFNQKLQQN
SFNHDKEMLQAQIQATKQLQADMMAIKQGVLTAGGFSPADAARGAVNAPMTQALDWSG
TRYWAPNSMRTTSYSGKFTSTAPVRQADFQHTQSRPSSGSSVSSFATQSSRPTLTTTT
GSSHGTVSSNSTRSTSLSQSTVSRVTSRTSEWVRDQNRNLEPYMHGALQTAFVTPPSS
RASDGTVSTVPKGVLDSWTPAFNTRRQPLFAHLRKRGESQA"
ORIGIN
1 tgaagatggc gtctaacgac gctaccgttg ccgttgcttg caacaacaac aacgacaaag
61 aaaaatcttc aggtgaaggc ttattcacaa atatgtcttc caccttaaag aaagccctcg
121 gggctaggcc caaacagcct gccccgagag acaaaccaca aaagccccca agaccaccaa
181 ctcccgagtt ggtcaagagg ataccccctc ctccacctaa tggcgaagaa gaagaagaac
241 cagtcattag gtacgagatt aagagtgggg tctctggcct gcccgagctc acaacagtcc
301 cccaaccgga cgtggccaac acagcattca gtgttccacc actgagcttg agagaaaaca
361 gggaggccaa ggaaccgcta acaggggcaa tattagagat gtgggatgga gagatatacc
421 attatggcct gtacgtagag aaaggcttag tgttgggtgt gcacaaacca cctgcagccg
481 taagcatggc aagagtggag ctgacgccgc tgtcattgta ctggcgtgtg gtgtacactc
541 cccaatacct catctcccct gaaactctca ggagactcaa cggagaggca ttcccttaca
601 ccgcctttga caataactgc tatgcctttt gctgctgggt gttagacctc aatgactcat
661 ggcttagcag gagaatggtg caaagaacaa cgggcttctt tagaccttac caagagtgga
721 acagaaaacc cctgcccacc atggatgact ccaaaattaa gaaggtagca aatatattcc
781 tatgctcatt gtccacatta ttcaccagac ccataaaaga cctcgtagga aaaattaaac
841 cattaaacat attgaatatc ctggcaacgt gtgactggac ttttgccgga atagtggagt
901 ctctgatatt aattgctgaa ctcttcggag ttttctggac acccccagat gtgtctgcta
961 tgatcgctcc cttactcggg gactacgagt tgcaggggcc agaagacctc gccgttgaac
1021 tcgtacccgt ggtaatgggg gggattggtt tggtgttggg attcaccaaa gagaaaattg
1081 gcaaaatgtt gtcctcagca gcatcaacac tcagggcttg caaagatctt ggtgcctatg
1141 gcttagagat attcaaattg gtcatgaagt ggttcttccc aaagaaagag gaggccaatg
1201 agctagccat ggtgagggcc atagaggatg ctgtactaga tcttgaggca atagaaaata
1261 accacatgac aaccctgtta aaagacaaag acagcttagc aacatacatg aaaacactgg
1321 acatggagga ggagaaagcc aggaggttgt ccacaaaatc tgcatcccct gacatagttg
1381 ggacaatcaa cgccctgctg gctcgaatag cagcggccag gtcattagtc cacagggcca
1441 aggaagagct atctagcagg ataagaccag tagttgttat gatatctggc aaaccaggaa
1501 taggcaaaac tcatctggcc agggaggtgg caagaaaggt ggcatccact ctcacagggg
1561 atcaaagagt cggactcata ccaagaaatg gtgtggacca ttgggatgca tacaaaggtg
1621 agagagtcgt gctgtgggac gactatggca tgagtaaccc cattcatgat gctcttcgca
1681 tacaagaatt ggctgatacg tgtcccctta ccttaaattg tgacagaatt gaaaataagg
1741 gaaaagtttt tgacagcgag gtcataataa ttacaacaaa ccttgccaat ccagccccac
1801 ttgattatgt taactttgag gcctgttcca ggagaattga tttcctggtg tacgctgagg
1861 caccagaagt agaaaaggca aaacgggact ttcctggtca gccagatatg tggaaggatg
1921 ccttcaagcc cgacttttca cacatcaagc tacagcttgc accccagggc ggctttgaca
1981 agaatggcaa caccccacat gggaaaggag tgatgaagac cctcactacc ggttctctga
2041 ttgcccgtgc atcaggccta ctgcatgaga ggatggatga atttgaactc caaggtccca
2101 caatcaccac cttcaatttc gaccggaaca gaatcacagc attcagacaa ttggctgcag
2161 aaaacaagta tggattggtg gataccatga aagttggcaa tcaactaaaa ggagtgaaaa
2221 ccatggagga acttaaacaa gcaatcagga atgtgaccat caagaagtgc cggatcatct
2281 acggtggctc cacgtatgac cttgaatctg atggcaaggg caaagttttg gtggaaaagg
2341 tcaagaacac ctctgtacag accaacaacg agttggctgg ggccctgcac catctcaaac
