Typing tool
|
|
|
|
|
|
Typing tool
|
Complete norovirus genomes
| MH218652 | GII.4 Sydney | |
|
|---|---|---|---|
| GII.P4 New Orleans |
ORF1: 5..5104
ORF2: 5085..6707
ORF3: 6707..7513
LOCUS MH218652 7560 bp RNA linear VRL 11-JUN-2018
DEFINITION Norovirus GII isolate NORO_184_23_09_2015, complete genome.
ACCESSION MH218652
VERSION MH218652.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7560)
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 7560)
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..7560
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="NORO_184_23_09_2015"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="United Kingdom"
/collection_date="23-Sep-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="AWR17614.1"
/translation="MKMASNDASAAAVANSNNDTAKSSSDGVLSSMAVTFKRALGARP
KQPPPREKPQRPPRPPTPELIKNVPPPPPNGEDEIVVSYSVKDGVSGLPDLSTVRQPE
ESNTAFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS
LAKVELAPLSLYWRPVYTPQYLISPDTLKRLSGETFPYTAFDNNCYAFCCWVLDLNDS
WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKIKKVANIFLCALSSLFTRPIKDIIGK
IRPLNILNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED
LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
KKEEANELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST
KSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREV
AKRIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC
PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPDVEK
AKRDFPGQPDMWKNAFSPDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA
SGLLHERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGKQLKDVKTM
PELKQALKNVSIKKCQIVYSGCTYILESDGKGNVKVDRIQSAAVQTNNELAGALHHLR
CARIRYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQDLWSKPQAENTEETTSKDGC
PKPKDDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERVSLGLV
TGSEIRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP
SLFITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPRPIRTDVTGMILEEGAPEG
TVVTLLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILG
PGSAPTLSTKTKFWRSSTASLPPGTYEPAYLGGKDPRVKGGPSLQQVMREQLKPFTEP
RGKPPKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCW
NGESFTGKLADQASKANLMFEEGKNMTPVYTAALKDELVKTDKIYGKIKKRLLWGSDL
ATMIRCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFERHSRYTYHYDADYSRWD
STQQRAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCT
SQWNSIAHWLLTLCALSEVTNLSPDTIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLR
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="AWR17615.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKVIFAAVPPNFPTEGLSPSQVTMFPHIVVDVRQLEPVLIPLPD
VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHIAGTHNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML
TQTTRTDGSTRGHKATVLTGSADFAPKLGRVQFGTDTDNDFVTNQNTKFTPVGVIQDG
NTTPRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGAGRRRVV"
gene 6707..7513
/gene="ORF3"
CDS 6707..7513
/gene="ORF3"
/codon_start=1
/product="VP2"
/protein_id="AWR17616.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGVINQKVDFENNRKLQQA
SFQFSSNSQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRDAVPARGSSSKSS
NSSTATSVYSNQTTSTRLGSTAGSGTSVSSLPSTARTRSWVEDQSRSLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRSRGESRV"
ORIGIN
1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgct gttgctaaca gcaacaacga
61 caccgcaaaa tcttcaagtg acggagtgct ttctagcatg gctgtcactt ttaaacgagc
121 cctcggggcg cggcctaaac aacctccccc gagggaaaaa ccacaaagac ccccacgacc
181 acctactcca gaactgatta aaaatgttcc ccccccccca cccaacggag aggatgaaat
241 agtggtttct tatagtgtca aagatggtgt ctccggcttg cctgaccttt ccaccgtcag
301 gcaaccggaa gaatccaaca cggccttcag tgtccctcca ctcaatcaga gggagaatag
361 agatgctaag gaaccactca ctggaacaat tctggaaatg tgggacgggg aaatctacca
421 ttatggcctg tatgtggagc gaggtcttgt gctaggcgtg cacaaaccgc cagctgctat
481 cagcctcgct aaggttgagt tagcaccact ctccttgtac tggagacctg tgtacactcc
541 tcagtacctc atctctccag acactctcaa gagattgtcc ggagaaacgt tcccctacac
601 agcctttgac aacaactgct atgccttttg ttgctgggtc ctggacctaa atgactcgtg
661 gctgagcagg agaatgatcc agagaacaac tggtttcttc aggccctacc aagattggaa
721 taggaaacct cttcccacta tggatgactc caaaataaag aaggtggcta acatatttct
781 gtgtgctctg tcctcactat tcaccaggcc cataaaagat ataataggga agataaggcc
841 tcttaacatc ctcaacatct tagcttcatg tgattggacc tttgcaggca tagtggagtc
901 cctgatactc ttggcagaac tctttggagt tttctggaca cccccagatg tgtctgcgat
961 gattgccccc ttacttggtg actacgagct acaagggcct gaggaccttg cagtggagct
1021 cgtccccgtg gtgatggggg gaattggttt ggtgctagga ttcaccaaag agaagattgg
1081 gaaaatgttg tcatcagctg cgtccacctt aagggcttgc aaagaccttg gtgcatatgg
1141 gctagagatc ctaaagttag tcatgaagtg gttcttcccg aagaaggagg aggcaaatga
1201 gctggctatg gtgaggtcca tcgaggatgc agtcctggac ctcgaagcaa ttgaaaacaa
1261 tcatatgacc accttgctta aagataaaga cagtctggca acctacatga gaacacttga
1321 ccttgaagag gagaaagcca ggaagctctc aaccaagtct gcctcacccg acatcgtggg
1381 cacaattaac gccctcctgg cgagaatcgc tgccgcacgt tcgctggtgc atcgagcgaa
1441 ggaggagctt tccagcagac caagacctgt ggtgttgatg atatcaggca ggccaggaat
1501 agggaagacc cacctcgcta gggaagtggc taagagaatc gcagcctccc ttacaggaga
1561 ccagcgtgtt ggcctcattc cacgcaatgg cgtcgaccac tgggatgcgt acaaggggga
1621 gagagtcgtc ctatgggacg attatggaat gagcaaccct attcacgatg ccctcaggct
1681 gcaagaactc gctgacactt gccccctcac tctgaactgt gacaggattg aaaataaagg
1741 aaaggtcttt gacagcgatg tcatcattat caccactaat ctggccaacc cagcaccact
1801 ggactatgtc aactttgaag catgctcgag gcgcattgac ttcctcgtgt atgcagaagc
1861 ccctgatgtc gaaaaggcga agcgtgactt cccaggccag cctgacatgt ggaagaacgc
1921 tttcagtcct gacttctcac acataaaact agcactggcc ccacagggtg gcttcgacaa
1981 gaacgggaac accccacacg gaaagggcgt catgaagact ctcaccactg gctcccttat
2041 tgcccgggca tcagggctac tccatgagag gttagatgaa tttgaactgc agggcccagc
2101 tctcaccacc ttcaacttcg atcgcaataa agtgcttgcc tttagacagc tcgctgctga
2161 aaataaatat ggattgatgg acacaatgag ggttgggaaa cagctcaagg atgtcaaaac
2221 catgccagaa ctcaaacaag cacttaagaa tgtctcaatc aagaagtgtc aaatagtgta
2281 tagtggttgc acctacatac ttgagtctga tggcaagggc aatgtgaaag ttgataggat
2341 ccaaagcgcc gccgtgcaga ccaacaatga gctggctggt gccctgcacc acttgaggtg
2401 cgccagaatc agatactatg tcaagtgtgt ccaggaagcc ctgtattcca tcatccaaat
