Typing tool
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Typing tool
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Complete norovirus genomes
| MH260506 | GII.4 Sydney | |
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| GII.P16 |
ORF1: 1..5099
ORF2: 5080..6702
ORF3: 6702..7508
LOCUS MH260506 7542 bp RNA linear VRL 16-JUN-2018
DEFINITION Norovirus GII isolate ST109 nonstructural polyprotein (ORF1) gene,
partial cds; and VP1 (ORF2) and VP2 (ORF3) genes, complete cds.
ACCESSION MH260506
VERSION MH260506.1
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 7542)
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JOURNAL Unpublished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 7542)
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..7542
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="ST109"
/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="AWT08374.1"
/translation="KMASNDATVAVACNNNNDKEKSSGEGLFTNMSSTLKKALGARPK
QPAPRDEPQKPPRPPTPELVKRIPPPPPNGEEEEEPVIRYGVKSGISGLPELTTVPQP
DVANTAFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAAI
SMARVELAPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLND
SWLSRRMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLIG
KIKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPE
DLAVELVPVVMGGIGLVLGFTKERIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFF
PKKEEANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRLS
TKSASPDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLARE
VARKVASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELADT
CPLTLNCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVE
KAKRDFPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIAR
ASGLLHERMDEFELQGPTITTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVKT
MEELKQAIRNVTIKRCRIIYGGSTYDLESDGKGKVLVEKVKNTSVQTNNELAGALHHL
KHARIRYYVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEEV
PKSEDDEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGK
YSIEEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLVT
GSEIRKRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSPS
LFITSTHVIPAGVTEAFGVPIKQIQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEGT
VATVLIKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDC
GCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILGP
GGAPKLSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPR
GKPPRPSVLEAAKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFWN
GETFTGKLADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDLS
TMIRCARSFGGLMDEMKTHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWDS
TQQRAVLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCTS
QWNSIAHWLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLKE
YGLKPTRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGPN
HEDPNETMIPHSQRPIQLMALLGEASLHGPSFYSKISKLVITELKEGGMDFYVPRQEP
MFRWMRFSDLSTWEGDRNLAPNFVNEDGVE"
gene 5080..6702
/gene="ORF2"
CDS 5080..6702
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="AWT08372.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSIPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML
TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDRDFEANQNTKFTPVGVIQDG
STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRVV"
gene 6702..7508
/gene="ORF3"
CDS 6702..7508
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="AWT08373.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAVLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRDAVPARGPSNKSS
NSSTATSVYSNQTISTRLGSTAGSGTSVSSLPSTARTRSWVEDQSRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRV"
ORIGIN
1 tgaagatggc gtctaacgac gctaccgttg ccgttgcttg caacaacaac aacgacaagg
61 aaaaatcttc aggtgaaggc ttattcacaa atatgtcttc caccttaaag aaagccctcg
121 gggctaggcc caaacagcct gccccgagag acgaaccaca aaagccccca agaccaccaa
181 ctcccgagtt ggtcaagagg ataccccctc ctccacctaa tggcgaagaa gaagaggaac
241 cagtcattag gtatggggtt aaaagtggga tctctggcct gcccgagctc acaacagtcc
301 cccaaccgga cgtggccaac acagcattca gtgttccacc actgagcttg agagaaaaca
361 gggaggccaa ggaaccgcta acaggggcga tattagagat gtgggatgga gagatatacc
421 actatggcct gtacgtggag aaaggcttag tgttgggtgt gcacaaacca cctgcagcca
481 taagcatggc aagagtggag ctggcgccgc tttcattgta ctggcgtgtg gtgtacactc
541 cccaatacct catctcccct gaaactctca ggaggctcaa cggagaggcg ttcccttaca
601 ccgccttcga caacaactgc tatgcctttt gctgctgggt gttagacctc aatgactcat
661 ggcttagcag gaggatggtg caaagaacga cgggcttctt cagaccttac caagagtgga
721 atagaaaacc cctgcctacc atggatgact ccaaaattaa gaaggtggca aatatattcc
781 tatgttcatt gtccacattg ttcaccagac ccataaaaga cctcataggg aaaattaaac
841 cattaaacat actgaacatc ctggcaacgt gtgactggac gtttgccgga atagtggagt
901 ctctgatatt acttgctgag ctcttcggag ttttctggac acccccagat gtgtctgcta
961 tgatcgctcc cttactcggg gactacgagt tgcaagggcc agaagacctt gccgttgaac
1021 tcgtacctgt ggtaatggga gggattggtt tggtgttggg attcaccaaa gagagaattg
1081 gcaaaatgtt gtcctcagca gcatcaacac tcagggcttg caaagatctt ggtgcctatg
1141 gcttagagat actcaaatta gtcatgaagt ggttcttccc aaagaaagag gaggccaatg
1201 agctagccat ggtgagggcc atagaggatg ccgtactaga tcttgaggca atagaaaata
1261 accacatgac aaccctgttg aaagacaaag acagcttagc aacatacatg aaaacactgg
1321 acatggagga ggagaaagcc agaaggttgt ccacaaaatc tgcatcccct gacatagttg
1381 ggacaatcaa cgccctactg gctcggatag cagcggccag gtcattagtc cacagggcca
1441 aggaagagct atctagcagg ataagaccag tagttgttat gatatctggc aaaccaggaa
1501 taggcaaaac tcatctggcc agggaggtgg caagaaaggt ggcatctact ctcacagggg
1561 atcaaagagt cggactcata ccaagaaacg gtgtggacca ttgggatgca tacaaaggtg
1621 agagagtcgt gctgtgggac gactatggca tgagtaaccc cattcatgat gctcttcgca
1681 tacaagaatt ggctgatacg tgtcccctca ccttaaactg tgacagaatt gaaaataagg
1741 gaaaagtttt tgacagtgaa gtcataataa ttacaacaaa ccttgccaat ccagccccac
1801 ttgattatgt caactttgag gcctgttcca ggagaattga tttcctggtg tacgctgagg
1861 caccagaagt agaaaaggca aaacgggatt ttcctggtca gccagatatg tggaaggatg
1921 cctttaagcc ggacttttca cacatcaagc tacagcttgc acctcagggc ggctttgaca
1981 agaatggcaa caccccacat gggaaaggag tgatgaagac cctcactacc ggttctctga
2041 ttgcccgtgc atcaggccta ctgcatgaga ggatggatga atttgaactc caaggtccca
2101 caatcaccac cttcaatttc gaccggaaca gaatcacagc attcagacaa ctggctgcag
2161 aaaacaagta tggattggtg gacaccatga aagttggcaa tcaactaaaa ggagtgaaaa