2401 acgcccgaat caggtactac gtcaaatgtg tgcaagaagc agtctattcc atcatacaaa
2461 ttgccggcgc tgcgtttgtc accacgcgca ttgcacgccg catgaacata caagaactct
2521 ggtcgaagcc acaattagat caaaatgaat cagagactaa ggaagaggcc cccaagtcag
2581 aagatgacga gttcatcata tcttctaagg acatcaagga ggaaggaaag aagggcaaaa
2641 acaaaactgg ccgtggcaag aaacacactg cattctccag caagggcttg agcgatgagg
2701 agtatgacga gtacaagagg ataagagaag agaggaatgg gaagtactcc atagaggagt
2761 atcttcaaga cagagacagg tactatgagg agctcgccat tgccaaggcc acggaagaag
2821 acttctgtga agaagaggag atcaaaatcc gtcagagaat tttccgtccc accaggaaac
2881 aaagaaagga agagagggcc acattagggc tagtaacagg ttcagaaatc agaaaaagga
2941 accctgatga cttcaaaccc aaagggaagc tgtgggctga tgacaacagg agtgttgact
3001 acaatgagaa actggacttt gaggcccccc caagcatatg gtctaggatt gtgagctttg
3061 gttctggctg gggcttctgg gtgtcaccaa gccttttcat aacatcaact catgtaatcc
3121 ccgcaggcat aacagaagca tttggagtcc ccatcaaaca aattcagatc cacaaatcag
3181 gtgaattttg ccgattcaga ttcccaaaac caattagacc agatgtaaca gggatgatct
3241 tggaagaagg tgcgcctgag ggcaccgtgg caactgtgct catcaaacgc cccaccgggg
3301 agctcatgcc ccttgcagcc agaatgggaa cacacgcaac catgagaatt caaggccgca
3361 tggttggcgg acagatgggt atgttgctca ctggatcaaa tgctaaagga atggatttgg
3421 gaacaactcc tggtgattgt ggctgtcctt acatctataa aagaggcaat gactatatag
3481 tcattggggt gcacactgca gcagcccgtg gtggaaacac cgtcatttgt gccacacagg
3541 gaagtgaggg tgaggcaact cttgagggtg gagatgacaa aggaacatac tgtggggcac
3601 ccattctagg ccctgggggt gcaccaaaat tgagcaccaa aaccaaattt tggaggtcat
3661 cgaacacgcc ccttccacca gggacatatg agcctgccta cctcggtggc cgtgatccgc
3721 gtgttaaggg tgggccctcc ctgcagcagg taatgagaga ccagttgaag ccattcactg
3781 aacccagggg caaacctcca agaccaagtg tattggaagc agccaaacaa accatcatca
3841 atgtcctcga acaaaccctg gaccctccac aaaaatggac atacgcacag gcgtgtgcct
3901 cacttgacaa aaccacctcc agtgggcatc cctatcacgt ccgaaagaat gaattctgga
3961 atggtgagac cttcactgga aaattggcag accaagcatc aaaagcaaac ctaatgtttg
4021 aggaggggaa acacatgaca ccagtgtaca cagcagcact caaggacgag ctagtcaaga
4081 ctgagaaaat ctatggaaag atcaagaaga gactgctctg gggctctgac ttgtccacta
4141 tgatccggtg cgctaggtca tttggtgggc tcatggacga gatgaaggca cactgcatat
4201 cactcccagt ccgagttggc atgaatatga atgaagatgg cccaataata tttgagaaac
4261 attccagata caaataccac tatgatgcag actactctcg ttgggattca acacaacaga
4321 gggcagtact agcagcagcc ttggaaatta tggtcagatt ctctgcagaa ccacaattgg
4381 cacaaatagt cgctgaggat ctgctggccc ctagtgtagt agatgtagga gacttcaaaa
4441 ttacaataaa tgaagggctc ccctctggtg tgccatgcac ttctcaatgg aactccatcg
4501 cacactggct gctaactctc tgtgccttgt ctgaagtcac caaactgtcc cctgacatta
4561 tacaggcaaa ttccatgttc tcattttacg gtgatgacga gattgtcagc accgacataa
4621 aactggaccc tgaacagtta accgccaaat tgaaagagta cggcctgaaa ccaacccgcc
4681 cagacaaaac cgagggaccc ctgattatca gtgaagattt gaacggactc actttcctcc
4741 gaaggacggt gactcgtgac ccagctggct ggtttggaaa attggaccaa agctcaattt
4801 tgaggcagat gtactggact agaggaccaa atcatgaaga ccccaatgag acaatgatac
4861 cccattctca aagacccata cagctcatgg cactgcttgg tgaagcctct cttcacggac
4921 cctctttcta cagtaaaatc agtaaattgg tcataactga actcaaagaa ggtgggatgg
