Typing tool
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Typing tool
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Complete norovirus genomes
| MH218679 | GII.3 | |
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| GII.P21 |
ORF1: 5..5104
ORF2: 5085..6731
ORF3: 6731..7495
LOCUS MH218679 7548 bp RNA linear VRL 11-JUN-2018
DEFINITION Norovirus GII isolate NORO_221_28_12_2015, complete genome.
ACCESSION MH218679
VERSION MH218679.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7548)
AUTHORS Brown,J.R., Roy,S., Shah,D., Williams,C.A., Williams,R., Dunn,H.,
Hartley,J., Harris,K. and Breuer,J.
TITLE Norovirus transmission dynamics in a paediatric hospital using full
genome sequences
JOURNAL Clin. Infect. Dis. (2018) In press
PUBMED 29800111
REMARK Publication Status: Available-Online prior to print
REFERENCE 2 (bases 1 to 7548)
AUTHORS Brown,J.R., Roy,S., Shah,D., Williams,C.A., Williams,R., Dunn,H.,
Hartley,J., Harris,K. and Breuer,J.
TITLE Direct Submission
JOURNAL Submitted (17-APR-2018) Division of Infection and Immunity,
University College London, 90 Gower St, London, London WC1E 6BT,
United Kingdom
COMMENT ##Assembly-Data-START##
Assembly Method :: CLC Genomics Workbench v. 10.1
Sequencing Technology :: Illumina
##Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..7548
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="NORO_221_28_12_2015"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="United Kingdom"
/collection_date="28-Dec-2015"
/note="genotype: GII.P21_GII.3"
gene 5..5104
/gene="ORF1"
CDS 5..5104
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="AWR17695.1"
/translation="MKMASNDASAAAAAKSNNDNAKSSSDGVLSNMAVTFKRALGARP
KQPPPSDKPPKPPRPPTPELVKAIPPPPPNGEDEPIISYNVKGGVSGLPELSTVTQLE
ENSTAFSVPPLSQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS
LAKIELTPLSLYWRPVYTPQYLISPDTLRKLHGETFPYTAFDNNCYAFCCWVLDLNDS
WLNRRMIQRTTGFFRPYQDWNRKPLPTMDDSKVKKVANVVLCALSSLFTRPIKDIIGK
LKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED
LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
KKEEKNELAMVRSIEDAVLDLEAIENNHMTALLKDKDSLATYMRTLDMEEEKARKLST
KSASPDIVGTINALLSRIAAARSLVHRAKEELSSRPRPVVLMISGKPGIGKTHLAREL
AKKIASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSSPVHDALRLQELADTC
PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYADAPEVEK
AKRDFPGQPDMWKDTFKPDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTASSLVARA
SGLLHERLDEYELQGPTPTTFNFDRNKVLAFRQLAAENKYGLVDTMRVGSQLKNVKTM
TELKQALKNISVKKCQLVYGGGTYTLESDGKGNVHVEKVNNTSVQTNNELSGVLHHLR
CARIRYYVKCVQEALYSILQIAGAAFITTRIAKRTNIQNLWSKPQAEDLEETNNEEGC
PKPKNDEEFVVSSDDIKSEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV
TGSEIRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP
SLFITSTHVIPQGAQEFFGVPIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG
TVATLLIKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGNEGEAMLEGGDNKGTYCGAPILG
PGNAPKLSTKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP
RGKPPKPSVLEAAKKTIINVLEQTIDPPQKWTYAQACASLDKTTSSGHPHHMRKNDCW
NGESFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGVVKKRLLWGSDL
STMIRCARAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWD
STQQRAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVMDVGDFRISINEGLPSGVPCT
SQWNSIAHWLLTLCALSEVTDLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLR
EYGLKPTRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTKGP
NHEDPFETMIPHSQRPIQLMSLLGEAALHGPSFYSKISKLVISELKEGGMDFYVPRQE
PMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE"
mat_peptide 5..994
/gene="ORF1"
/product="p48"
mat_peptide 995..2092
/gene="ORF1"
/product="NTPase"
mat_peptide 2093..2629
/gene="ORF1"
/product="p22"
mat_peptide 2630..3028
/gene="ORF1"
/product="VPg"
mat_peptide 3029..3571
/gene="ORF1"
/product="Pro"
mat_peptide 3572..5101
/gene="ORF1"
/product="RdRp"
gene 5085..6731
/gene="ORF2"
CDS 5085..6731
/gene="ORF2"
/codon_start=1
/product="VP1"
/protein_id="AWR17696.1"
/translation="MKMASNDAAPSNDGAAGLVPEINNEAMALEPVAGAAIAAPLTGQ
QNIIDPWIMNNFVQAPGGEFTVSPRNSPGEVLLNLELGPEINPYLAHLARMYNGYAGG
FEVQVVLAGNAFTAGKIIFAAIPPNFPVDNLSAAQITMCPHVIVDVRQLEPVNLPMPD
VRNNFFHYNQGSDSRLRLIAMLYTPLRANNSGDDVFTVSCRVLTRPSPDFSFNFLVPP
TVESKTKPFSLPILTISEMSNSRFPVPIDSLHTSPTENVVVQCQNGRVTLDGELMGTT
QLLPSQICAFRGVLTRSTSRASDQADTATPRLFNYYWHIQLDNLNGTPYDPAEDIPGP
LGTPDFRGKVFGVASQRNPDATTRAHEAKIDTTSGRFTPKLGSLEISTESSDFDQSQP
TRFTPVGIGVDHEADFQQWALPDYAGQFTHNMNLAPAVAPNFPGEQLLFFRSHLPSSG
GRSNGILDCLVPQEWVQHFYQESASSQSQVALVRYVNPDTGRVLFEAKLHKLGFMTIA
KNGDSPITVPPNGYFRFESWVNPFYTLAPMGTGNGRRRIQ"
gene 6731..7495
/gene="ORF3"
CDS 6731..7495
/gene="ORF3"
/codon_start=1
/product="VP2"
/protein_id="AWR17697.1"
/translation="MAGAFIAGLAGDMLTNTVGSLVNAGANAINQTIDFENNKYLQNA
SFNHDKEMLNAQIEATKKLQADMIAIKQGVLTAGGFSPTDAARGAINAPMTKVLDWSG
TRNWAPGATSTTSMSGGFTHQTVHRSTPNFKTNQAPKSTPSSGSSVRSNSTQITSLSS
HSSGSSRSSGSTVISSIPSSNRTRDWVNQQNFNLEPHMPGSLRTAFVTPPSSTASSSG
TVSTVPKNVLDSWTSAFNTRRQPLFAHLRRRGESNV"
ORIGIN
1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgct gctgccaaaa gcaacaacga
61 caacgcaaaa tcttcaagtg acggagtatt atctaatatg gctgtcactt ttaaacgagc
121 cctcggggcg cggcctaaac agccgccccc gagtgacaaa ccaccaaaac ccccaagacc
181 acccacacca gagttggtta aggcaattcc ccctccccca cccaacgggg aggacgaacc
241 aatcatctct tacaacgtca aagggggtgt ttctggtttg cctgagctct caactgtcac
301 ccaactggaa gagaactcta cagcattcag cgtcccccct cttagtcaga gggagaacag
361 agatgcaaag gaaccattga ctggaaccat cctggagatg tgggacgggg agatctacca
421 ttatggctta tacgtagaac gagggttagt gctcggtgta cacaaaccac cagcagccat
481 cagccttgct aagattgagc tgaccccttt gtctttgtat tggagaccag tgtacacccc
