Typing tool
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Typing tool
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Complete norovirus genomes
| MH260496 | GII.4 Sydney | |
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| GII.P16 |
ORF1: 1..5077
ORF2: 5058..6680
ORF3: 6680..7449
LOCUS MH260496 7449 bp RNA linear VRL 16-JUN-2018
DEFINITION Norovirus GII isolate ST165 nonstructural polyprotein (ORF1) gene,
partial cds; VP1 (ORF2) gene, complete cds; and VP2 (ORF3) gene,
partial cds.
ACCESSION MH260496
VERSION MH260496.1
DBLINK BioProject: PRJNA338014
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norovirus norwalkense.
REFERENCE 1 (bases 1 to 7449)
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JOURNAL Unpublished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 7449)
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..7449
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="ST165"
/host="Homo sapiens"
/db_xref="taxon:122929"
/geo_loc_name="USA"
/collection_date="2017"
/note="genotype: GII"
gene <1..5077
/gene="ORF1"
CDS <1..5077
/gene="ORF1"
/codon_start=2
/product="nonstructural polyprotein"
/protein_id="AWT08342.1"
/translation="TVAVACNNNNDKEKSSGEGLFTNMSSTLKKALGARPKQPAPRDE
PQKPPRPPTPELVKRIPPPPPNGEEEEEPVIRYEVKSGISGLPELTTVPQPDVANTAF
SVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAAISMARVEL
APLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLNDSWLSRRM
VQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLIGKIKPLNI
LNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVELV
PVVMGGIGLVLGFTKERIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEAN
ELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKALDMEEEKARRLSTKSASPD
IVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAREVARKVAS
TLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELADTCPLTLNC
DRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRDFP
GQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLHE
RMDEFELQGPTITTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVKTMEELKQA
IRNVTIKRCRIIYGGSTYDLESDGKGKVLVEKVKNTSVQTNNELAGALHHLKHARIRY
YVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEEVPKSEDDE
FIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEEYL
QDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLVTGSEIRKR
NPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSPSLFITSTH
VIPAGVTEAFGVPIKQIQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEGTVATVLIK
RPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDCGCPYIYK
RGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILGPGGAPKLS
TKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPRGKPPRPN
VLEAAKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFWNGETFTGK
LADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDLSTMIRCAR
SFGGLMDEMKTHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWDSTQQRAVL
AAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCTSQWNSIAH
WLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLKEYGLKPTR
PDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGPNHEDPNET
MIPHSQRPIQLMALLGEASLHGPSFYSKISKLVITELKEGGMDFYVPRQEPMFRWMRF
SDLSTWEGDRNLAPNFVNEDGVE"
mat_peptide <1..973
/gene="ORF1"
/product="p48"
mat_peptide 974..2071
/gene="ORF1"
/product="NTPase"
mat_peptide 2072..2602
