Typing tool
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Typing tool
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Complete norovirus genomes
| MH260503 | GII.4 Sydney | |
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| GII.P16 |
ORF1: 1..4875
ORF2: 4856..6478
ORF3: 6478..7284
LOCUS MH260503 7300 bp RNA linear VRL 16-JUN-2018
DEFINITION Norovirus GII isolate ST114 nonstructural polyprotein (ORF1) gene,
partial cds; and VP1 (ORF2) and VP2 (ORF3) genes, complete cds.
ACCESSION MH260503
VERSION MH260503.1
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 7300)
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JOURNAL Unpublished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 7300)
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..7300
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="ST114"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="USA"
/collection_date="2017"
/note="genotype: GII"
gene <1..4875
/gene="ORF1"
CDS <1..4875
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="AWT08365.1"
/translation="EEEEEPVIRYGVKSGISGLPELTTVPQPDVANTAFSVPPLSLRE
NREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAAISMARVELAPLSLYWRV
VYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLNDSWLSRRMVQRTTGFFR
PYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLIGKIKPLNILNILATCDW
TFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLALELVPVVMGGIGL
VLGFTKERIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEANELAMVRAIE
DAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRLSTKSASPDIVGTINALL
ARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAREVARKVASTLTGDQRVG
LIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELADTCPLTLNCDRIENKGKV
FDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRDFPGQPDMWKDA
FKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLHERMDEFELQG
PTITTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVKTMEELKQAIRNVTIKRC
RIIYGGSTYDLESDGKGKVLVEKVKNTSVQTNNELAGALHHLKHARIRYYVKCVQEAV
YSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEEVPKSEDDEFIISSKDIK
EEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEEYLQDRDRYYEE
LAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLVTGSEIRKRNPDDFKPKG
KLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSPSLFITSTHVIPAGVTEA
FGVPIKQIQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEGTVATVLIKRPTGELMPL
AARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDCGCPYIYKRGNDYVVIG
VHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILGPGGAPKLSTKTKFWRSS
NTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPRGKPPRPSVLEAAKQTI
INVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFWNGETFTGKLADQASKAN
LMFEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDLSTMIRCARSFGGLMDEM
KTHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWDSTQQRAVLAAALEIMVR
FSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCTSQWNSIAHWLLTLCALS
EVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLKEYGLKPTRPDKTEGPLI
ISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGPNHEDPNETMIPHSQRPI
QLMALLGEASLHGPSFYSKISKLVITELKEGGMDFYVPRQEPMFRWMRFSDLSTWEGD
RNLAPNFVNEDGVE"
mat_peptide <1..771
/gene="ORF1"
/product="p48"
mat_peptide 772..1869
