Typing tool
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Typing tool
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Complete norovirus genomes
| MH260505 | GII.4 Sydney | |
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| GII.P16 |
ORF1: 1..4985
ORF2: 4966..6588
ORF3: 6588..7191
LOCUS MH260505 7191 bp RNA linear VRL 16-JUN-2018
DEFINITION Norovirus GII isolate ST110 nonstructural polyprotein (ORF1) gene,
partial cds; VP1 (ORF2) gene, complete cds; and VP2 (ORF3) gene,
partial cds.
ACCESSION MH260505
VERSION MH260505.1
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 7191)
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JOURNAL Unpublished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 7191)
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..7191
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="ST110"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="USA"
/collection_date="2017"
/note="genotype: GII"
gene <1..4985
/gene="ORF1"
CDS <1..4985
/gene="ORF1"
/codon_start=3
/product="nonstructural polyprotein"
/protein_id="AWT08369.1"
/translation="LGARPKQPAPRDEPQKPPRPPTPELVKRIPPPPPNGEEEEEPVI
RYGVKSGISGLPELTTVPQPDVANTAFSVPPLSLRENREAKEPLTGAILEMWDGEIYH
YGLYVEKGLVLGVHKPPAAISMARVELAPLSLYWRVVYTPQYLISPETLRRLNGEAFP
YTAFDNNCYAFCCWVLDLNDSWLSRRMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVA
NIFLCSLSTLFTRPIKDLIGKIKPLNILNILATCDWTFAGIVESLILLAELFGVFWTP
PDVSAMIAPLLGDYELQGPEDLAVELVPVVMGGIGLVLGFTKERIGKMLSSAASTLRA
CKDLGAYGLEILKLVMKWFFPKKEEANELAMVRAIEDAVLDLEAIENNHMTTLLKDKD
SLATYMKTLDMEEEKARRLSTKSASPDIVGTINALLARIAAARSLVHRAKEELSSRIR
PVVVMISGKPGIGKTHLAREVARKVASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWD
DYGMSNPIHDALRIQELADTCPLTLNCDRIENKGKVFDSEVIIITTNLANPAPLDYVN
FEACSRRIDFLVYAEAPEVEKAKRDFPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNG
NTPHGKGVMKTLTTGSLIARASGLLHERMDEFELQGPTITTFNFDRNRITAFRQLAAE
NKYGLVDTMKVGNQLKGVKTMEELKQAIRNVTIKRCRIIYGGSTYDLESDGKGKVLVE
KVKNTSVQTNNELAGALHHLKHARIRYYVKCVQEAVYSIIQIAGAAFVTTRIARRMNI
QELWSKPQLDQNESETKEEVPKSEDDEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSK
GLSDEEYDEYKRIREERNGKYSIEEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQR
IFRPTRKQRKEERATLGLVTGSEIRKRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPP
SIWSRIVSFGSGWGFWVSPSLFITSTHVIPAGVTEAFGVPIKQIQIHKSGEFCRFRFP
KPIRPDVTGMILEEGAPEGTVATVLIKRPTGELMPLAARMGTHATMKIQGRMVGGQMG
MLLTGSNAKGMDLGTTPGDCGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGE
ATLEGGDDKGTYCGAPILGPGGAPKLSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVK
GGPSLQQVMRDQLKPFTEPRGKPPRPSVLEAAKQTIINVLEQTLDPPQKWTYAQACAS
LDKTTSSGHPHHVRKNEFWNGETFTGKLADQASKANLMFEEGKHMTPVYTAALKDELV
KTEKIYGKIKKRLLWGSDLSTMIRCARSFGGLMDEMKTHCISLPVRVGMNMNEDGPII
FEKHSRYKYHYDADYSRWDSTQQRAVLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVD
VGDFKITINEGLPSGVPCTSQWNSIAHWLLTLCALSEVTKLSPDIIQANSMFSFYGDD
EIVSTDIKLDPEQLTAKLKEYGLKPTRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGW
FGKLDQSSILRQMYWTRGPNHEDPNETMIPHSQRPIQLMALLGEASLHGPSFYSKISK
LVITELKEGGMDFYVPRQEPMFRWMRFSDLSTWEGDRNLAPNFVNEDGVE"
mat_peptide <1..881
/gene="ORF1"
/product="p48"
mat_peptide 882..1979
/gene="ORF1"