2461 tgctggggct gcatttgtca ccacgcgcat tgccaagcgc atgaacatac aagacctatg
2521 gtccaagcca caagcggaaa acacagagga gaccaccagc aaggacgggt gcccaaaacc
2581 taaggatgat gaggagtttg tcatttcatc cgacgacatc aaaactgagg gcaagaaagg
2641 gaagaacaag actggccgtg gcaagaagca cacagcattt tcaagcaaag gcctcagtga
2701 tgaagagtac gatgaataca agaggatcag agaagaaagg aatggcaagt actctataga
2761 agagtacctt caggacaggg acaaatatta tgaggaggtg gccattgcca gagcgaccga
2821 ggaagacttc tgtgaggagg aggaagccaa gatccgacaa aggatcttta ggccaacaag
2881 gaaacaacgc aaggaggaaa gagtctccct cggcttggtc acaggttctg aaattaggaa
2941 aagaaaccca gatgatttca aacccaaggg gaaattgtgg gctgacgatg acaggagtgt
3001 ggactacaat gagaaactca gttttgaggc cccaccaagc atttggtcaa gaatagtcaa
3061 ctttggttca ggctggggat tctgggtctc ccccagcttg ttcataacat caacccatgt
3121 tataccccag ggcgcaaagg agttctttgg agtccccatc aaacaaatac aggtacacaa
3181 gtcaggcgag ttctgtcgcc tgagattccc tagaccaatc agaactgatg tgacgggcat
3241 gatcttagaa gaaggcgcac ctgagggcac cgtggttaca ctactcatca aaaggtccac
3301 tggggaactt atgcctctag cagctaggat ggggacccat gcgaccatga agatccaagg
3361 gcgtactgtt gggggccaga tgggcatgct tctgacagga tccaacgcca agagtatgga
3421 cctgggtact acaccaggtg attgtggttg cccctacatc tacaagagag gtaatgacta
3481 tgtggttatt ggagtccaca cggctgccgc acgtgggggg aacactgtca tatgtgccac
3541 ccaggggagt gaaggggagg ctacacttga gggtggcgac aacaagggga catactgtgg
3601 tgcaccaatc ctaggcccag ggagtgcccc aacacttagc accaagacca aattctggag
3661 atcgtccaca gcatcactcc cacctggcac ctatgaacca gcctatcttg gtggcaagga
3721 ccccagagtc aagggtggcc cttcactgca gcaagtcatg agggaacagt tgaagccatt
3781 cacagagccc aggggtaagc caccaaaacc aagtgtgtta gaagctgcca agaaaaccat
3841 cattaatgtc cttgagcaga caattgatcc acctgagaaa tggtcgttcg cacaagcttg
3901 cgcgtccctt gacaagacca cttccagtgg tcatccgcac cacatgcgga agaacgactg
3961 ctggaacggg gagtccttca caggcaagct ggcagaccag gcctccaaag ccaacctgat
4021 gtttgaagaa gggaagaaca tgaccccagt ctacacagct gcgctcaagg atgagttagt
4081 taaaactgac aaaatttatg gtaagatcaa gaagaggctc ctttggggct cagacttggc
4141 gaccatgatc cggtgtgctc gagcattcgg aggcctaatg gatgaactca aagcgcactg
4201 tgttacactt cccattagag ttggcatgaa tatgaatgag gatggcccca tcatcttcga
4261 gaggcattct aggtacacgt accactatga tgctgattac tctcgatggg attcaacaca
4321 acagagagcc gtgttggcag cagctctaga aatcatggta aaattctccc cagaaccaca
4381 tttggctcag gtagtcgcgg aagaccttct ttctcctagc gtggtggatg tgggcgactt
4441 cacaatatca atcaacgagg gtcttccctc tggggtgccc tgcacctccc aatggaactc
4501 catcgcccac tggcttctca ctctctgtgc gctctccgaa gtcacaaacc tgtctcccga
4561 taccatacag gctaattctc tcttctcttt ttatggtgat gatgaaattg ttagcacaga
4621 cataaaattg gacccagaga aattgacagc aaagctcaga gaatatgggt taaagccaac
4681 ccgccctgac aaaactgaag gacccctcgt catctctgaa gacctgaatg gcctaacttt
4741 cctacggaga actgtgaccc gcgacccagc tggttggttc ggaaaactag agcagagttc
4801 aatactcagg caaatgtact ggactagggg tcccaaccat ggagacccat ctgaaacaat
4861 gattccacac tcccaaagac ccatacaatt gatgtcccta ctgggggagg ccgctctcca
4921 cggcccagca ttttacagta aaatcagcaa attggtcatt gcagagctaa aagaaggtgg
