Typing tool
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Typing tool
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Complete norovirus genomes
| MH260494 | GII.3 | |
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| GII.P12 |
ORF1: 1..5068
ORF2: 5049..6695
ORF3: 6695..7459
LOCUS MH260494 7498 bp RNA linear VRL 16-JUN-2018
DEFINITION Norovirus GII isolate ST173 nonstructural polyprotein (ORF1) gene,
partial cds; and VP1 (ORF2) and VP2 (ORF3) genes, complete cds.
ACCESSION MH260494
VERSION MH260494.1
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 7498)
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JOURNAL Unpublished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 7498)
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..7498
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="ST173"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="USA"
/collection_date="2017"
/note="genotype: GII"
gene <1..5068
/gene="ORF1"
CDS <1..5068
/gene="ORF1"
/codon_start=2
/product="nonstructural polyprotein"
/protein_id="AWT08336.1"
/translation="AAANSNNDNAKSSSDGVLSSMAVTFKRALGARHKQPPPRETSQR
PPRPPTPELVKKIPPPPPNGEDELVVSYSAKDGVSGLPELTTVRQPDEANTAFSVPPL
NQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAISLAKVELAPLSL
FWRPVYTPQYLISPDTLRRLHGESFPYTAFDNNCYAFCCWVLDLNDSWLCRRMIQRTT
GFFRPYQEWNRKPLPTMDDSKLKKVANIFLCALSSLFTRPIKDIIGKVRPLNILNILA
SCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVELVPVVMG
GIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEANELAMV
RSIEDAVLDLEAIENNHMTALLKDKDSLATYMRTLDLEEEKARKLSTKSASPDIVGTI
NALLARIAAARSLVHRAKEELSSRPRPVVVMISGKPGIGKTHLARELAKKIAASLTGD
QRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCPLTLNCDRIEN
KGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRDFPGQPDM
WKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLHERLDEY
ELQGPTPTTFNFDRNKVLAFRQLAAENKYGLLDTMRVGKQLKDVKTMPELKQALKNVA
IKSCQIVYGGCTYRLESDGKGDVRVDRVQNATVQTNNELAGALHHLRCARIRYYVKCV
QEALYSIIQIAGAAFVTTRIVKRMNIQDLWSKPQVEDTEEITSKDGCPKPQDDEEFVV
SSDDIKTEGKKGKNKSGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEEYLQDR
DRYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLVTGSEIRKRNPD
DFKPKGKLWADDDRSVDYNERLNFEAPPSIWSRIVNFGSGWGFWVSPSLFITSTHVIP
QGAQEFFGVSIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVVTLLIKRPT
GELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCGCPYIYKRGN
DYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDSKGTYCGAPILGPGSAPKLSTKT
KFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRGRPPKPSVLE
AAKKTIVNVLEQTIDPPQKWSFAQACASLDKTTSSGHPHHMRKNDCWNGESFTGKLAD
QASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDLATMIRCARAFG
GLMEELKAHCVTLPVRVGMNMNEDGPIIFERHSRYKYHYDADYSRWDSTQQRAVLAAA
LEIMVKFSPEPHLAQKVAEDLLSPSVMDVGDFKISINEGLPSGVPCTSQWNSIAHWLL
TLCALSEVTNLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLKEYGLKPTRPDK
TEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHEDPSETMIP
HSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQEPMFRWMRFSDL
STWEGDRNLAPSFVNEDGVE"
mat_peptide <1..958
/gene="ORF1"
/product="p48"
mat_peptide 959..2056
/gene="ORF1"
/product="NTPase"
mat_peptide 2057..2593
/gene="ORF1"
/product="p22"
mat_peptide 2594..2992
/gene="ORF1"
/product="VPg"
mat_peptide 2993..3535
/gene="ORF1"
/product="Pro"
mat_peptide 3536..5065
/gene="ORF1"
/product="RdRp"
gene 5049..6695
/gene="ORF2"
CDS 5049..6695
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="AWT08337.1"
/translation="MKMASNDATPSNDGAAGLVPEINNEAMALEPVAGAAIAAPLTGQ
QNIIDPWIMNNFVQAPGGEFTVSPRNSPGEVLLNLELGPEINPYLAHLARMYNGYAGG
FEVQVVLAGNAFTAGKIIFAAIPPNFPIDNLSAAQITMCPHVIVDVRQLEPVNLPMPD
VRNNFFHYNQGSDSRLRLVAMLYTPLRANNSGDDVFTVSCRVLTRPSPEFSFNFLVPP
TVESKTKPFTLPILTISEMSNSRFPVPIDSLHTSPTENIVVQCQNGRVTLDGELMGTT
QLLPSQICAFRGVLTRSTSRASDQADTATPRLFNYYWHIQLDNLNGTPYDPAEDIPGP
LGTPDFRGKVFGVASQRNPDSTTRAHEAKVDTTAGRFTPKLGSLEISTESDDFDQNQP
TRFTPVGIGVDHEADFQQWSLPDYSGQFTHNMNLAPAVAPNFPGEQLLFFRSQLPSSG
GRSNGILDCLVPQEWVQHFYQESAPAQTQVALVRYVNPDTGRVLFEAKLHKLGFMTIA
KNGDSPITVPPNGYFRFESWVNPFYTLAPMGTGNGRRRVQ"
gene 6695..7459
/gene="ORF3"
CDS 6695..7459
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="AWT08338.1"
/translation="MAGAFIAGLAGDIFTNTVGSLVNAGANAINQKVDFENNKYLQNA
SFNHDKEMLNAQIEATKRLQADMIAIKQGVLTAGGFSPTDAARGAINAPMTKVLDWNG
TRYWAPSATSTTSMSGGFTNQAVYRTTPNFKMNQAPKSTPSSGSSVRSLSTQVTSLSS
HSSGSSRSSESTVASSLPSSNRTRDWVNQQNFNLEPHMPGSLRTAFVTPPSSTASSSG
TVSTVPKNVLDSWTSAFNTRRQPLFAHLRRRGESNV"
ORIGIN
1 cgctgctgct aacagcaaca acgacaacgc aaaatcttca agtgacggag tgctttctag
61 catggctgtc acttttaaac gagccctcgg ggcgcggcat aaacagcccc ccccgaggga
121 aacatcacaa aggcctccac gaccacccac cccagaactg gtgaaaaaga tccctcctcc
181 cccacccaac ggggaggacg agctagtggt ctcttacagc gccaaagatg gcgtttctgg
241 tttgcctgaa cttaccactg tccggcaacc ggatgaggcc aacacggcgt tcagtgttcc
301 ccctctcaac cagagggaga acagggacgc caaggagccg ctgaccggaa caatcctgga
361 aatgtgggac ggggagatat accattacgg tctgtatgtg gagcgaggtc ttgtacttgg
421 tgtgcacaaa ccaccagctg ccatcagcct cgccaaggtt gaactggcac cactctctct
481 attttggagg ccagtgtaca caccacagta cctcatctct ccagacactc ttaggagact
541 gcatggagag tcgttcccct atacagcttt tgacaacaac tgctatgcct tctgttgttg
601 ggtcctggac ctaaacgact cgtggttgtg caggagaatg attcagagaa caactggctt
661 cttcagacct taccaagagt ggaataggaa acccctcccc accatggatg actctaaatt
721 gaaaaaggta gccaacatat tcttgtgtgc gctatcttcg ctattcacta ggcccatcaa
