Typing tool
|
|
|
|
|
|
Typing tool
|
Complete norovirus genomes
| MH218669 | GII.4 San Francisco | |
|
|---|---|---|---|
| GII.P4 Yerseke |
ORF1: 5..5104
ORF2: 5085..6707
ORF3: 6707..7513
LOCUS MH218669 7564 bp RNA linear VRL 11-JUN-2018
DEFINITION Norovirus GII isolate NORO_211_16_12_2015, complete genome.
ACCESSION MH218669
VERSION MH218669.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7564)
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 7564)
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..7564
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="NORO_211_16_12_2015"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="United Kingdom"
/collection_date="16-Dec-2015"
/note="genotype: GII.P4_GII.4"
gene 5..5104
/gene="ORF1"
CDS 5..5104
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="AWR17665.1"
/translation="MKMASNDASAAAVANSNNDTAKSSSDGVLSSMAVTFKRALGARP
KQPPPREIPQRPPRPPTPELVKKIPPPPPNGEDEIVVSYSVKDGVSGLPDLSTVKQPE
ESNTAFSVPPLSQRENRDAKEPLTGSILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS
LARIELAPLSLYWRTVYTPQYLISPDTLKKLHGETFPYTAFDNNCYAFCCWVLDLNDS
WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCTLSSLFTRPIKDIIGK
LKPLNILNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED
LAVELVPVVMGGIGLVLGFTKEKVGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
KKEEANELAIVRSIEDAVLDLEAIENNHLTTLLKDKDSLATYMRTLDLEEEKARKLST
KSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVMMISGKPGIGKTHLAREV
AKRIATSLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPVHDALRLQELADTC
PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK
AKRDFPGQPDMWKNAFSSDFSHIKLTLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA
SGLLHERLDEFELQGPTLTTFNFDRNKVLAFRQLAAENKYGLMDTMRIGKQLKGVKTM
PELKQALKNVSIRKCQIVYSGCTYMLESDGKGNVKVDKTQSASVQTNNELTGALHHLR
CARIRYYVKCVQEALYSIIQIAGAAFVTTRIVKRMNIQDLWSKPQVENTEETTNKDGC
PKPKDDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV
TGSEIRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP
SLFITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG
TVVTLLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGNDKGTYCGAPILG
PGSAPTLSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMREQLKPFTEP
RGKPPKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCW
NGESFTGKLADQASKANLMYEEGKSMTPVYTAALKDELVKTDKIYGKIKKRLLWGSDL
ATMIRCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFERHSRYTYHYDADYSRWD
STQQRAVLAAALEILVKFSPEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCT
SQWNSVAHWLLTLCALSEVTNLSPDTIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLR
EYGLKPTRPDKTEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP
NHGDPSETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQE
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..6707
/gene="ORF2"
CDS 5085..6707
/gene="ORF2"
/codon_start=1
/product="VP1"
/protein_id="AWR17666.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPILTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHIKDSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGVL
TQTTKSNGSTRGHKATVLTGSTDFTPKLGRIQFATDTDHDFEANQNTKFTPVGVIQDG
DTAHQNEPQQWMLPSYSGRDIHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGRHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAV"