541 acagtacctc atctcccctg acactctcag aaagttgcat ggggagacgt tcccttatac
601 agcctttgac aacaactgtt atgccttctg ctgttgggtg cttgacttga acgattcatg
661 gctgaacaga aggatgatac agaggacaac aggcttcttc cgaccctacc aggattggaa
721 caggaaaccc ctccccacga tggatgactc taaagtgaaa aaggtggcca atgttgttct
781 atgtgctctc tcatcattgt tcacaagacc aattaaggac attattggga agttaaaacc
841 cctaaacatt ctcaacatct tagccacatg tgattggact tttgcaggca tagtagaatc
901 cctgatcctt ttggctgaac tttttggagt tttctggaca cccccagatg tgtctgcgat
961 gatcgctccc ttactgggtg attatgaact acagggaccc gaggacctcg ctgtggaact
1021 cgtacccgta gtaatgggag ggataggttt ggtgctggga ttcaccaaag agaaaatcgg
1081 caagatgctt tcttctgctg cttcaaccct gagggcatgt aaagatctcg gtgcatatgg
1141 gttggagatc ctcaaattgg ttatgaaatg gtttttccca aagaaagaag agaaaaacga
1201 attggcaatg gtgagatcca tcgaggacgc agtgctagat cttgaagcca ttgagaacaa
1261 ccatatgaca gctctactca aggataaaga cagccttgca acctacatga ggactcttga
1321 catggaagag gagaaggcga gaaaactttc caccaagtct gcctctccgg atattgtggg
1381 cacgataaat gccctactgt caaggattgc agctgcccgg tctctagtgc acagggctaa
1441 ggaggagctg tcaagcaggc cccgaccggt cgtcttaatg atttcaggga aaccgggtat
1501 aggaaaaacc catctagcta gagagttggc aaagaagatc gcctccacac tcacaggtga
1561 ccagagggtg ggtcttatcc cacgtaacgg ggtcgaccac tgggatgcat acaaaggtga
1621 aagagtcgtt ctctgggacg actacgggat gagcagccct gtccacgacg ccctcagact
1681 ccaggagctc gctgatacct gtcctctcac actcaactgt gacaggattg agaacaaagg
1741 taaagtcttt gacagtgacg tcataataat aaccaccaat ttagccaacc cagcaccact
1801 ggattatgtc aactttgaag cttgctcgag acgcatagac ttcctcgtct atgctgatgc
1861 tcctgaagtt gagaaggcta agcgggactt cccaggccaa ccagacatgt ggaaagacac
1921 cttcaaaccc gacttctcac atataaaatt ggcattggcc ccgcaaggag gttttgacaa
1981 gaatggtaac actcctcacg ggaagggagt catgaagacc ctcactgcca gttccctcgt
2041 tgcccgagca tcagggctcc tccacgagag attagacgag tatgagctgc agggcccaac
2101 tcccacaaca ttcaacttcg accgcaacaa ggtgcttgct tttaggcagc ttgctgctga
2161 aaacaagtac ggtcttgttg acacaatgag ggtcgggtca caactcaaga atgtcaaaac
2221 tatgacagaa ctcaagcagg ccctcaagaa catctcagtc aagaaatgtc agcttgtgta
2281 cggtgggggc acatacacac ttgaatctga tggtaaaggc aatgtacacg tcgaaaaggt
2341 gaacaacacc agtgtacaaa ctaacaacga gctctccggg gttttgcacc atctcaggtg
2401 tgctagaatc aggtactatg ttaagtgtgt tcaggaagct ctctactcca tcttacaaat
2461 tgccggggct gcattcataa ccacgcgcat tgcaaagcgc acaaacatac aaaacctctg
2521 gtctaaacca caagcagaag atctagagga gactaacaac gaggagggtt gtccaaaacc
2581 taaaaatgat gaagaatttg tcgtctcctc tgatgacatc aaatctgagg gtaagaaagg
2641 aaagaacaag actggccgtg gtaagaagca cacagccttt tccagcaaag gactcagtga
2701 tgaggagtac gatgagtata agagaatcag ggaagagaga aatggtaagt actccataga
2761 ggaataccta caggacagag acaaatacta tgaggaggtg gccatagcca gggcaactga
2821 ggaagatttc tgtgaagaag aggaggccaa gatccgacag aggatattca gaccaacaag