/gene="ORF1"
/product="p22"
mat_peptide 2603..3001
/gene="ORF1"
/product="VPg"
mat_peptide 3002..3544
/gene="ORF1"
/product="Pro"
mat_peptide 3545..5074
/gene="ORF1"
/product="RdRp"
gene 5058..6680
/gene="ORF2"
CDS 5058..6680
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="AWT08343.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYSQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSIPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML
TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG
STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRVV"
gene 6680..>7449
/gene="ORF3"
CDS 6680..>7449
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="AWT08344.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAVLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRDTVPARGPSNKSS
NSSTATSVYSNQTISTRLGSTAGSGTSVSSLPSTARTRSWVEDQSRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPL"
ORIGIN
1 taccgttgcc gttgcttgca acaacaacaa cgacaaggaa aaatcttcag gtgaaggctt
61 attcacaaat atgtcttcca ccttaaagaa agccctcggg gctaggccca aacagcctgc
121 cccgagagac gaaccacaaa agcccccaag accaccaact cccgagttgg tcaagaggat
181 accccctcct ccacctaatg gcgaagaaga agaggaacca gtcattaggt atgaggttaa
241 gagtgggatc tctggcctgc ccgagctcac aacagtcccc caaccggacg tggccaacac
301 agcattcagt gttccaccac tgagcttgag agaaaacagg gaggccaagg aaccgctaac
361 aggggcgata ttagagatgt gggatggaga gatataccac tatggcctgt acgtggagaa
421 aggcttagtg ttgggtgtgc acaaaccacc tgcagccata agcatggcaa gagtggagct
481 ggcgccgctt tcattgtact ggcgtgtggt gtacactccc caatacctca tctcccctga
541 aactctcagg aggctcaacg gagaggcgtt cccttacacc gccttcgaca acaactgcta
601 tgccttttgc tgctgggtgt tagacctcaa tgactcatgg cttagcagga ggatggtgca
661 aagaacgacg ggcttcttca gaccttacca agagtggaac agaaaacccc tgcctaccat
721 ggatgactcc aaaattaaga aggtggcaaa tatattccta tgttcattgt ccacattgtt
781 caccagaccc ataaaagacc tcatagggaa aattaaacca ttaaacatac tgaacatcct
841 ggcaacgtgt gactggacgt ttgccggaat agtggagtct ctgatattac ttgctgagct
901 cttcggagtt ttctggacac ccccagatgt gtctgctatg atcgctccct tactcgggga
961 ctacgagttg caagggccag aagaccttgc cgttgaactc gtacctgtgg taatgggagg
1021 gattggtttg gtgttgggat tcaccaaaga gagaattggc aaaatgttgt cctcagcagc
1081 atcaacactc agggcttgca aagatcttgg tgcctatggc ttagagatac tcaaattagt
1141 catgaagtgg ttcttcccaa agaaagagga ggccaatgag ctagccatgg tgagggccat
1201 agaggatgcc gtactagatc ttgaggcaat agaaaataac cacatgacaa ccctgttgaa
1261 agacaaagac agcttagcaa catacatgaa agcactggac atggaggagg agaaagccag
1321 aaggttgtcc acaaaatctg catcccctga catagttggg acaatcaacg ccctactggc
1381 tcggatagca gcggccaggt cattagtcca cagggccaag gaagagctat ctagcaggat
1441 aagaccagta gttgttatga tatctggcaa accaggaata ggcaaaactc atctggccag
1501 ggaggtggca agaaaggtgg catctactct cacaggggat caaagagtcg gactcatacc
1561 aagaaacggt gtggaccatt gggatgcata caaaggtgag agagtcgtgc tgtgggacga
1621 ctatggcatg agtaacccca ttcatgatgc tcttcgcata caagaattgg ctgatacgtg
1681 tcccctcacc ttaaactgtg acagaattga aaataaggga aaagtttttg acagtgaagt
1741 cataataatt acaacaaacc ttgccaatcc agccccactt gattatgtca actttgaggc
1801 ctgttccagg agaattgatt tcctggtgta cgctgaggca ccagaagtag aaaaggcaaa
1861 acgggatttt cctggtcagc cagatatgtg gaaggatgcc tttaaaccgg acttttcaca
1921 catcaagcta cagcttgcac ctcagggcgg ctttgacaag aatggcaaca ccccacatgg