781 agacataata ggaaaggtga gaccgctcaa catccttaac atcctggcct catgtgattg
841 gacttttgca ggcatagtgg aatctttgat cctcttggca gagctctttg gagttttctg
901 gacaccccca gatgtgtctg cgatgatcgc ccccttacta ggtgactacg agctgcaggg
961 gcctgaggac cttgcagtgg aactcgtacc agtagtgatg ggagggattg gtttggtgtt
1021 aggattcact aaagagaaga tcggaaaaat gttgtcatct gctgcttcca ccttaagagc
1081 ttgtaaagac cttggtgcat acggactgga aatcctaaaa ttggtcatga aatggttctt
1141 cccaaagaaa gaggaagcaa atgagctagc tatggtgagg tccatcgagg atgcggtgct
1201 ggacctcgaa gcaattgaga acaatcacat gactgccctc ctcaaagaca aagacagtct
1261 ggcaacctac atgaggaccc ttgacctcga ggaggagaaa gccaggaagc tttcaaccaa
1321 gtctgcttca cctgacatcg tgggcacaat caacgctctt ctggcgagaa tcgccgctgc
1381 acgttccctg gtgcatcggg cgaaagagga actctccagc aggccaagac ctgttgttgt
1441 tatgatatca ggtaagccag ggatagggaa aactcacctt gccagggagc tagccaagaa
1501 gatcgcagct tcgctcacag gggaccagcg cgtgggcctc atccctcgca atggcgttga
1561 ccattgggat gcatacaagg gagaaagagt cgtcctatgg gacgattatg gaatgagcaa
1621 tcccatccac gacgccctca ggttacagga acttgctgac acctgccccc tcacgctaaa
1681 ctgtgacagg attgagaaca aaggaaaggt ctttgacagt gatgccataa tcatcaccac
1741 caatctagcc aacccagcac cattggacta tgtcaacttt gaagcatgct cgaggcgcat
1801 tgacttcctc gtgtacgcag aagcccctga ggtcgagaaa gcaaagcgtg acttcccagg
1861 tcaacctgac atgtggaaga acgcatttag ttctgacttc tcgcacataa aactggcgtt
1921 ggctccgcaa ggtggtttcg acaagaacgg aaacacccca cacgggaaag gcgttatgaa
1981 aactctcacc actggttccc tcatcgcccg agcatcaggg ctactccatg agaggttaga
2041 tgagtacgag ctgcagggcc caactcccac cacctttaat tttgaccgca acaaggtgct
2101 tgcgttcaga caacttgctg ccgaaaacaa gtacggattg ttggacacaa tgagagttgg
2161 aaaacagctc aaggatgtta agaccatgcc agagctcaaa caggcactca agaatgtcgc
2221 aatcaagagt tgtcagatag tgtatggtgg ctgcacctac aggcttgagt ctgatggcaa
2281 gggtgatgta agagttgaca gagttcagaa cgccactgta cagaccaaca atgagcttgc
2341 cggcgcacta caccatctta ggtgcgccag aatcagatat tatgtcaagt gtgttcagga
2401 ggccctgtat tccatcatcc aaattgctgg ggccgcattt gtcaccacgc gcattgtcaa
2461 gcgcatgaac atacaagatc tctggtccaa gccacaggtg gaggatacag aggaaatcac
2521 tagcaaggat ggatgcccaa aaccccagga tgatgaagag tttgttgtct catccgatga
2581 catcaaaacc gagggcaaga aagggaaaaa caagtctggc cgtggcaaga agcacacagc
2641 attctcaagt aaaggtctca gtgatgaaga gtacgatgag tacaaaagaa tcagagaaga
2701 aagaaatggc aaatactcca tagaggaata cctccaggac agagacaggt attatgagga
2761 ggtggccatc gccagggcaa ccgaagagga cttctgtgaa gaagaagagg ccaagatccg
2821 acagaggatc ttcaggccaa caaggaaaca acgcaaagag gagagagcct ctctcggttt
2881 ggtcacaggt tctgaaatca ggaagaggaa cccagacgac ttcaagccta aaggaaagct
2941 gtgggctgat gatgacagga gtgttgacta caatgagaga ctcaattttg aagccccacc
3001 aagcatctgg tcgaggatag tcaactttgg ttcaggttgg ggcttttggg tttcccccag