gene 6707..7513
/gene="ORF3"
CDS 6707..7513
/gene="ORF3"
/codon_start=1
/product="VP2"
/protein_id="AWR17667.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAVLLEGGFSETDAARGAIN
APMTKTLDWSGTRYWAPDARTTTYNAGRFSTPQPPGALPGRANLRDAVPARGSSSKSS
NSSTVTSVYSNQTVSTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRSLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTHRQPLFAHIRKRGESRA"
ORIGIN
1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgct gttgccaaca gcaacaacga
61 caccgcaaaa tcttcaagtg acggagtgct ttccagcatg gctgtcactt ttaaacgagc
121 cctcggggcg cggcctaaac agcccccccc gagggaaata ccacaaagac ccccacgacc
181 acccacccca gaattggtta aaaagatccc ccctcccccg cccaacggag aggatgaaat
241 agtggtctct tatagtgtca aagatggcgt ttccggtttg cctgaccttt ccaccgtcaa
301 gcaaccggaa gaatctaaca cggctttcag tgtcccccca ctcagtcaga gggagaatag
361 agacgccaag gagccactta ctgggtcaat tctggaaatg tgggatggag aaatctacca
421 ttatggcctg tatgtggagc gaggtctcgt gctaggcgtg cacaaaccac cagctgccat
481 cagcctcgct aggattgagc tagcaccact ctccctgtac tggagaactg tgtacactcc
541 tcagtacctc atctctccag acactctcaa gaaattacac ggagagacgt tcccctacac
601 agcctttgac aacaattgtt atgccttctg ttgctgggtc ctggacctaa acgactcgtg
661 gctgagcagg agaatgatcc aaagaacaac tggtttcttt agaccctacc aagactggaa
721 taggaaaccc cttcccacta tggatgactc caaattaaag aaggtagcta acatatttct
781 gtgtactctg tcctcgttat tcaccaggcc cataaaagac ataataggga agttaaagcc
841 cctcaatatc ctcaacatct tagcctcatg tgattggacc ttcgcaggta tcgtggagtc
901 cctgatactc ttggcagagc tctttggggt tttctggaca cccccagatg tgtctgcgat
961 gattgccccc ttactcggtg actacgagct gcaaggacct gaggaccttg cggtggagct
1021 cgtccccgta gtgatgggtg gaattggttt ggtactagga ttcaccaaag agaaggttgg
1081 gaaaatgttg tcatctgctg catccacctt gagagcttgc aaagacctcg gtgcatatgg
1141 gctagaaatc ctaaagttgg tcatgaagtg gttcttcccg aaaaaggagg aagcaaatga
1201 actggctata gtgagatcta tcgaggatgc agtcttggat ctcgaggcaa ttgaaaacaa
1261 ccacttgacc accctgctca aagacaaaga cagtctggca acctacatga gaactcttga
1321 ccttgaggag gagaaagcca ggaaactttc aaccaagtct gcctcgcctg acattgtggg
1381 cacaatcaac gcccttctgg cgagaatcgc cgctgcacgc tctctagtgc atcgggcgaa
1441 ggaggaactt tccagcagac caagacctgt agtgatgatg atatcaggca agccaggaat
1501 agggaagacc caccttgcta gggaagtggc taagagaatc gcaacctccc ttacaggaga
1561 ccagcgcgta ggcctcatcc cacgtaacgg cgtcgaccat tgggatgctt acaaggggga
1621 gagggttgtc ctttgggatg attatggaat gagcaacccc gttcatgatg ccctcagatt
1681 gcaggaactc gctgacacct gccccctcac tctaaactgt gacaggattg agaacaaagg
1741 aaaggtcttt gacagcgatg tcatcattat caccactaac ctggccaacc cagcaccact
1801 agactatgtc aactttgaag catgctcgag gcgcatcgac ttcctcgtgt acgcagaagc
1861 ccctgaagtc gaaaaggcga agcgtgactt cccaggtcag cctgacatgt ggaagaacgc
1921 cttcagttct gatttctcac acataaaact gacactggcc ccacaaggtg gcttcgacaa
1981 gaacgggaac accccacacg gaaagggtgt catgaagacc ctcaccactg gctccctcat
2041 tgcccgggca tctgggttac tccatgagag gttagatgag tttgagctac aaggcccaac
2101 cctcaccacc ttcaatttcg accgcaataa agtgcttgcc tttagacaac ttgctgctga
2161 gaacaaatat gggttgatgg acacaatgag aattgggaaa cagctcaagg gtgtcaaaac
2221 catgccagaa ctcaaacaag cacttaagaa tgtctcaatc aggaaatgcc aaatagtgta