1981 gaaaggagtg atgaagaccc tcactaccgg ttctctgatt gcccgtgcat caggcctact
2041 gcatgagagg atggatgaat ttgaactcca aggtcccaca atcaccacct tcaatttcga
2101 ccggaacaga atcacagcat tcagacaact ggctgcagaa aacaagtatg gattggtgga
2161 caccatgaaa gttggcaatc aactaaaagg agtgaaaacc atggaagaac tcaaacaagc
2221 aatcaggaat gtgaccatca agaggtgccg gatcatctac ggtggctcca cgtatgacct
2281 tgaatctgat ggcaagggta aagttttggt ggaaaaggtc aagaacacct ctgtacagac
2341 caacaacgag ttggccgggg ccctgcacca tctcaaacac gcccgaatca ggtactatgt
2401 caaatgtgtg caagaagcag tctattccat catacaaatt gccggcgctg cgttcgtcac
2461 cacgcgcatt gcacgccgca tgaacataca agaactctgg tcgaaaccac aattagatca
2521 aaatgaatca gagactaagg aagaggtccc caagtcagaa gatgacgagt tcatcatatc
2581 ttctaaggac atcaaggagg aaggaaagaa gggcaaaaac aaaactggcc gtggtaagaa
2641 acacactgca ttctccagca agggtttgag cgatgaggag tatgacgagt acaagaggat
2701 aagagaagag agaaatggga agtactctat agaggagtat cttcaagaca gagacaggta
2761 ctatgaggag ctcgccattg ccaaggccac ggaagaagac ttctgtgaag aggaggagat
2821 caaaatccgt cagagaattt tccgtcccac caggaaacaa agaaaggaag agagggccac
2881 attagggcta gtaacaggtt cagaaatcag aaaaagaaac cctgatgact tcaaacccaa
2941 agggaagctg tgggccgacg acaacagaag tgttgactac aatgagaaac tggactttga
3001 ggccccccca agcatatggt ctaggattgt gagctttggt tctggctggg gcttctgggt
3061 atcaccaagc ctgttcataa catcaactca cgtgatcccc gcaggcgtaa cagaagcgtt
3121 tggagtcccc atcaaacaaa ttcagatcca caaatcaggt gaattttgtc gattcagatt
3181 cccaaaacca attagaccag atgtgacagg aatgatcttg gaagaaggtg cgcctgaagg
3241 caccgtggca actgtgctca tcaaacgccc caccggagag ctcatgcctc ttgcagccag
3301 aatgggaaca cacgcaacca tgaaaattca aggccgcatg gttggtggac agatgggtat
3361 gttgctcact gggtcaaatg ctaaagggat ggatttgggg acaactcctg gtgactgtgg
3421 ctgtccctac atctataaaa ggggcaatga ctatgtagtc attggggtgc acactgcagc
3481 agcccgtggt ggaaacaccg tcatctgtgc cacacaggga agtgagggtg aggcaactct
3541 tgagggtgga gatgacaaag gaacatactg tggggcaccc attctaggcc ctgggggtgc
3601 accaaaattg agcaccaaaa ccaaattttg gaggtcatcg aacacgcccc ttccaccagg
3661 gacatatgag cctgcctacc tcggtggccg tgatccgcgt gttaagggtg ggccctcctt
3721 gcagcaggta atgagagacc agttgaagcc attcactgaa cccaggggca aacctccaag
3781 accaaatgta ttggaagcag ccaaacaaac cattatcaat gtcctcgaac aaactctgga
3841 ccctccacaa aaatggacat acgcacaggc gtgtgcctca cttgacaaaa ccacctccag
3901 cgggcatccc catcacgtcc gaaagaatga attctggaat ggtgagacct tcactggtaa
3961 attggcagac caagcatcaa aagcaaacct aatgtttgag gaagggaaac acatgacacc
4021 agtgtataca gcagcactca aggacgagct agtcaagacc gagaaaatct atggaaagat
4081 caagaagaga ctgctctggg gctctgactt gtccaccatg atccggtgcg ctaggtcatt
4141 tggtgggctc atggatgaga tgaagacaca ctgcatatca ctcccagtac gagttggcat
4201 gaatatgaat gaagatggcc caataatatt tgagaaacat tccagataca aataccacta
4261 tgatgcagac tactctcgtt gggattcaac acaacagagg gcagtactag cagcagcctt
4321 ggaaatcatg gtcagattct ctgcagaacc acaattggca caaatagtcg ctgaggatct
4381 gctggcccct agtgtggtag atgtaggaga ctttaagatc acaataaatg aagggctccc
4441 atctggtgtg ccatgcactt ctcaatggaa ctccatcgca cactggctgc taactctctg
4501 tgccttgtct gaagtcacca aactgtcccc tgacattata caagcaaatt ccatgttctc
4561 attttacggt gatgacgaga ttgtcagcac cgacataaaa ttggaccctg aacagttaac
4621 cgccaagttg aaggagtacg gcctgaaacc aacccgccca gacaagaccg agggaccctt
4681 gatcatcagt gaagatttga acggactcac tttcctccga agaacggtga ctcgtgaccc