/gene="ORF1"
/product="NTPase"
mat_peptide 1870..2400
/gene="ORF1"
/product="p22"
mat_peptide 2401..2799
/gene="ORF1"
/product="VPg"
mat_peptide 2800..3342
/gene="ORF1"
/product="Pro"
mat_peptide 3343..4872
/gene="ORF1"
/product="RdRp"
gene 4856..6478
/gene="ORF2"
CDS 4856..6478
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="AWT08363.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSIPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML
TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDRDFEANQNTKFTPVGVIQDG
STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRVV"
gene 6478..7284
/gene="ORF3"
CDS 6478..7284
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="AWT08364.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAVLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRDAVPARGPSNKSS
NSSTATSVYSNQTISTRLGSTAGSGTSVSSLPSTARTRSWVEDQSRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRV"
ORIGIN
1 gaagaagaag aggaaccagt cattaggtat ggggttaaaa gtgggatctc tggcctgccc
61 gagctcacaa cagtccccca accggacgtg gccaacacag cattcagtgt tccaccactg
121 agcttgagag aaaacaggga ggccaaggaa ccgctaacag gggcgatatt agagatgtgg
181 gatggagaga tataccacta tggcctgtac gtggagaaag gcttagtgtt gggtgtgcac
241 aaaccacctg cagccataag catggcaaga gtggagctgg cgccgctttc attgtactgg
301 cgtgtggtgt acactcccca atacctcatc tcccctgaaa ctctcaggag gctcaacgga
361 gaggcgttcc cttacaccgc cttcgacaac aactgctatg ccttttgctg ctgggtgtta
421 gacctcaatg actcatggct tagcaggagg atggtgcaaa gaacgacggg cttcttcaga
481 ccttaccaag agtggaatag aaaacccctg cctaccatgg atgactccaa aattaagaag
541 gtggcaaata tattcctatg ttcattgtcc acattgttca ccagacccat aaaagacctc
601 ataggaaaaa ttaaaccatt aaacatattg aacatcctgg caacgtgtga ctggacgttt
661 gccggaatag tggagtctct gatattactt gctgagctct tcggagtttt ctggacaccc
721 ccagatgtgt ctgctatgat cgctccctta ctcggggact acgagttgca agggccagaa
781 gaccttgccc ttgaactcgt acctgtggta atgggaggga ttggtttggt gttgggattc
841 accaaagaga gaattggcaa aatgttgtcc tcagcagcat caacactcag ggcttgcaaa
901 gatcttggtg cctatggctt agagatactc aaattagtca tgaagtggtt cttcccaaag
961 aaagaggagg ccaatgagct agccatggtg agggccatag aggatgccgt actagatctt
1021 gaggcaatag aaaataacca catgacaacc ctgttgaaag acaaagacag cttagcaaca
1081 tacatgaaaa cactggacat ggaggaggag aaagccagaa ggttgtccac aaaatctgca
1141 tcccctgaca tagttgggac aatcaacgcc ctactggctc ggatagcagc ggccaggtca
1201 ttagtccaca gggccaagga agagctatct agcaggataa gaccagtagt tgttatgata
1261 tctggcaaac caggaatagg caaaactcat ctggccaggg aggtggcaag aaaggtggca
1321 tctactctca caggggatca aagagtcgga ctcataccaa gaaacggtgt ggaccattgg
1381 gatgcataca aaggtgagag agtcgtgctg tgggacgact atggcatgag taaccccatt
1441 catgatgctc ttcgcataca agaattggct gatacgtgtc ccctcacctt aaactgtgac
1501 agaattgaaa ataagggaaa agtttttgac agtgaagtca taataattac aacaaacctt
1561 gccaatccag ccccacttga ttatgtcaac tttgaggcct gttccaggag aattgatttc
1621 ctggtgtacg ctgaggcacc agaagtagaa aaggcaaaac gggattttcc tggtcagcca
1681 gatatgtgga aggatgcctt taagccggac ttttcacaca tcaagctaca gcttgcacct
1741 cagggcggct ttgacaagaa tggcaacacc ccacatggga aaggagtgat gaagaccctc
1801 actaccggtt ctctgattgc ccgtgcatca ggcctactgc atgagaggat ggatgaattt
1861 gaactccaag gtcccacaat caccaccttc aatttcgacc ggaacagaat cacagcattc