4981 tatggatttt tacgtgccca gacaagagcc aatgttcaga tggatgagat tctcagatct
5041 gagcacgtgg gagggcgatc gcaatctggc tcccagtttt gtgaatgaag atggcgtcga
5101 gtgacgccaa cccatctgat gggtccgcag ccaacctcgt cccagaggtc aacaatgagg
5161 ttatggctct ggagcccgtt gttggtgccg ccattgcggc acctgtagcg ggccaacaaa
5221 atgtaattga cccctggatt agaaacaatt ttgtacaagc ccctggtgga gagtttacag
5281 tgtcccctag aaacgctcca ggtgaaatac tatggagcgc gcccttaggc cctgatttaa
5341 atccctacct atcccatttg gccagaatgt ataatggtta tgcaggtggt tttgaagtgc
5401 aggtaattct cgcggggaac gcgttcaccg ccgggaaggt catatttgca gcagtcccac
5461 caaattttcc aactgaaggc ttgagcccta gtcaggtcac tatgtttccc catatagtag
5521 tagatgttag gcaactagaa cctgtgttga ttcccttacc cgatgttagg aataacttct
5581 atcattataa tcaatcaaat gactccacca ttaagttgat agcaatgttg tatacaccac
5641 ttagagctaa taatgctggg gacgatgtct tcacagtttc ttgccgagtt ctcacgaggc
5701 catcccccga ttttgatttc atatttctag tgccacccac agttgagtct aggactaaac
5761 cattctctgt tccagtctta actgttgagg agatgaccaa ttcaaggttc cccattcctt
5821 tggaaaagtt gttcacgggt cccagcagtg cctttgttgt tcaaccacaa aacggtaggt
5881 gtacgactga tggcgtactc ctaggcacca cccaattgtc tcctgtcaat atctgcacct
5941 tcagagggga cgtcacccac attgcaggta ctcataacta cacaatgaat ttggcttctc
6001 aaaattggaa taattatgac ccaacagaag agattccagc ccctctagga actccagact
6061 ttgtggggaa gattcaaggc atgctcaccc aaaccacaag gacagatggc tcaacacgcg
6121 gccacaaagc tacggtgctc actgggagcg ccgactttgc tccaaaactg ggcagagttc
6181 aatttggaac tgacacagac aatgattttg taaccaacca aaacacaaaa ttcaccccag
6241 tcggtgtcat ccaagatggt aacaccaccc cccgaaatga accccaacag tgggtgctcc
6301 caagttattc aggcagaaat actcataatg ttcacctggc ccccgctgta gcccccactt
6361 ttccgggtga gcaacttctc ttcttcagat ccaccatgcc cggatgtagc gggtacccca
6421 acatggattt ggactgtctg ctcccccagg aatgggtgca gtacttctac caagaggcag
6481 ccccagcaca atctgatgtg gctctgctaa gatttgtgaa tccagacaca ggtagggttt
6541 tgtttgagtg taaacttcat aaatcaggct atgttacagt ggctcacact ggccaacatg
6601 atttggttat cccccccaat ggctatttta ggtttgattc ctgggtcaac cagttctaca
6661 cgcttgcccc catgggaaat ggagcggggc gtagacgtgt agtataatgg ctggagcttt
6721 ctttgctgga ttagcatctg atgtccttgg ctctggactt ggttccctta tcaatgctgg
6781 ggctggggtc attaatcaaa aagttgattt tgaaaacaac agaaaattgc aacaagcatc
6841 cttccaattt agcagcaatt cacaacaggc ttcctttcaa catgacaaag aaatgctcca
6901 agcacaaatt gaggccacca aaaagctaca acaggaaatg atgaaagtta agcaggcaat
6961 gctcctggag ggtgggttct ctgagacaga tgcagcccgc ggggcaatca acgcccccat
7021 gacaaaagct ttggactgga gcgggacaag gtactgggct cccgatgcta ggactacaac
7081 atacaatgca ggccgctttt caacccctca gccatcgggg gcactgccag gaagagctaa
7141 tcttagggat gctgtccctg ctcggggctc ctccagtaaa tcttctaact cttctactgc
7201 tacttctgtg tactcaaatc aaaccacttc aacgagactt ggttctacag ctggttctgg
7261 taccagtgtc tcgagtctcc cgtcaactgc aaggactagg agctgggttg aggatcaaag
7321 taggagtttg tctcctttca tgaggggggc ccacaacata tcgtttgtca ccccaccatc
7381 tagcagatcc tctagccaag gcacagtctc aaccgtgcct aaagaggttt tggactcctg
7441 gactggcgct ttcaacacgc gcaggcagcc tctcttcgct cacattcgta gtcgagggga
7501 gtcacgggtg taatgtgaaa agacaaaatt gattatcttt ctttttcttt agtgtctttt
//