2221 ccatggaaga actcaaacaa gcaatcagga atgtgaccat caagaggtgc cggatcatct
2281 acggtggctc cacgtatgac cttgaatctg atggcaaggg taaagttttg gtggaaaagg
2341 tcaagaacac ctctgtacag accaacaacg agttggccgg ggccctgcac catctcaaac
2401 acgcccgaat caggtactat gtcaaatgtg tgcaagaagc agtctattcc atcatacaaa
2461 ttgccggcgc tgcgttcgtc accacgcgca ttgcacgccg catgaacata caagaactct
2521 ggtcgaaacc acaattagat caaaatgaat cagagactaa ggaagaggtc cccaagtcag
2581 aagatgacga gttcatcata tcttctaagg acatcaagga ggaaggaaag aagggcaaaa
2641 acaaaactgg ccgtggtaag aaacacactg cattctccag caagggtttg agcgatgagg
2701 agtatgacga gtacaagagg ataagagaag agagaaatgg gaagtactct atagaggagt
2761 atcttcaaga cagagacagg tactatgagg agctcgccat tgccaaggcc acggaagaag
2821 acttctgtga agaggaggag atcaaaatcc gtcagagaat tttccgtccc accaggaaac
2881 aaagaaagga agagagggcc acattagggc tagtaacagg ttcagaaatc agaaaaagaa
2941 accctgatga cttcaaaccc aaagggaagc tgtgggccga cgacaacaga agtgttgact
3001 acaatgagaa actggacttt gaggcccccc caagcatatg gtctaggatt gtgagctttg
3061 gttctggctg gggcttctgg gtatcaccaa gcctgttcat aacatcaact cacgtgatcc
3121 ccgcaggcgt aacagaagcg tttggagtcc ccatcaaaca aattcagatc cacaaatcag
3181 gtgaattttg tcgattcaga ttcccaaaac caattagacc agatgtgaca ggaatgatct
3241 tggaagaagg tgcgcctgaa ggcaccgtgg caactgtgct catcaaacgc cccaccggag
3301 agctcatgcc tcttgcagcc agaatgggaa cacacgcaac catgaaaatt caaggccgca
3361 tggttggtgg acagatgggt atgttgctca ctgggtcaaa tgctaaaggg atggatttgg
3421 ggacaactcc tggtgactgt ggctgtccct acatctataa aaggggcaat gactatgtag
3481 tcattggggt gcacactgca gcagcccgtg gtggaaacac cgtcatctgt 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 ttgcagcagg taatgagaga ccagttgaag ccattcactg
3781 aacccagggg caaacctcca agaccaagtg tattggaagc agccaaacaa accattatca
3841 atgtcctcga acaaactctg gaccctccac aaaaatggac atacgcacag gcgtgtgcct
3901 cacttgacaa aaccacctcc agcgggcatc cccatcacgt ccgaaagaat gaattctgga
3961 atggtgagac cttcactggt aaattggcag accaagcatc aaaagcaaac ctaatgtttg
4021 aggaagggaa acacatgaca ccagtgtata cagcagcact caaggacgag ctagtcaaga
4081 ccgagaaaat ctatggaaag atcaagaaga gactgctctg gggctctgac ttgtccacca
4141 tgatccggtg cgctaggtca tttggtgggc tcatggatga gatgaagaca cactgcatat
4201 cactcccagt acgagttggc atgaatatga atgaagatgg cccaataata tttgagaaac
4261 attccagata caaataccac tatgatgcag actactctcg ttgggattca acacaacaga
4321 gggcagtact agcagcagcc ttggaaatca tggtcagatt ctctgcagaa ccacaattgg
4381 cacaaatagt cgctgaggat ctgctggccc ctagtgtggt agatgtagga gactttaaga
4441 tcacaataaa tgaagggctc ccatctggtg tgccatgcac ttctcaatgg aactccatcg
4501 cacactggct gctaactctc tgtgccttgt ctgaagtcac caaactgtcc cctgacatta
4561 tacaagcaaa ttccatgttc tcattttacg gtgatgacga gattgtcagc accgacataa
4621 aattggaccc tgaacagtta accgccaagt tgaaggagta cggcctgaaa ccaacccgcc
4681 cagacaagac cgagggaccc ttgatcatca gtgaagattt gaacggactc actttcctcc
4741 gaagaacggt gactcgtgac ccagctggct ggtttggaaa actggaccaa agctcaattt
4801 tgaggcagat gtactggact agaggaccaa atcatgaaga ccccaatgag acaatgatac
4861 cccattctca aagacccata cagctcatgg cactgcttgg tgaagcctct ctccacggac
4921 cctctttcta cagcaaaatc agtaaattgg tcataactga actcaaagaa ggtgggatgg
