Typing tool
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Typing tool
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Complete norovirus genomes
| MH218606 | GII.4 Sydney | |
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| GII.P4 New Orleans |
ORF1: 5..5104
ORF2: 5085..6707
ORF3: 6707..7513
LOCUS MH218606 7513 bp RNA linear VRL 11-JUN-2018
DEFINITION Norovirus GII isolate NORO_135_30_01_2015, complete genome.
ACCESSION MH218606
VERSION MH218606.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7513)
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 7513)
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..7513
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="NORO_135_30_01_2015"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="United Kingdom"
/collection_date="30-Jan-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="AWR17476.1"
/translation="MKMASNDASAAAVANSNNDTAKTSSDGVLSSMAVTFKRALGARP
KQPPPREIPQRPPRPPTPELVKNIPPPPPNGEDEIVVSYSVKNGVSGLPDLSTVRQPE
ETNTAFSVPPLNQRENKDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS
LAKIELTPLSLYWRPVYTPQYLISPDSLKKLAGETFPYTAFDNNCYAFCCWVLDLNDS
WLSRRMIQRTTGFFRPYQDWNRKPLPTMDSSKIKKVADIFLCTLSSLFTRPIKDIIGK
IRPLNILNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED
LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
KKEEANELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST
KSASPDIVGTVNALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREV
AKRIATSLTGDQRVGLVPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC
PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK
AKRDFPGQPDMWKNAFSSDFSHIKLTLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA
SGLLHERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGKQLKDVKTM
PELKQALKNVSIKKCQIVYSGCTYMLESDGKGNVKVDKIQSAAVQTNNELTGALHHLR
CARIRYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQDLWSKPQVENTEETTSKDGC
PKPKDDEEFVITSDDIKAEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERVSLGLV
TGSEIRKRNPDDFKPKGKLWADDDRNVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP
SLFITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG
TVVTLLIKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILG
PGSAPTLSTKTKFWRSSTASLPPGTYEPAYLGGKDPRVKGGPSLQQVMREQLKPFTEP
RGKPPKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCW
NGESFTGKLADQASKANLMYEEGKNMTPVYTAALKDELVKTDKIYGKIKKRLLWGSDL
ATMIRCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFERHSRYTYHYDADYSRWD
STQQRAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCT
SQWNSIAHWLLTLCALSEVTNLSPDTIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLR
EYGLKPTRPDKTEGPLAISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP
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"
/note="predicted CDS stop by homology is invalid; there
may be a valid stop in a different location due to
truncation (trc) or extension (ext) (TAG|TAA|TGA) [TAT
ending at position 6705 on + strand];first in-frame stop
codon exists 3' of stop position predicted by homology to
reference [homology search predicted 5085..6705 revised to
5085..6707 (stop shifted 2 nt)]"
/codon_start=1
/product="VP1"