2881 gaaacaacgc aaagaggaaa gagcttctct tggtttggtt acaggctctg agatcaggaa
2941 gagaaaccca gatgacttca agcccaaagg gaaactatgg gctgatgatg acaggagtgt
3001 tgactacaat gagaaactta gtttcgaggc tccaccaagc atttggtcac gaatagtcaa
3061 ctttggctca gggtggggct tttgggtctc gcccagcctc ttcataacat caacccatgt
3121 cattccccaa ggcgcgcagg agttctttgg agtgcccatc aaacaaatac aaatccacaa
3181 gtcaggtgag ttctgccggc ttaggttccc gaaaccaatc aggacagatg ttacaggcat
3241 gatcttggag gaaggtgctc cagaaggcac tgttgccaca cttctcatca agagaccaac
3301 tggggaactc atgcccttgg cagccaggat gggcacccac gctaccatga aaattcaggg
3361 tcgcactgtt ggtggacaga tgggcatgct actcacaggg tctaacgcta agagcatgga
3421 tttgggcaca actcctggcg attgtggttg tccctatatc tacaagagag ggaacgacta
3481 cgtggtcatt ggagttcaca ctgccgccgc tcgtggagga aacaccgtca tctgtgcaac
3541 ccaaggaaac gagggtgagg ccatgctaga aggtggtgac aacaagggaa cttattgtgg
3601 ggcaccaata ttaggccctg gaaatgcccc caaactcagc accaaaacca aattttggag
3661 gtcttccacc acccccctgc cacccggaac ctatgagcca gcttatctgg gtggcaagga
3721 ccctagagtg aaaggtggtc cctcactgca acaggttatg agagaccaac taaaaccatt
3781 cactgagccc agaggcaaac cacccaaacc aagtgtgcta gaagctgcca agaagactat
3841 aatcaatgtg cttgaacaaa caatagaccc acctcaaaaa tggacatacg cacaagcgtg
3901 tgcatcacta gacaaaacca cttccagcgg tcaccctcac cacatgcgga agaacgattg
3961 ctggaatggg gaatctttca caggaaaact ggcagaccaa gcatcaaagg ccaacctaat
4021 gtttgaggaa ggaaagaaca tgactccagt atacacagga gctctgaaag atgagctagt
4081 caagactgac aagatctatg gggtagtcaa gaagaggctc ctgtggggtt cagacctatc
4141 aaccatgata cggtgtgcac gagccttcgg tgggctaatg gacgagctca aggcccattg
4201 cgtcacacta ccagtcaggg ttggtatgaa catgaatgag gatggaccca taatatttga
4261 gaaacactcc agatacaaat accattatga tgcagattac tcccgctggg actcaacaca
4321 acaaagagca gtgctagccg cagccctgga aataatggtt aaattctcac cagaacccca
4381 cctggcccag gtggttgcag aagacctttt gtcccccagt gtgatggacg tgggtgattt
4441 caggatatca atcaacgagg gattgccctc tggtgttccc tgtacttcac aatggaactc
4501 cattgctcac tggctcctca cactatgtgc actgtctgaa gtcacagacc tgtcccctga
4561 catcatccag gcgaattccc tgttttcctt ttatggtgat gatgaaatag tgagcacaga
4621 catcaaatta gacccagaga aactgacagc aaagctgagg gaatacgggc ttaaaccaac
4681 tcgccctgac aaaacagagg gacccttaat tatctctgaa gatttgaatg gcctgacctt
4741 cttgcggaga acagtgaccc gcgatccggc cggatggttt ggcaaactgg accaaagttc
4801 aatactcagg cagatgtact ggaccaaggg gccaaaccat gaagacccct ttgaaacaat
4861 gataccacac tcccaaagac ccatacaact gatgtcatta cttggtgaag ctgcattgca
4921 tggtccatca ttctacagta aaatcagcaa attggtcatc tcagaattga aagagggtgg
4981 aatggatttt tacgtgccca gacaagaacc aatgttcagg tggatgagat tctcagattt
5041 gagcacgtgg gagggcgatc gcaatctggc tcccagtttt gtgaatgaag atggcgtcga
5101 atgacgccgc tccatctaat gatggtgccg ccggcctcgt cccagagatc aacaatgagg
5161 caatggcgct agagccagtg gcgggtgcag cgatagcagc acccctcact ggtcagcaaa