4981 acttttacgt gccaaggcag gaacccatgt tcaggtggat gaggttttct gacttgagca
5041 cgtgggaggg cgatcgcaat ctggctccca attttgtgaa tgaagatggc gtcgagtgac
5101 gccaacccat ctgatgggtc cgcagccaac ctcgtaccag aggtcaacaa tgaggttatg
5161 gctttggaac ccgttgttgg tgccgctatt gcggcacctg tagcgggcca acaaaatgta
5221 attgacccct ggattagaaa taattttgta caagcccctg gtggggagtt tacagtatcc
5281 cctagaaacg ctccaggtga aatactatgg agcgcgcccc taggccctga cctaaatccc
5341 tacctatccc atttggccag aatgtataat ggttatgcag gtggttttga agtgcaggta
5401 attctcgcgg ggaacgcgtt caccgccggg aagatcatat ttgcagcagt cccaccaaat
5461 tttccaactg aaggcttaag tcctagccag gtcactatgt tcccccatat aatagtagat
5521 gttagacaat tagaacctgt gctgattccc ttacccgatg ttaggaataa tttctatcat
5581 tataatcagt caaatgattc cactattaag ttgatagcaa tgttgtatac accacttagg
5641 gctaataatg ctggggatga tgttttcaca gtttcgtgcc gagttctcac gagaccatcc
5701 cccgattttg atttcatatt tttagtgcca cccacagttg agtcaagaac taaaccattc
5761 tctatcccag tcttaactgt tgaggagatg accaattcaa gattccccat tcctttggaa
5821 aagttgttca cgggccccag cagtgccttt gttgttcaac cacaaaacgg caggtgcaca
5881 actgatggcg tgctcctagg caccacccaa ctgtctcctg tcaacatctg caccttcaga
5941 ggggatgtca ctcacatcac aggtagtcgc aactacacaa tgaatttggc ttctcaaaat
6001 tggaacaact atgacccaac agaagaaatc ccagcccctc taggaactcc agattttgtg
6061 gggaagattc aaggcatgct cacccaaacc acaaggacag atggttcaac acgcggccac
6121 aaagctacag tgtacactgg gagcgccgac tttgctccaa aactgggtag agttcaattt
6181 gaaactgaca cagaccgtga ttttgaggct aatcaaaaca caaagttcac cccagtcggt
6241 gtcatccaag atggtagcac cacccaccga aacgaacccc aacagtgggt gctcccaagt
6301 tactcaggca gaaacactca caatgtacat ctggcccccg ctgtagcccc cacctttccg
6361 ggtgagcaac ttctcttctt cagatccacc atgcccggat gcagcgggta ccccaacatg
6421 gatttggact gtctgctccc ccaggaatgg gtgcagtact tttaccaaga ggcagcccca
6481 gcacaatctg atgtggccct gctaagattt gtgaatccag acacaggtag ggttttgttt
6541 gagtgcaagc ttcacaaatc aggctatgtt acagtggctc acactggcca acatgatctg
6601 gttatccccc ccaatggtta ctttaggttt gactcctggg tcaaccagtt ctacacactt
6661 gcccccatgg gaaatggaac ggggcgtagg cgtgtagtat aatggctgga gctttctttg
6721 ctggattggc atctgatgtc cttggctctg gacttggttc ccttatcaat gctggggctg
6781 gggccatcaa ccaaaaagtt gagtttgaaa ataacagaaa attgcaacaa gcatccttcc
6841 aatttagcag caatctgcaa caggcttcct ttcaacatga taaagagatg ctccaagcac
6901 aaattgaggc caccaaaaag ctacaacagg aaatgatgaa agtcaagcag gcagtgctcc
6961 tagagggtgg gttctctgag acagatgcag cccgcggggc aattaacgcc cccatgacaa
7021 aagctttgga ctggagcggg acaaggtact gggctcccga tgctaggact acaacataca
7081 atgcaggccg cttttccacc cctcaaccat cgggggcact gccagggaga gctaacctta
7141 gggatgctgt ccctgctcgg ggaccctcca acaaatcttc taactcttcc actgccacct
7201 ctgtgtattc aaatcaaact atttcaacga gacttggttc tacagctggt tctggaacca
7261 gtgtctcgag cctcccgtca actgcaagga ctaggagctg ggttgaggat caaagtagga
7321 atttgtcacc tttcatgagg ggggcccaca atatatcatt tgtcacccca ccatctagca
7381 gatcctctag ccaaggcaca gtctcaaccg tgcctaaaga gattttggac tcctggactg
7441 gcgccttcaa cacgcgcagg cagcctctct tcgctcacat tcgtaagcga ggggagtcac
7501 gggtgtaatg tgaaaagaca aaactgatta tctttctttt tc
//