2281 tagtggttgc acttacatgc ttgaatctga tggcaagggc aatgtgaaag ttgacaaaac
2341 tcagagcgcc tccgtgcaga ccaacaatga gctgactggt gccctgcacc atttgaggtg
2401 cgccaggatc agatactatg tcaagtgtgt ccaggaggcc ctgtactcca tcatccaaat
2461 tgccggagct gcatttgtca ccacgcgcat cgtcaagcgc atgaacatac aagacttgtg
2521 gtccaaacca caagtggaaa acacagagga aaccaccaac aaagacggat gcccaaaacc
2581 caaagatgat gaggagtttg tcatctcatc cgacgacatc aagactgagg gtaagaaagg
2641 gaagaacaaa actggccgcg gcaagaaaca tacagccttc tcaagtaaag gtctcagtga
2701 cgaagagtac gatgagtaca agaggattag ggaagaaagg aatggcaagt actccataga
2761 ggagtacctt caggacaggg acaaatacta tgaggaggta gccattgcca gggcgactga
2821 ggaagacttc tgtgaagagg aggaagccaa gatccggcaa aggattttca ggccaacaag
2881 gaaacaacga aaggaggaga gagcttctct cggtctagtc acaggttctg aaattaggaa
2941 aagaaaccca gatgatttca aacccaaggg gaaactgtgg gctgacgatg acaggagtgt
3001 ggattataac gagaaactca gttttgaggc cccaccaagc atctggtcga ggatagtcaa
3061 ctttggttca ggttggggat tttgggtctc ccctagcctg ttcataacat caacccatgt
3121 cataccccag ggtgcaaaag agttctttgg agtccccatc aaacaaattc aggtacacaa
3181 gtcaggcgaa ttctgtcgct tgagattccc aaaaccaatc aggactgatg tgacaggcat
3241 gatcttagaa gaaggcgcac ctgagggcac cgtagttaca ctacttatca agaggtccac
3301 tggggaactt atgcccctag cagctaggat ggggacccat gcaactatga agatccaagg
3361 gcgcactgtt gggggccaaa tgggcatgct tctgacaggg tccaacgcca aaagcatgga
3421 tctgggtact acaccaggtg attgtggctg tccctacatc tacaagagag gtaatgacta
3481 tgtggtcatt ggagtccaca cggctgccgc tcgcggagga aacactgtca tatgtgccac
3541 ccaggggagt gaaggagagg ccacacttga aggtggtaac gacaagggga catactgtgg
3601 tgcacccatc ctaggcccag ggagtgcccc aacacttagc accaagacca aattctggag
3661 atcatccaca gcaccactcc cacccggcac ctatgaacca gcctatcttg gtggcaagga
3721 ccccagagtc aagggtggcc cttcactgca gcaagtcatg agggaacagt taaagccatt
3781 cacagagccc aggggcaaac caccaaagcc aagtgtgttg gaagctgcca agaagaccat
3841 catcaatgtc cttgagcaaa caattgatcc acctgagaaa tggtcattcg cacaagcttg
3901 cgcgtccctt gacaagacta cttccagcgg tcatccccac cacatgcgga aaaacgattg
3961 ctggaacggg gaatccttca cgggcaagct ggctgaccag gcttccaaag ccaacctgat
4021 gtatgaagaa gggaagagca tgaccccagt ctacacagct gcactcaagg atgaattggt
4081 taaaactgac aaaatttatg gtaagatcaa gaagaggctt ctctggggct cggacttggc
4141 gaccatgatc cgttgcgctc gagcgttcgg aggcctaatg gatgaactca aagcacactg
4201 tgtcacactc cccattagag ttggtatgaa tatgaatgag gatggcccca tcatcttcga
4261 gaggcattcc aggtacacat atcactatga cgctgattac tctcgatggg attcaacaca
4321 acagagagcc gtgttggcag cagctctaga aatcctggtt aaattctccc cagaaccaca
4381 tttggctcag gtagttgcgg aagacctcct ttctcctagc gtggtggacg tgggcgactt
4441 cacaatatca atcaacgagg gtcttccctc tggggtgccc tgcacctctc agtggaattc
4501 tgtcgcccat tggcttctca cactctgcgc gctctctgaa gtcacaaact tgtcccccga
4561 caccatacag gctaactccc tcttctcttt ttatggtgat gatgaaattg ttagcacaga
4621 cataaaattg gacccagaga aattaacagc aaagctcagg gagtatgggt tgaaaccaac
4681 ccgccctgat aaaaccgaag gaccccttgt catctctgaa gacttgaatg gcctaacttt
4741 cctgcggagg actgtgaccc gcgacccagc tggttggttt ggaaaactgg agcagagttc
4801 aatactcagg caaatgtact ggactagggg ccccaaccat ggagacccat ctgaaacaat
4861 gattccacac tcccaaaggc ctatacaatt gatgtcccta ttgggggagg ccgctcttca