/product="NTPase"
mat_peptide 1980..2510
/gene="ORF1"
/product="p22"
mat_peptide 2511..2909
/gene="ORF1"
/product="VPg"
mat_peptide 2910..3452
/gene="ORF1"
/product="Pro"
mat_peptide 3453..4982
/gene="ORF1"
/product="RdRp"
gene 4966..6588
/gene="ORF2"
CDS 4966..6588
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="AWT08370.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSIPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML
TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDRDFEANQNTKFTPVGVIQDG
STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRVV"
gene 6588..>7191
/gene="ORF3"
CDS 6588..>7191
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="AWT08371.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAVLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRDAVPARGPSNKSS
NSSTATSVYSNQTISTRLGSTAGSGTSVSSLPSTARTRSWV"
ORIGIN
1 ccctcggggc taggcccaaa cagcctgccc cgagagacga accacaaaag cccccaagac
61 caccaactcc cgagttggtc aagaggatac cccctcctcc acctaatggc gaagaagaag
121 aggaaccagt cattaggtat ggggttaaaa gtgggatctc tggcctgccc gagctcacaa
181 cagtccccca accggacgtg gccaacacag cattcagtgt tccaccactg agcttgagag
241 aaaacaggga ggccaaggaa ccgctaacag gggcgatatt agagatgtgg gatggagaga
301 tataccacta tggcctgtac gtggagaaag gcttagtgtt gggtgtgcac aaaccacctg
361 cagccataag catggcaaga gtggagctgg cgccgctttc attgtactgg cgtgtggtgt
421 acactcccca atacctcatc tcccctgaaa ctctcaggag gctcaacgga gaggcgttcc
481 cttacaccgc cttcgacaac aactgctatg ccttttgctg ctgggtgtta gacctcaatg
541 actcatggct tagcaggagg atggtgcaaa gaacgacggg cttcttcaga ccttaccaag
601 agtggaatag aaaacccctg cctaccatgg atgactccaa aattaagaag gtggcaaata
661 tattcctatg ttcattgtcc acattgttca ccagacccat aaaagacctc atagggaaaa
721 ttaaaccatt aaacatactg aacatcctgg caacgtgtga ctggacgttt gccggaatag
781 tggagtctct gatattactt gctgagctct tcggagtttt ctggacaccc ccagatgtgt
841 ctgctatgat cgctccctta ctcggggact acgagttgca agggccagaa gaccttgccg
901 ttgaactcgt acctgtggta atgggaggga ttggtttggt gttgggattc accaaagaga
961 gaattggcaa aatgttgtcc tcagcagcat caacactcag ggcttgcaaa gatcttggtg
1021 cctatggctt agagatactc aaattagtca tgaagtggtt cttcccaaag aaagaggagg
1081 ccaatgagct agccatggtg agggccatag aggatgccgt actagatctt gaggcaatag
1141 aaaataacca catgacaacc ctgttgaaag acaaagacag cttagcaaca tacatgaaaa
1201 cactggacat ggaggaggag aaagccagaa ggttgtccac aaaatctgca tcccctgaca
1261 tagttgggac aatcaacgcc ctactggctc ggatagcagc ggccaggtca ttagtccaca
1321 gggccaagga agagctatct agcaggataa gaccagtagt tgttatgata tctggcaaac
1381 caggaatagg caaaactcat ctggccaggg aggtggcaag aaaggtggca tctactctca
1441 caggggatca aagagtcgga ctcataccaa gaaacggtgt ggaccattgg gatgcataca
1501 aaggtgagag agtcgtgctg tgggacgact atggcatgag taaccccatt catgatgctc
1561 ttcgcataca agaattggct gatacgtgtc ccctcacctt aaactgtgac agaattgaaa
1621 ataagggaaa agtttttgac agtgaagtca taataattac aacaaacctt gccaatccag
1681 ccccacttga ttatgtcaac tttgaggcct gttccaggag aattgatttc ctggtgtacg
1741 ctgaggcacc agaagtagaa aaggcaaaac gggattttcc tggtcagcca gatatgtgga
1801 aggatgcctt taagccggac ttttcacaca tcaagctaca gcttgcacct cagggcggct
1861 ttgacaagaa tggcaacacc ccacatggga aaggagtgat gaagaccctc actaccggtt