4741 agctggctgg tttggaaaac tggaccaaag ctcaattttg aggcagatgt actggactag
4801 aggaccaaat catgaagacc ccaatgagac aatgataccc cattctcaaa gacccataca
4861 gctcatggca ctgcttggtg aagcctctct ccacggaccc tctttctaca gcaaaatcag
4921 taaattggtc ataactgaac tcaaagaagg tgggatggac ttttacgtgc caaggcagga
4981 acccatgttc aggtggatga ggttttctga cttgagcacg tgggagggcg atcgcaatct
5041 ggctcccaat tttgtgaatg aagatggcgt cgagtgacgc caacccatct gatgggtccg
5101 cagccaacct cgtaccagag gtcaacaatg aggttatggc tttggaaccc gttgttggtg
5161 ccgctattgc ggcacctgta gcgggccaac aaaatgtaat tgacccctgg attagaaata
5221 attttgtaca agcccctggt ggggagttta cagtatcccc tagaaacgct ccaggtgaaa
5281 tactatggag cgcgccccta ggccctgacc taaatcccta cctatcccat ttggccagaa
5341 tgtataatgg ttatgcaggt ggttttgaag tgcaggtaat tctcgcgggg aacgcgttca
5401 ccgccgggaa gatcatattt gcagcagtcc caccaaattt tccaactgaa ggcttaagtc
5461 ctagccaggt cactatgttc ccccatataa tagtagatgt tagacaatta gaacctgtgc
5521 tgattccctt acccgatgtt aggaataatt tctatcatta tagtcagtca aatgattcca
5581 ctattaagtt gatagcaatg ttgtatacac cacttagggc taataatgct ggggatgatg
5641 ttttcacagt ttcgtgccga gttctcacga gaccatcccc cgattttgat ttcatatttt
5701 tagtgccacc cacagttgag tcaagaacta aaccattctc tatcccagtc ttaactgttg
5761 aggagatgac caattcaaga ttccccattc ctttggaaaa gttgttcacg ggccccagca
5821 gtgcctttgt tgttcaacca caaaacggca ggtgcacaac tgatggcgtg ctcctaggca
5881 ccacccaact gtctcctgtc aacatctgca ccttcagagg ggatgtcact cacatcacag
5941 gtagtcgcaa ctacacaatg aatttggctt ctcaaaattg gaacaactat gacccaacag
6001 aagaaatccc agcccctcta ggaactccag attttgtggg gaagattcaa ggcatgctca
6061 cccaaaccac aaggacagat ggttcaacac gcggccacaa agctacagtg tacactggga
6121 gcgccgactt tgctccaaaa ctgggtagag ttcaatttga aactgacaca gaccatgatt
6181 ttgaggctaa tcaaaacaca aagttcaccc cagtcggtgt catccaagat ggtagcacca
6241 cccaccgaaa cgaaccccaa cagtgggtgc tcccaagtta ctcaggcaga aacactcaca
6301 atgtacatct ggcccccgct gtagccccca cctttccggg tgagcaactt ctcttcttca
6361 gatccaccat gcccggatgc agcgggtacc ccaacatgga tttggactgt ctgctccccc
6421 aggaatgggt gcagtacttt taccaagagg cagccccagc acaatctgat gtggccctgc
6481 taagatttgt gaatccagac acaggtaggg ttttgtttga gtgcaagctt cacaaatcag
6541 gctatgttac agtggctcac actggccaac atgatctggt tatccccccc aatggttact
6601 ttaggtttga ctcctgggtc aaccagttct acacacttgc ccccatggga aatggaacgg
6661 ggcgtaggcg tgtagtataa tggctggagc tttctttgct ggattggcat ctgatgtcct
6721 tggctctgga cttggttccc ttatcaatgc tggggctggg gccatcaacc aaaaagttga
6781 gtttgaaaat aacagaaaat tgcaacaagc atccttccaa tttagcagca atctgcaaca
6841 ggcttccttt caacatgata aagagatgct ccaagcacaa attgaggcca ccaaaaagct
6901 acaacaggaa atgatgaaag tcaagcaggc agtgctccta gagggtgggt tctctgagac
6961 agatgcagcc cgcggggcaa ttaacgcccc catgacaaaa gctttggact ggagcgggac
7021 aaggtactgg gctcccgatg ctaggactac aacatacaat gcaggccgct tttccacccc
7081 tcaaccatcg ggggcactgc cagggagagc taaccttagg gatactgtcc ctgctcgggg
7141 accctccaac aaatcttcta actcttccac tgccacctct gtgtattcaa atcaaactat
7201 ttcaacgaga cttggttcta cagctggttc tggaaccagt gtctcgagcc tcccgtcaac
7261 tgcaaggact aggagctggg ttgaggatca aagtaggaat ttgtcacctt tcatgagggg
7321 ggcccacaat atatcatttg tcaccccacc atctagcaga tcctctagcc aaggcacagt
7381 ctcaaccgtg cctaaagaga ttttggactc ctggactggc gccttcaaca cgcgcaggca
7441 gcctctctt
//