4981 acttttacgt gccaaggcag gaacccatgt tcaggtggat gaggttttct gacttgagca
5041 cgtgggaggg cgatcgcaat ctggctccca attttgtgaa tgaagatggc gtcgaatgac
5101 gccgctccat ctactgatgg tgcagccggc ctcgtgccag aaagtaacaa tgaggtcatg
5161 gctcttgaac ccgtggctgg tgccgccttg gcagccccgg tcactggtca aacaaatatt
5221 atagaccctt ggattagagc aaattttgtc caggccccca atggtgaatt tacagtctct
5281 ccccgtaatg cccctggtga agtgctactg agtctagagt tgggtccaga attaaatcct
5341 tatctggcac atttagcaag aatgtacaat gggtatgccg gtgggatgga ggtgcaggtc
5401 atgttggctg ggaacgcgtt cacagccggc aagttggtct tcgccgccgt gccacctcac
5461 ttcccggttg aaaaccttag cccacagcaa atcaccatgt tccctcatgt gatcatagat
5521 gtgagaacct tggaacctgt tttattacca ctccctgatg ttagaaataa tttcttccat
5581 tataatcaga aagatgatcc caagatgaga attgtggcta tgctttatac ccccctcagg
5641 tctaatggtt caggtgatga tgtgtttaca gtctcctgca gagtgttgac tagaccttcc
5701 cctgactttg acttcacata cctggtgcca ccaacagtgg agtctaaaac aaaaccattc
5761 accctcccaa tcctcacact tggggaactt tccaattcca ggttcccagt gtccatagac
5821 cagatgtata ccagccctaa tgaagttata tcagtgcagt gtcaaaatgg taggtgcaca
5881 ctggacgggg agctccaggg gacaacacaa ctccaagtca gtggcatttg tgctttcaaa
5941 ggtgaagtga ccgcccactt gcatgacaat gatcacctat ataatgttac catcacaaac
6001 ttgaatgggt ccccttttga tccctccgag gatatccctg cccctctggg tgtgcctgac
6061 ttccagggaa gggtttttgg tatcatctcc caaagagaca aacacaatag tcctgggcat
6121 aatgaaccag caaacagggg acacgacgct gtggttccca cttacacagc acagtacact
6181 ccaaaactgg gacaaattca aattggcaca tggcagactg acgatcttgc agtcaaccaa
6241 ccagccaaat tcaccccagt tggactcaat gacactgaac atttcaacca atgggtggtc
6301 cctaggtatg ctggtgccct aaacctcaat acaaaccttg ccccttctgt tgctccagta
6361 tttccaggag agcgtctgct cttcttcaga tcatacattc ccctcaaggg cggttatgga
6421 aacccagcca ttgattgcct actaccacaa gagtgggtgc aacacttcta tcaggaagca
6481 gccccttcaa tgagtgaggt ggccctcgtc aggtacatca acccggacac tggtcgggca
6541 ctgtttgagg ccaagctcca cagagctggt ttcatgacag tctcgagcaa caccagtgcc
6601 ccggtggttg tgcctgccaa cggatacttc agatttgatt cttgggtgaa ccaattctat
6661 tctctcgccc ccatgggaac tgggaatggg cgtagaaggg ttcaataatg gctggagctt
6721 ttgtagctgg tcttgcaggg gatgtgctca gcaatgggct tagttcatta atcaatgcag
6781 gtgctaatgc aataaatcag agggcagaat ttgattttaa tcagaaattg cagcaaaatt
6841 cttttaatca tgataaggag atgttgcagg ctcagattca ggcaactaag cagctgcagg
6901 cagacatgat ggctataaaa caaggggtct tgaccgctgg cggcttttcc cctgctgatg
6961 cagccagagg tgctgtgaac gcgcccatga cacaagcgct ggattggagt ggtacaaggt
7021 attgggcacc aaactccatg aggaccacat cttactctgg aaaattcaca tcaaccgccc
7081 cagtgaggca ggccgacttc cagcacaccc aaagccggcc ttcgagtggc tcctctgtgt
7141 cctcctttgc cactcagtct tcaaggccaa ctctgaccac aaccactggt tcctcacatg
7201 gcacagtctc atcaaattca actcgcagca caagcctctc ccaatcaacg gtctccagag
7261 tcacatctag gactagtgag tgggttagag atcaaaatag aaatttggaa ccctacatgc
7321 atggtgcctt acagacagcc tttgtcaccc caccttccag cagggcatct gacgggacag
7381 tctcaaccgt cccgaaaggt gttttggact cctggacacc tgcgtttaac acccgcaggc
7441 agccgctttt tgcacacctc cgtaagaggg gggagtcaca agcttagtga aaaggtgaag
7501 atttatttag gat
//