3061 cctgttcata acatcaactc atgtcatacc ccagggcgca caggagttct ttggtgtatc
3121 catcaaacaa attcagatac acaaatcagg tgaattctgc cgcttgaggt ttccaaagcc
3181 gatcagaact gatgtgacag gcatgatctt ggaagaaggt gcacccgaag gaaccgtggt
3241 cacattactc atcaaaagac caactggaga gctcatgccc ctggcagcca gaatgggaac
3301 ccacgcaacc atgaagatac aagggcgcac cgttggaggt caaatgggca tgctcctaac
3361 aggatccaac gccaagagca tggacctggg caccacacca ggtgactgtg gttgccccta
3421 catttacaag agggggaatg actacgtggt cattggggtc cacacagccg ccgcccgcgg
3481 aggaaacact gtcatttgtg ccacccaggg gagcgaggga gaagccacac ttgaaggcgg
3541 tgatagcaag gggacctact gcggtgcacc aatcttaggt ccaggaagtg ccccaaaact
3601 cagcaccaag accaagttct ggaggtcatc cacggcacca ctcccacctg gtacctatga
3661 accagcttac ctcggcggca aggatcccag agtcaagggt ggcccttcac tgcaacaagt
3721 tatgagggat caactgaaac cattcactga gcctaggggt aggccaccaa aaccaagtgt
3781 gctagaagct gccaagaaaa ccatcgtcaa tgtccttgaa cagacaattg acccacctca
3841 aaaatggtcg tttgcgcagg catgcgcatc ccttgataag accacttcta gcggtcatcc
3901 gcaccatatg cggaagaacg actgctggaa cggggagtcc ttcacaggaa aattggcaga
3961 ccaggcttcc aaagccaacc tgatgtttga ggagggaaag aacatgacac cagtttacac
4021 gggtgcgctt aaggacgagc tggtcaagac tgacaagatt tatggtaaga tcaaaaagag
4081 acttctctgg ggttcggacc tggcgaccat gattcggtgc gctcgagcat tcgggggtct
4141 gatggaggaa ctcaaagcac actgtgtcac actacctgtt agggtgggta tgaatatgaa
4201 tgaggatggc cctatcatct ttgagagaca ctctagatat aaatatcatt atgatgctga
4261 ctactctcgg tgggattcaa cacaacaaag agccgtgttg gcagcagcct tagaaattat
4321 ggtcaagttt tccccagagc cgcacctggc ccaaaaggtt gcagaagacc ttctttctcc
4381 cagcgtgatg gacgtaggtg atttcaaaat atcaatcaat gagggtctcc cctccggggt
4441 gccctgcacc tcccaatgga attccatcgc ccactggctc ctcaccctct gtgcactctc
4501 cgaagttaca aacctgtccc ctgacattat tcaggccaac tctctctttt ctttctacgg
4561 tgatgatgaa attgtgagta cagacataaa attagaccca gaaaaactga cagcaaaact
4621 taaggaatac gggttgaaac cgacccgccc tgacaagact gaagggcctc ttgtcatttc
4681 cgaagacctg aatggcctaa ccttcctgcg gaggaccgtg acccgtgacc cagcaggctg
4741 gtttggaaag ttggaacaga gctcaatact cagacaaatg tactggacta ggggccccaa
4801 ccatgaagat ccatctgaaa caatgatacc acactcccag aggcccatac aattgatgtc
4861 tttgctgggt gaggcagcac tccacggccc agcattctac agcaaaatca gcaaactggt
4921 cattgcagag ttgaaggaag gtggcatgga tttttacgtg ccaagacaag agccaatgtt
4981 cagatggatg agattctcgg atctgagcac gtgggagggc gatcgcaatc tggctcccag
5041 ttttgtgaat gaagatggcg tcgaatgacg ccactccatc taatgatggt gccgccggcc
5101 tcgtcccaga gatcaacaat gaggcaatgg cgctagaacc agtggcgggt gcagcgatag
5161 cagcacccct cactggccag caaaatataa ttgatccctg gattatgaat aattttgtgc
5221 aagcacctgg tggtgagttc acagtgtctc ctaggaattc ccctggtgaa gtgctcctca