/protein_id="AWR17477.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKVIFAAVPPNFPTEGLSPSQVTMFPHIVVDVRQLEPVLIPLPD
VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHTTGSHNYTMNLASLNWNNYDPTEEIPAPLGTPDFVGKIQGVL
TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFATDTDHDFEANQNTKFTPVGVIQDG
STTHRNEPQQWVLPSYSGRNIHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAV"
gene 6707..7513
/gene="ORF3"
CDS 6707..7513
/gene="ORF3"
/codon_start=1
/product="VP2"
/protein_id="AWR17478.1"
/translation="MAGAVFAGLASDVLSSGLGSLINAGAGAINQTIEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIESTKKLQQEMMKVKQAVLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRDAVPARGSSSKSS
NSSTVTSVYSNQTTSTRLGSTAGSGASVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRKRGESRV"
ORIGIN
1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgct gttgctaaca gcaacaacga
61 caccgcaaaa acttcaagtg acggagtgct ttctagcatg gctgtcactt ttaaacgagc
121 cctcggggcg cggcctaaac agcctccccc gagggaaata ccacaaagac ccccacgacc
181 acctactcca gaactggtta agaacatccc ccctcccccg cccaacgggg aagatgaaat
241 agtggtctct tatagtgtca aaaatggtgt ctccggcttg cctgaccttt ctaccgtcag
301 gcaaccggaa gaaaccaaca cagccttcag tgtccctccg ctcaatcaga gggagaataa
361 agatgctaag gagccactca ctggaacaat tctggaaatg tgggacgggg aaatctatca
421 ttatggcctg tatgtggagc gaggccttgt actaggtgtg cacaaaccgc cagctgccat
481 cagccttgct aagattgagc tgacaccact ctccttgtac tggagacctg tgtacactcc
541 tcagtacctc atctctccag acagtctcaa gaaattggcc ggagagacgt tcccctacac
601 agcctttgat aacaactgtt atgccttttg ctgctgggtt ctggacctga atgactcgtg
661 gctgagcaga agaatgatcc agagaacaac tggtttcttc aggccctacc aggactggaa
721 caggaaaccc ctccccacta tggatagctc caaaataaag aaggtggctg acatatttct
781 gtgtaccctg tcctcgctat tcaccagacc cataaaagat ataataggga agataaggcc
841 tcttaacatc ctcaacatct tggcctcatg tgattggacc tttgcgggca tagtggagtc
901 cctgatactc ttggcagaac tctttggagt tttctggaca cccccagatg tgtctgcgat
961 gattgccccc ttactcggtg actacgagct acaaggacct gaggaccttg cagtggagct
1021 tgtccccgtg gtgatggggg gaattggttt ggtgctagga ttcaccaaag agaagattgg
1081 gaaaatgttg tcatctgctg cgtccacttt gagagcttgc aaagaccttg gtgcatatgg
1141 gctagagatc ctaaagttag tcatgaaatg gttcttccca aagaaggagg aggcaaatga
1201 gctggctatg gtgaggtcca tcgaggatgc agtcctggat ctcgaggcaa ttgaaaacaa
1261 tcacatgacc accttgctta aagataaaga cagtctggca acctacatga gaacacttga
1321 ccttgaagag gagaaagcca ggaaactctc aaccaagtct gcctcacccg acatcgtggg
1381 tacagtcaac gccctcctgg cgagaatcgc cgccgcacgt tctctggtgc atcgagcgaa
1441 ggaggagctt tccagcagac caagacctgt ggtgctgatg atatcaggca ggccaggaat
1501 agggaagacc cacctcgcta gggaagtggc taagagaatc gcaacctccc ttacagggga
1561 tcagcgcgtg ggcctcgtcc cacgcaatgg tgtcgaccat tgggatgcgt acaaggggga
1621 gagggtcgtc ctgtgggacg attatggaat gagcaaccct attcacgatg ccctcaggct
1681 gcaagaactc gctgacactt gtcccctcac tctgaactgt gacaggattg aaaacaaagg
1741 aaaggtcttt gacagcgatg tcatcattat caccactaat ctggccaacc cagcaccact
1801 ggactatgtc aactttgaag catgctcgag gcgcattgac tttctcgtgt atgcagaggc
1861 ccctgaagtc gaaaaggcga agcgtgactt cccaggccag cctgacatgt ggaagaacgc
1921 tttcagttct gatttctcac acataaaact aacactggcc ccacaaggtg gtttcgataa
1981 gaacgggaac accccacacg gaaagggcgt catgaagacc ctcaccactg gctcccttat