1921 ctctgattgc ccgtgcatca ggcctactgc atgagaggat ggatgaattt gaactccaag
1981 gtcccacaat caccaccttc aatttcgacc ggaacagaat cacagcattc agacaactgg
2041 ctgcagaaaa caagtatgga ttggtggaca ccatgaaagt tggcaatcaa ctaaaaggag
2101 tgaaaaccat ggaagaactc aaacaagcaa tcaggaatgt gaccatcaag aggtgccgga
2161 tcatctacgg tggctccacg tatgaccttg aatctgatgg caagggtaaa gttttggtgg
2221 aaaaggtcaa gaacacctct gtacagacca acaacgagtt ggccggggcc ctgcaccatc
2281 tcaaacacgc ccgaatcagg tactatgtca aatgtgtgca agaagcagtc tattccatca
2341 tacaaattgc cggcgctgcg ttcgtcacca cgcgcattgc acgccgcatg aacatacaag
2401 aactctggtc gaaaccacaa ttagatcaaa atgaatcaga gactaaggaa gaggtcccca
2461 agtcagaaga tgacgagttc atcatatctt ctaaggacat caaggaggaa ggaaagaagg
2521 gcaaaaacaa aactggccgt ggtaagaaac acactgcatt ctccagcaag ggtttgagcg
2581 atgaggagta tgacgagtac aagaggataa gagaagagag aaatgggaag tactctatag
2641 aggagtatct tcaagacaga gacaggtact atgaggagct cgccattgcc aaggccacgg
2701 aagaagactt ctgtgaagag gaggagatca aaatccgtca gagaattttc cgtcccacca
2761 ggaaacaaag aaaggaagag agggccacat tagggctagt aacaggttca gaaatcagaa
2821 aaagaaaccc tgatgacttc aaacccaaag ggaagctgtg ggccgacgac aacagaagtg
2881 ttgactacaa tgagaaactg gactttgagg cccccccaag catatggtct aggattgtga
2941 gctttggttc tggctggggc ttctgggtat caccaagcct gttcataaca tcaactcacg
3001 tgatccccgc aggcgtaaca gaagcgtttg gagtccccat caaacaaatt cagatccaca
3061 aatcaggtga attttgtcga ttcagattcc caaaaccaat tagaccagat gtgacaggaa
3121 tgatcttgga agaaggtgcg cctgaaggca ccgtggcaac tgtgctcatc aaacgcccca
3181 ccggagagct catgcctctt gcagccagaa tgggaacaca cgcaaccatg aaaattcaag
3241 gccgcatggt tggtggacag atgggtatgt tgctcactgg gtcaaatgct aaagggatgg
3301 atttggggac aactcctggt gactgtggct gtccctacat ctataaaagg ggcaatgact
3361 atgtagtcat tggggtgcac actgcagcag cccgtggtgg aaacaccgtc atctgtgcca
3421 cacagggaag tgagggtgag gcaactcttg agggtggaga tgacaaagga acatactgtg
3481 gggcacccat tctaggccct gggggtgcac caaaattgag caccaaaacc aaattttgga
3541 ggtcatcgaa cacgcccctt ccaccaggga catatgagcc tgcctacctc ggtggccgtg
3601 atccgcgtgt taagggtggg ccctccttgc agcaggtaat gagagaccag ttgaagccat
3661 tcactgaacc caggggcaaa cctccaagac caagtgtatt ggaagcagcc aaacaaacca
3721 ttatcaatgt cctcgaacaa actctggacc ctccacaaaa atggacatac gcacaggcgt
3781 gtgcctcact tgacaaaacc acctccagcg ggcatcccca tcacgtccga aagaatgaat
3841 tctggaatgg tgagaccttc actggtaaat tggcagacca agcatcaaaa gcaaacctaa
3901 tgtttgagga agggaaacac atgacaccag tgtatacagc agcactcaag gacgagctag
3961 tcaagaccga gaaaatctat ggaaagatca agaagagact gctctggggc tctgacttgt
4021 ccaccatgat ccggtgcgct aggtcatttg gtgggctcat ggatgagatg aagacacact
4081 gcatatcact cccagtacga gttggcatga atatgaatga agatggccca ataatatttg
4141 agaaacattc cagatacaaa taccactatg atgcagacta ctctcgttgg gattcaacac
4201 aacagagggc agtactagca gcagccttgg aaatcatggt cagattctct gcagaaccac
4261 aattggcaca aatagtcgct gaggatctgc tggcccctag tgtggtagat gtaggagact
4321 ttaagatcac aataaatgaa gggctcccat ctggtgtgcc atgcacttct caatggaact
4381 ccatcgcaca ctggctgcta actctctgtg ccttgtctga agtcaccaaa ctgtcccctg
4441 acattataca agcaaattcc atgttctcat tttacggtga tgacgagatt gtcagcaccg
4501 acataaaatt ggaccctgaa cagttaaccg ccaagttgaa ggagtacggc ctgaaaccaa