5281 atttggaatt gggcccagag ataaacccct atctggccca tcttgctaga atgtataatg
5341 gttatgcagg tgggtttgaa gtgcaggtag tcctagctgg aaatgcgttt acagcaggaa
5401 agataatctt tgcagctata ccccctaact tcccaattga caatctaagt gcagcacaga
5461 tcacaatgtg tccacatgtg attgtggatg tcaggcagtt ggaaccggtc aacctcccga
5521 tgcctgacgt tcgcaataac ttcttccact acaaccaagg gtctgattcg agattgcgct
5581 tggttgcgat gctgtacaca cctcttaggg caaataactc tggggatgat gttttcactg
5641 tgtcttgtag agtgttgact agacctagcc ctgaattttc atttaacttc cttgtgccac
5701 ccactgtgga gtcaaagaca aaacccttta ccctcccaat tctgactatt tctgaaatgt
5761 ctaattctag gtttccagtg ccgattgatt ccctgcacac cagcccaact gagaatattg
5821 ttgtccagtg ccaaaatgga cgcgtcactc ttgatggtga gttgatgggc accactcagc
5881 tcttacctag tcaaatctgt gctttcaggg gcgtgctcac tagatcaaca agcagggcta
5941 gtgaccaggc cgacacagca acccctagat tgtttaatta ttattggcac atacaattgg
6001 ataatctaaa tgggactcct tatgatcctg cagaagacat accaggcccc ctggggacac
6061 cagatttccg gggcaaagtc ttcggcgtgg ccagccaaag aaaccccgac agtacaacta
6121 gagcacatga agcaaaggtg gacacaacag ctggtcgctt caccccaaaa ctaggctcat
6181 tagagatatc cactgaatct gatgactttg atcaaaatca accaacaaga ttcaccccag
6241 ttggcattgg ggttgaccac gaggcagact tccaacaatg gtccttaccc gactactctg
6301 gccagttcac tcacaacatg aacttagccc cagctgttgc tcccaacttc cctggtgagc
6361 agctcctttt cttccgctca cagttaccat cttctggtgg gcgatccaat gggattctag
6421 actgcctggt cccccaagaa tgggttcagc acttctacca agaatcagcc cccgcccaaa
6481 cccaggtggc tctggttaga tatgtcaacc ctgacactgg tagagtgttg tttgaggcaa
6541 agctgcacaa attaggcttc atgactatag ctaagaatgg tgactctcca ataactgtcc
6601 ccccaaatgg atactttagg tttgaatctt gggtgaaccc attttataca cttgccccca
6661 tgggaactgg gaatgggcgt agaagagttc aataatggct ggagctttta tagcaggatt
6721 agctggtgat atattcacaa atactgtagg gtctctagtt aatgcagggg ctaatgctat
6781 taatcaaaaa gttgattttg aaaataataa atatttgcaa aatgcttcct tcaatcatga
6841 taaggaaatg ttaaatgcac agattgaggc aacaaagagg ttacaggctg acatgattgc
6901 tatcaaacag ggggttttga ccgctggcgg cttttccccc actgatgcag ctcgcggggc
6961 aattaatgcc cccatgacaa aagtcctaga ttggaatgga acaaggtact gggcaccgag
7021 tgccacctct acaacctcga tgtcgggtgg cttcacaaac caggctgtgt acagaactac
7081 accaaatttt aaaatgaacc aggcccccaa atccacaccc agcagtgggt cttcagtgag
7141 gtcactctca acccaagtca ctagtctgag ctcacactcg tccgggtcgt ctcgatccag
7201 cgagtctaca gttgctagct cattaccatc ctctaacagg actagggact gggtcaatca
7261 gcaaaatttc aatttggaac cacacatgcc tgggtcactt aggacggctt ttgtcactcc
7321 accatctagt acagcctcta gttcaggcac tgtctcaacc gtgcccaaaa atgttttgga
7381 ctcctggaca tctgcgttta acacgcgcag acagccgcta ttcgcacacc ttcgtagaag
7441 gggggagtca aatgtttagt gaaaaggtta ttttaaattt gatttaaatt ggatttga
//