1921 agacaactgg ctgcagaaaa caagtatgga ttggtggaca ccatgaaagt tggcaatcaa
1981 ctaaaaggag tgaaaaccat ggaagaactc aaacaagcaa tcaggaatgt gaccatcaag
2041 aggtgccgga tcatctacgg tggctccacg tatgaccttg aatctgatgg caagggtaaa
2101 gttttggtgg aaaaggtcaa gaacacctct gtacagacca acaacgagtt ggccggggcc
2161 ctgcaccatc tcaaacacgc ccgaatcagg tactatgtca aatgtgtgca agaagcagtc
2221 tattccatca tacaaattgc cggcgctgcg ttcgtcacca cgcgcattgc acgccgcatg
2281 aacatacaag aactctggtc gaaaccacaa ttagatcaaa atgaatcaga gactaaggaa
2341 gaggtcccca agtcagaaga tgacgagttc atcatatctt ctaaggacat caaggaggaa
2401 ggaaagaagg gcaaaaacaa aactggccgt ggtaagaaac acactgcatt ctccagcaag
2461 ggtttgagcg atgaggagta tgacgagtac aagaggataa gagaagagag aaatgggaag
2521 tactctatag aggagtatct tcaagacaga gacaggtact atgaggagct cgccattgcc
2581 aaggccacgg aagaagactt ctgtgaagag gaggagatca aaatccgtca gagaattttc
2641 cgtcccacca ggaaacaaag aaaggaagag agggccacat tagggctagt aacaggttca
2701 gaaatcagaa aaagaaaccc tgatgacttc aaacccaaag ggaagctgtg ggccgacgac
2761 aacagaagtg ttgactacaa tgagaaactg gactttgagg cccccccaag catatggtct
2821 aggattgtga gctttggttc tggctggggc ttctgggtat caccaagcct gttcataaca
2881 tcaactcacg tgatccccgc aggcgtaaca gaagcgtttg gagtccccat caaacaaatt
2941 cagatccaca aatcaggtga attttgtcga ttcagattcc caaaaccaat tagaccagat
3001 gtgacaggaa tgatcttgga agaaggtgcg cctgaaggca ccgtggcaac tgtgctcatc
3061 aaacgcccca ccggagagct catgcctctt gcagccagaa tgggaacaca cgcaaccatg
3121 aaaattcaag gccgcatggt tggtggacag atgggtatgt tgctcactgg gtcaaatgct
3181 aaagggatgg atttggggac aactcctggt gactgtggct gtccctacat ctataaaagg
3241 ggcaatgact atgtagtcat tggggtgcac actgcagcag cccgtggtgg aaacaccgtc
3301 atctgtgcca cacagggaag tgagggtgag gcaactcttg agggtggaga tgacaaagga
3361 acatactgtg gggcacccat tctaggccct gggggtgcac caaaattgag caccaaaacc
3421 aaattttgga ggtcatcgaa cacgcccctt ccaccaggga catatgagcc tgcctacctc
3481 ggtggccgtg atccgcgtgt taagggtggg ccctccttgc agcaggtaat gagagaccag
3541 ttgaagccat tcactgaacc caggggcaaa cctccaagac caagtgtatt ggaagcagcc
3601 aaacaaacca ttatcaatgt cctcgaacaa actctggacc ctccacaaaa atggacatac
3661 gcacaggcgt gtgcctcact tgacaaaacc acctccagcg ggcatcccca tcacgtccga
3721 aagaatgaat tctggaatgg tgagaccttc actggtaaat tggcagacca agcatcaaaa
3781 gcaaacctaa tgtttgagga agggaaacac atgacaccag tgtatacagc agcactcaag
3841 gacgagctag tcaagaccga gaaaatctat ggaaagatca agaagagact gctctggggc
3901 tctgacttgt ccaccatgat ccggtgcgct aggtcatttg gtgggctcat ggatgagatg
3961 aagacacact gcatatcact cccagtacga gttggcatga atatgaatga agatggccca
4021 ataatatttg agaaacattc cagatacaaa taccactatg atgcagacta ctctcgttgg
4081 gattcaacac aacagagggc agtactagca gcagccttgg aaatcatggt cagattctct
4141 gcagaaccac aattggcaca aatagtcgct gaggatctgc tggcccctag tgtggtagat
4201 gtaggagact ttaagatcac aataaatgaa gggctcccat ctggtgtgcc atgcacttct
4261 caatggaact ccatcgcaca ctggctgcta actctctgtg ccttgtctga agtcaccaaa
4321 ctgtcccctg acattataca agcaaattcc atgttctcat tttacggtga tgacgagatt
4381 gtcagcaccg acataaaatt ggaccctgaa cagttaaccg ccaagttgaa ggagtacggc
4441 ctgaaaccaa cccgcccaga caagaccgag ggacccttga tcatcagtga agatttgaac
4501 ggactcactt tcctccgaag aacggtgact cgtgacccag ctggctggtt tggaaaactg
4561 gaccaaagct caattttgag gcagatgtac tggactagag gaccaaatca tgaagacccc