4921 cggcccagca ttctacagca aaatcagtaa attggtcatt gcagagctaa aagaaggtgg
4981 catggatttt tacgtgccca gacaagagcc aatgttcagg tggatgagat tctcagacct
5041 gagcacgtgg gagggcgatc gcaatctggc tcccagtttt gtgaatgaag atggcgtcga
5101 gtgacgccaa cccatctgat gggtccgcag ccaacctcgt cccagaggtc aacaatgagg
5161 ttatggcttt ggagcccgtt gttggtgccg ccattgcggc gcccgtagcg ggccaacaaa
5221 atgtaattga cccctggatt agaaataatt ttgtgcaagc ccctggtgga gagtttacag
5281 tgtcccctag aaacgctcca ggtgagatac tatggagcgc gcccttaggc cctgatttaa
5341 atccctacct atcccatttg gctagaatgt acaatggtta tgcaggtggc tttgaagtgc
5401 aggtaattct cgcggggaac gcgtttaccg ccgggaagat catatttgca gcagtcccac
5461 caaattttcc aactgaaggc ttgagcccca gccaggtcac tatgttcccc catataatag
5521 tagatgttag gcaattagaa cctgtgttga ttcccttacc cgatgttagg aataatttct
5581 atcattataa tcaatcaaat gaccccacta ttaagttgat agcaatgttg tacacaccac
5641 ttagggctaa taatgctggg gatgatgtct tcacggtttc ttgccgagtt ctcacgagac
5701 catcccccga ttttgatttc atattcctag tgccacccac agttgagtca agaactaaac
5761 cattctctgt cccaatctta actgtcgagg agatgaccaa ttcaagattt cccattcctt
5821 tggaaaagtt gttcacgggt cccagcagtg cctttgttgt ccaaccacaa aatggcaggt
5881 gcacgactga tggcgtgctt ctaggtacca cccaactgtc tcctgtcaac atttgcacct
5941 tcagagggga tgtcacccat atcaaagata gtcgtaacta cacaatgaat ttggcttctc
6001 aaaattggaa caattatgac ccaacagaag aaatcccagc ccctctagga actccagatt
6061 ttgtggggaa gattcaaggt gtgctcactc aaaccacgaa atcgaatggc tcgacacgcg
6121 gccacaaagc cacagtgctc actgggagca ccgactttac tccaaaactg ggtagaattc
6181 aatttgcaac tgacacagac catgattttg aagctaacca aaatacaaaa ttcaccccag
6241 tcggtgtcat ccaagatggt gacactgccc accaaaatga acctcaacag tggatgctcc
6301 caagttattc aggcagggac attcataatg tgcatctggc ccccgctgta gcccccactt
6361 ttccgggtga gcagctgctc ttcttcaggt ccactatgcc cggatgcagc gggtatccca
6421 acatggattt ggactgtctg cttccccagg aatgggtgca gtacttctac caagaggcag
6481 ccccagcaca atctgatgtg gctctgttaa gatttgtgaa cccagacaca ggtagggttt
6541 tgtttgagtg caaactccat aaatcaggct atgtcacagt ggctcacact ggtcgacatg
6601 atttggttat tccccctaat ggttacttta gatttgattc ctgggttaat cagttctaca
6661 cgcttgcccc catgggaaat ggaacggggc gtagacgtgc ggtataatgg ctggagcttt
6721 ctttgctgga ttggcatctg atgtccttgg ctctggactt ggttccctca tcaatgctgg
6781 ggctggggcc atcaaccaaa aagttgaatt tgaaaataac agaaaattgc aacaagcttc
6841 cttccaattt agcagcaatc tacaacaagc ttcctttcaa catgacaagg agatgctcca
6901 agcacaaatt gaggccacca aaaagctaca acaggaaatg atgaaagtta agcaggcagt
6961 gctcctagag ggtgggttct ctgagacaga tgcagcccgc ggggcaatca acgcccccat
7021 gacaaaaact ttggactgga gtgggacaag gtactgggct cccgacgcta ggactacaac
7081 atacaatgca ggtcgctttt ccacccccca accaccgggg gcactgccag gaagagctaa
7141 tcttagggat gctgtccccg ctcggggttc ctctagtaaa tcttctaact cttctactgt
7201 cacttctgtg tattcaaatc aaactgtttc aacgagactt ggttctacag ctggttctgg
7261 taccagtgtc tcgagtctcc cgtcgactgc aaggactagg agctgggttg aggatcaaaa
7321 taggagtttg tcacctttca tgaggggggc ccacaacata tcgtttgtca ccccaccatc
7381 tagcagatcc tctagccaag gcacagtctc aaccgtgcct aaagaaattt tggactcctg
7441 gactggtgct ttcaacacgc acaggcagcc tctcttcgct cacattcgta agcgagggga
7501 gtcacgggct taatgtgaaa agacaaaatt gattattttt ctttttcttt ctttagtgtc
7561 tttt
//