4561 cccgcccaga caagaccgag ggacccttga tcatcagtga agatttgaac ggactcactt
4621 tcctccgaag aacggtgact cgtgacccag ctggctggtt tggaaaactg gaccaaagct
4681 caattttgag gcagatgtac tggactagag gaccaaatca tgaagacccc aatgagacaa
4741 tgatacccca ttctcaaaga cccatacagc tcatggcact gcttggtgaa gcctctctcc
4801 acggaccctc tttctacagc aaaatcagta aattggtcat aactgaactc aaagaaggtg
4861 ggatggactt ttacgtgcca aggcaggaac ccatgttcag gtggatgagg ttttctgact
4921 tgagcacgtg ggagggcgat cgcaatctgg ctcccaattt tgtgaatgaa gatggcgtcg
4981 agtgacgcca acccatctga tgggtccgca gccaacctcg taccagaggt caacaatgag
5041 gttatggctt tggaacccgt tgttggtgcc gctattgcgg cacctgtagc gggccaacaa
5101 aatgtaattg acccctggat tagaaataat tttgtacaag cccctggtgg ggagtttaca
5161 gtatccccta gaaacgctcc aggtgaaata ctatggagcg cgcccctagg ccctgaccta
5221 aatccctacc tatcccattt ggccagaatg tataatggtt atgcaggtgg ttttgaagtg
5281 caggtaattc tcgcggggaa cgcgttcacc gccgggaaga tcatatttgc agcagtccca
5341 ccaaattttc caactgaagg cttaagtcct agccaggtca ctatgttccc ccatataata
5401 gtagatgtta gacaattaga acctgtgctg attcccttac ccgatgttag gaataatttc
5461 tatcattata atcagtcaaa tgattccact attaagttga tagcaatgtt gtatacacca
5521 cttagggcta ataatgctgg ggatgatgtt ttcacagttt cgtgccgagt tctcacgaga
5581 ccatcccccg attttgattt catattttta gtgccaccca cagttgagtc aagaactaaa
5641 ccattctcta tcccagtctt aactgttgag gagatgacca attcaagatt ccccattcct
5701 ttggaaaagt tgttcacggg ccccagcagt gcctttgttg ttcaaccaca aaacggcagg
5761 tgcacaactg atggcgtgct cctaggcacc acccaactgt ctcctgtcaa catctgcacc
5821 ttcagagggg atgtcactca catcacaggt agtcgcaact acacaatgaa tttggcttct
5881 caaaattgga acaactatga cccaacagaa gaaatcccag cccctctagg aactccagat
5941 tttgtgggga agattcaagg catgctcacc caaaccacaa ggacagatgg ttcaacacgc
6001 ggccacaaag ctacagtgta cactgggagc gccgactttg ctccaaaact gggtagagtt
6061 caatttgaaa ctgacacaga ccgtgatttt gaggctaatc aaaacacaaa gttcacccca
6121 gtcggtgtca tccaagatgg tagcaccacc caccgaaacg aaccccaaca gtgggtgctc
6181 ccaagttact caggcagaaa cactcacaat gtacatctgg cccccgctgt agcccccacc
6241 tttccgggtg agcaacttct cttcttcaga tccaccatgc ccggatgcag cgggtacccc
6301 aacatggatt tggactgtct gctcccccag gaatgggtgc agtactttta ccaagaggca
6361 gccccagcac aatctgatgt ggccctgcta agatttgtga atccagacac aggtagggtt
6421 ttgtttgagt gcaagcttca caaatcaggc tatgttacag tggctcacac tggccaacat
6481 gatctggtta tcccccccaa tggttacttt aggtttgact cctgggtcaa ccagttctac
6541 acacttgccc ccatgggaaa tggaacgggg cgtaggcgtg tagtataatg gctggagctt
6601 tctttgctgg attggcatct gatgtccttg gctctggact tggttccctt atcaatgctg
6661 gggctggggc catcaaccaa aaagttgagt ttgaaaataa cagaaaattg caacaagcat
6721 ccttccaatt tagcagcaat ctgcaacagg cttcctttca acatgataaa gagatgctcc
6781 aagcacaaat tgaggccacc aaaaagctac aacaggaaat gatgaaagtc aagcaggcag
6841 tgctcctaga gggtgggttc tctgagacag atgcagcccg cggggcaatt aacgccccca
6901 tgacaaaagc tttggactgg agcgggacaa ggtactgggc tcccgatgct aggactacaa
6961 catacaatgc aggccgcttt tccacccctc aaccatcggg ggcactgcca gggagagcta
7021 accttaggga tgctgtccct gctcggggac cctccaacaa atcttctaat tcttctactg
7081 ccacctctgt gtattcaaat caaactattt caacgagact tggttctaca gctggttctg
7141 gaaccagtgt ctcgagcctc ccgtcaactg caaggactag gagctgggtt g
//