4621 aatgagacaa tgatacccca ttctcaaaga cccatacagc tcatggcact gcttggtgaa
4681 gcctctctcc acggaccctc tttctacagc aaaatcagta aattggtcat aactgaactc
4741 aaagaaggtg ggatggactt ttacgtgcca aggcaggaac ccatgttcag gtggatgagg
4801 ttttctgact tgagcacgtg ggagggcgat cgcaatctgg ctcccaattt tgtgaatgaa
4861 gatggcgtcg agtgacgcca acccatctga tgggtccgca gccaacctcg taccagaggt
4921 caacaatgag gttatggctt tggaacccgt tgttggtgcc gctattgcgg cacctgtagc
4981 gggccaacaa aatgtaattg acccctggat tagaaataat tttgtacaag cccctggtgg
5041 ggagtttaca gtatccccta gaaacgctcc aggtgaaata ctatggagcg cgcccctagg
5101 ccctgaccta aatccctacc tatcccattt ggccagaatg tataatggtt atgcaggtgg
5161 ttttgaagtg caggtaattc tcgcggggaa cgcgttcacc gccgggaaga tcatatttgc
5221 agcagtccca ccaaattttc caactgaagg cttaagtcct agccaggtca ctatgttccc
5281 ccatataata gtagatgtta gacaattaga acctgtgctg attcccttac ccgatgttag
5341 gaataatttc tatcattata atcagtcaaa tgattccact attaagttga tagcaatgtt
5401 gtatacacca cttagggcta ataatgctgg ggatgatgtt ttcacagttt cgtgccgagt
5461 tctcacgaga ccatcccccg attttgattt catattttta gtgccaccca cagttgagtc
5521 aagaactaaa ccattctcta tcccagtctt aactgttgag gagatgacca attcaagatt
5581 ccccattcct ttggaaaagt tgttcacggg ccccagcagt gcctttgttg ttcaaccaca
5641 aaacggcagg tgcacaactg atggcgtgct cctaggcacc acccaactgt ctcctgtcaa
5701 catctgcacc ttcagagggg atgtcactca catcacaggt agtcgcaact acacaatgaa
5761 tttggcttct caaaattgga acaactatga cccaacagaa gaaatcccag cccctctagg
5821 aactccagat tttgtgggga agattcaagg catgctcacc caaaccacaa ggacagatgg
5881 ttcaacacgc ggccacaaag ctacagtgta cactgggagc gccgactttg ctccaaaact
5941 gggtagagtt caatttgaaa ctgacacaga ccgtgatttt gaggctaatc aaaacacaaa
6001 gttcacccca gtcggtgtca tccaagatgg tagcaccacc caccgaaacg aaccccaaca
6061 gtgggtgctc ccaagttact caggcagaaa cactcacaat gtacatctgg cccccgctgt
6121 agcccccacc tttccgggtg agcaacttct cttcttcaga tccaccatgc ccggatgcag
6181 cgggtacccc aacatggatt tggactgtct gctcccccag gaatgggtgc agtactttta
6241 ccaagaggca gccccagcac aatctgatgt ggccctgcta agatttgtga atccagacac
6301 aggtagggtt ttgtttgagt gcaagcttca caaatcaggc tatgttacag tggctcacac
6361 tggccaacat gatctggtta tcccccccaa tggttacttt aggtttgact cctgggtcaa
6421 ccagttctac acacttgccc ccatgggaaa tggaacgggg cgtaggcgtg tagtataatg
6481 gctggagctt tctttgctgg attggcatct gatgtccttg gctctggact tggttccctt
6541 atcaatgctg gggctggggc catcaaccaa aaagttgagt ttgaaaataa cagaaaattg
6601 caacaagcat ccttccaatt tagcagcaat ctgcaacagg cttcctttca acatgataaa
6661 gagatgctcc aagcacaaat tgaggccacc aaaaagctac aacaggaaat gatgaaagtc
6721 aagcaggcag tgctcctaga gggtgggttc tctgagacag atgcagcccg cggggcaatt
6781 aacgccccca tgacaaaagc tttggactgg agcgggacaa ggtactgggc tcccgatgct
6841 aggactacaa catacaatgc aggccgcttt tccacccctc aaccatcggg ggcactgcca
6901 gggagagcta accttaggga tgctgtccct gctcggggac cctccaacaa atcttctaac
6961 tcttccactg ccacctctgt gtattcaaat caaactattt caacgagact tggttctaca
7021 gctggttctg gaaccagtgt ctcgagcctc ccgtcaactg caaggactag gagctgggtt
7081 gaggatcaaa gtaggaattt gtcacctttc atgagggggg cccacaatat atcatttgtc
7141 accccaccat ctagcagatc ctctagccaa ggcacagtct caaccgtgcc taaagagatt
7201 ttggactcct ggactggcgc cttcaacacg cgcaggcagc ctctcttcgc tcacattcgt
7261 aagcgagggg agtcacgggt gtaatgtgaa aagacaaaac
//