2041 tgcccgggca tcagggctac tccatgagag gttggatgaa tttgaactgc agggcccagc
2101 tctcaccacc ttcaacttcg atcgcaataa agtgcttgcc tttagacagc ttgctgctga
2161 aaacaaatat ggattgatgg acacaatgag ggttgggaaa cagctcaagg atgtcaaaac
2221 catgccagaa ctcaagcaag cactcaagaa tgtctcaatc aagaagtgcc aaatagtgta
2281 tagtggctgc acttacatgc ttgagtctga tggcaagggc aatgtgaaag ttgacaaaat
2341 ccaaagcgcc gccgtgcaga ccaacaatga gctgactggc gccctgcacc acttgaggtg
2401 cgccagaatc agatactatg tcaagtgtgt tcaggaggcc ctgtattcca tcatccaaat
2461 cgctggggct gcatttgtca ccacgcgcat tgccaagcga atgaacatac aagacctgtg
2521 gtccaagcca caagtggaaa acacagagga gactaccagc aaggatgggt gcccaaaacc
2581 caaggatgat gaggagttcg tcattacatc cgacgacatc aaagctgagg gcaagaaagg
2641 gaagaacaag actggccgtg gcaagaagca cacagcattc tcaagcaaag gtctcagtga
2701 tgaagagtat gatgaataca agaggattag agaagaaagg aatggcaagt actctataga
2761 agagtacctt caggacagag acaaatacta tgaggaggtg gccattgcca gggcgactga
2821 ggaagacttc tgtgaagagg aggaggccaa gatccggcaa aggatcttta ggccaacgag
2881 gaaacaacgc aaggaggaaa gagtctctct tggtctggtc acaggctctg aaattaggaa
2941 aagaaaccca gatgacttca aacccaaggg gaaattgtgg gctgacgatg acaggaatgt
3001 ggactacaat gagaaactca gctttgaggc cccaccaagc atttggtcga gaatagtcaa
3061 ctttggctca ggctggggat tctgggtctc ccccagtctg ttcataacat caacccatgt
3121 cataccccag ggcgcaaagg agttctttgg agtccccatc aaacaaatac aggtacacaa
3181 gtcaggcgag ttctgtcgct tgagattccc taaaccaatc aggactgatg tgacgggtat
3241 gatcttggaa gaaggcgctc ctgagggcac cgtggtcaca ctgctcatca agaggcccac
3301 tggggaactc atgcccctag cagctaggat ggggacccat gcgaccatga agatccaagg
3361 acgcactgtt ggaggccaga tgggcatgct tctgacagga tccaacgcca agagcatgga
3421 cctgggtaca acaccaggtg attgtggctg cccctacatc tacaagagag gtaatgacta
3481 tgtggtcatt ggagtccaca cggctgccgc acgtggggga aacactgtca tatgtgccac
3541 ccaagggagt gaaggggagg ctacacttga gggtggtgac aacaagggga catactgtgg
3601 tgcaccaatc ctaggcccag ggagtgcccc gacacttagc accaaaacca aattctggag
3661 gtcgtccaca gcatcacttc cacctggcac ctatgaacca gcctatcttg gtggcaagga
3721 ccctagagtc aagggtggcc cttcactgca gcaagtcatg agagaacagt tgaagccatt
3781 cacagagccc aggggcaagc caccaaaacc aagtgtacta gaagctgcca agaagaccat
3841 cattaatgtc cttgagcaaa caattgatcc accagagaaa tggtcgttcg cacaagcttg
3901 cgcgtccctc gacaagacca cttccagtgg ccatccgcac cacatgcgga aaaacgactg
3961 ctggaacggg gagtccttca cgggcaagct ggcagaccag gcttccaagg ccaacctgat
4021 gtatgaagaa gggaagaaca tgaccccagt ctacacagct gcgctcaagg atgagttggt
4081 taaaactgac aaaatctatg gtaagatcaa gaagaggctt ctctggggct cggatctggc
4141 aaccatgatt cggtgtgctc gagcattcgg aggcctaatg gatgaactca aagcgcactg
4201 tgtcacactc cccattagag ttggcatgaa tatgaatgag gatggcccca tcatcttcga
4261 gaggcattcc aggtacacgt accactatga tgctgactac tctcggtggg attcaacaca
4321 acagagagcc gtgctggcag cagctctgga aatcatggtt aaattctccc cagaaccaca
4381 tttggctcag gtagtcgcgg aagaccttct ctcccccagc gtggtggacg tgggcgactt
4441 cacaatatca atcaatgagg gtcttccctc tggggtgccc tgcacctccc aatggaactc
4501 catcgcccac tggcttctca ctctctgtgc gctctctgaa gtcacaaacc tgtctcctga
4561 caccatacag gctaattccc tcttctcttt ttatggtgat gatgaaattg ttagcacaga
4621 cataaaattg gacccagaga aattgacagc aaaactcaga gaatatgggt taaaaccaac