5221 atataattga tccctggatt atgaataatt ttgtgcaagc tcctggtggt gagtttacag
5281 tgtcccccag aaattcccct ggtgaagtcc ttcttaattt ggaattgggc ccagaaataa
5341 atccctactt ggcccatctt gctagaatgt ataatggtta tgcaggtgga tttgaagtgc
5401 aggtggtcct agctggaaat gcgtttacag caggaaagat aatctttgca gctattcccc
5461 ccaactttcc agttgacaat ttgagtgcag cacagatcac aatgtgccca catgtgattg
5521 tggatgtcag acagttggaa ccagtcaacc tcccgatgcc tgacgttcgc aataacttct
5581 ttcattataa tcaagggtct gattcgaggt tacgcctaat tgcaatgcta tatacacctc
5641 ttagagcaaa caattctggg gatgatgttt ttactgtatc ttgtagagtg ctaactagac
5701 ctagtcctga tttctcattc aatttccttg tgccacctac tgtggagtca aagacaaaac
5761 ccttctccct ccctatcctg actatctctg aaatgtctaa ttctaggttc ccagtaccaa
5821 ttgattctct gcacaccagt cctactgaga atgttgttgt tcagtgccaa aatgggcgcg
5881 tcacccttga tggtgagttg atgggcacca cccaactctt gcctagccaa atctgtgctt
5941 tcaggggcgt tctcaccaga tcaacaagca gggccagtga ccaggccgat acagcaactc
6001 ctagattgtt taattattat tggcatatac aattggataa tctaaatgga accccttatg
6061 atcctgcaga agacatacca ggccccctag ggacaccaga tttccgtggc aaagtctttg
6121 gcgtggccag ccagagaaat cctgatgcca cgactagggc acatgaagca aagatagaca
6181 ccacatctgg ccgcttcacc cctaagttag gctcattaga gatatccact gaatctagtg
6241 attttgacca aagccaacca acaagattca ccccagttgg cattggagtt gaccatgagg
6301 cagactttca acaatgggcc ctacccgatt acgctggtca gttcacacac aacatgaact
6361 tagccccagc tgttgctccc aactttcctg gtgagcagct ccttttcttc cgctcacatt
6421 tgccatcttc tggtgggcga tccaacggga ttctagattg cctggtcccc caagaatggg
6481 tacagcactt ctaccaagag tcagcctcct ctcagtctca agtggccctg gttaggtatg
6541 ttaatcctga cactggtaga gtgttatttg aggccaagct acacaaatta ggtttcatga
6601 ctatagctaa gaatggtgat tctccaataa ctgttcctcc aaatggatac tttaggtttg
6661 aatcttgggt gaaccccttt tacacacttg cccccatggg aactgggaat gggcgtagaa
6721 ggattcaata atggctggag cttttatagc aggattggct ggtgacatgc tcacaaatac
6781 tgtaggatct ttagttaatg caggggctaa tgctattaat caaacaattg attttgaaaa
6841 taataaatat ttgcaaaatg cttcttttaa tcatgataag gagatgttga atgcacaaat
6901 tgaggcaaca aagaagttac aggctgacat gattgctatc aagcaagggg tcttgaccgc
6961 tggcggcttc tcccctactg atgcagcccg tggggcaatt aatgccccca tgacaaaagt
7021 cctagattgg agtggaacga gaaactgggc accaggtgcc acctccacaa cctcgatgtc
7081 gggtggcttt acacatcaaa ctgtacacag atccacacca aattttaaaa cgaaccaggc
7141 tcccaaatcc acacccagca gtgggtcttc agtgaggtca aactcaaccc aaatcactag
7201 cctgagctca cactcgtccg ggtcgtctcg atccagcggg tctacagtta tcagctcaat
7261 accatcctct aacaggacta gggactgggt caaccaacaa aattttaatt tggaaccaca
7321 catgcctgga tctcttagga cagcttttgt cactccacca tctagtacag cctctagctc
7381 aggcacagtc tcaactgtgc ccaaaaatgt tttggactcc tggacatctg cgtttaacac
7441 gcgcagacag ccgctattcg cacaccttcg cagaaggggg gagtcaaatg tttagtgaaa
7501 agattatttt aaatttggtt taaaattaga tttaatttgg aatctttt
//