4681 ccgccctgac aaaactgaag gaccccttgc catctctgaa gacctggatg gcctaacttt
4741 cctgcggaga actgtgaccc gcgacccagc tggttggttt ggaaaactgg agcagagttc
4801 aatactcagg caaatgtact ggactagggg tcccaaccat ggagacccat ctgaaacaat
4861 gattccacac tcccaaaggc ccatacaatt gatgtcccta ctaggggagg ccgctctcca
4921 cggcccagca ttttacagca 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 ctattgcggc acctgtagcg ggccaacaaa
5221 atgtaattga cccctggatt agaaacaatt ttgtacaagc ccctggtgga gagtttacag
5281 tatcccctag aaacgctcca ggtgaaatac tatggagcgc gcccttaggc cctgatctaa
5341 acccctacct atcccattta gccagaatgt acaatggtta tgcaggtggc tttgaagtgc
5401 aggtaattct cgcggggaac gcgttcaccg ccgggaaggt catatttgca gcagtcccac
5461 caaattttcc aactgaaggc ttaagcccca gccaggtcac catgttcccc catatagtgg
5521 tagatgttag gcaactagaa cctgtgttga ttcccttacc cgatgttagg aataatttct
5581 atcattataa ccaatcaaat gactccacca ttaagctgat agcaatgttg tatacaccac
5641 ttagggctaa taatgctggg gacgatgttt tcacagtttc ttgccgagtt ctcacaaggc
5701 catcccccga ttttgatttc atatttttgg tgccccccac agttgagtca agaactaaac
5761 cattctctgt cccagtttta actgttgagg agatgaccaa ttcaagattc cccattcctt
5821 tggaaaagct gttcacgggt cccagcagtg cctttgttgt tcaaccacaa aacggcaggt
5881 gcacgactga tggcgtgctt ctaggcacca cccaactgtc tcctgtcaac atctgcacct
5941 tcagagggga tgtcacccat accacaggca gtcacaacta cacaatgaat ttggcttctc
6001 taaattggaa caattatgac ccaacagaag aaatcccagc ccctctagga actccagact
6061 ttgtggggaa gattcaaggc gtgctcaccc aaaccacaag gacagatggc tcaacacgcg
6121 gccacaaagc cacagtgtac actgggagtg ccgattttgc tccaaaactg ggtagagttc
6181 aatttgcaac tgacacagac catgattttg aagctaacca aaacacaaag ttcaccccag
6241 tcggtgtcat tcaagatggt agcaccaccc accgaaatga acctcaacag tgggtgcttc
6301 ctagttactc aggcagaaat attcataatg tgcatctggc ccccgctgta gcccccactt
6361 ttccaggtga gcaacttctc tttttcagat ccaccatgcc cggatgcagc gggtacccca
6421 acatggattt ggactgcttg ctcccccagg aatgggtgca gcacttctac caagaggcag
6481 ccccagcaca atctgatgtg gccctgctga gatttgtgaa tccagacaca ggtagggttt
6541 tgtttgagtg caagcttcat aaatcaggct atgttacagt ggctcacact ggccaacacg
6601 atctggttat cccccccaat ggttatttta ggtttgattc ttgggtcaac cagttctaca
6661 cgcttgcccc catgggaaat ggaacggggc gtagacgtgc agtataatgg ctggagctgt
6721 ctttgctgga ttggcatctg atgtcctcag ctctggactt ggttccctta tcaatgctgg
6781 ggccggggcc atcaaccaaa caattgagtt tgaaaataac agaaaattgc aacaagcatc
6841 attccaattt agcagcaatc tgcaacaggc ttccttccaa catgacaaag agatgctcca
6901 agcacaaatt gagtctacca aaaagctaca acaggaaatg atgaaagtta agcaggcagt
6961 gctcctagag ggtgggttct ctgagacaga tgcagcccgc ggggcaatca acgcccccat
7021 gacaaaagct ttggactgga gcgggacaag gtactgggct cccgatgcca ggaccacaac
7081 atacaatgca ggccgctttt ccacccctca accatcgggg gcactgccag gaagagctaa
7141 tcttagggat gctgtccctg ctcggggttc ctccagcaaa tcttctaact cttctactgt
7201 tacttctgtg tattcaaatc aaaccacttc aacgagactt ggttctacag ctggttctgg
7261 tgccagtgtc tcgagcctcc cgtcaactgc aaggactagg agctgggttg aggatcaaaa
7321 taggaatttg tcacctttca tgaggggggc ccacaatata tcgtttgtca ccccaccatc
7381 tagcagatcc tctagccaag gcacagtctc aaccgtgcct aaagaggttt tggactcctg
7441 gactggcgct ttcaacacgc gcaggcagcc tctcttcgct cacattcgta agcgagggga
7501 gtcacgggtg taa
//