Typing tool
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Typing tool
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Complete norovirus genomes
| MH218620 | GII.4 Sydney | |
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| GII.P31 |
ORF1: 5..5104
ORF2: 5085..6707
ORF3: 6707..7513
LOCUS MH218620 7560 bp RNA linear VRL 11-JUN-2018
DEFINITION Norovirus GII isolate NORO_149_22_01_2015, complete genome.
ACCESSION MH218620
VERSION MH218620.1
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_149_22_01_2015"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="United Kingdom"
/collection_date="22-Jan-2015"
/note="genotype: GII.Pe_GII.4"
gene 5..5104
/gene="ORF1"
CDS 5..5104
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="AWR17518.1"
/translation="MKMASNDASAAAVANSNNDIAKSSSDGVFSNMADTFKRALGARP
KQPPPREIPPRPPRPPTPELVKKIPPPPPNGEDELVVSYSAKDGVSGLPELTTVRQPE
ETNTAFSVPPLNQRESRDAKEPLTGTIIEMWDGEIYHYGLYVERGLILGVHKPPAAIS
LAKVELAPLSLFWRPVYTPQYLISPDTLRRLHGESFPYTAFDNNCYAFCCWVLDLNDS
WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCTLSSLFTRPIKDIIGK
LKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED
LAVELVPIVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
KKEEANELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST
KSASPDIVGTINSLLARIAAARSLVHRAKEELSSRPRPVVVMISGRPGIGKTHLAREL
AKKIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC
PLTLNCDRIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK
AKRDFPGQPDMWKNAFSPDFSHIKLSLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA
SGLLHERLDEYELQGPTLTTFNFDRNKILAFRQLAAENKYGLMDTMRVGKQLKDVKTM
SDLKQALKNIAIKKCQIVYNGSTYTLEADGKGNVKVDKVQSATVQTNNELAGALHHLR
CARIRYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQNLWSKPQVEDTEEMANKDGC
LKPKDDEEFVVSSDDIKTEGKKGKNKSGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
KYSIEEYLQDRDRYYEEVAIARATEEDFCEEEEAKIRQRVFRPTRKQRKEERASLGLV
TGSEIRKRNPEDFKPKGKLWADDDRSVDYNEKLNFEAPPSIWSRIVNFGSGWGFWVSP
SLFITSTHVIPQGAKEFFGVPIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG
TVATLLIKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDSKGTYCGAPILG
PGSAPKLSTKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP
RGKPPRPNVLEAAKKTIINVLEQTIDPPQKWSFAQACASLDKTTSSGHPHHMRKNDCW
NGESFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKVYGKVKKRLLWGSDL
ATMIRCARAFGGLMEELKAHCVTLPVRVGMNMNEDGPIIFEKHSRYRYHYDADYSRWD
STQQRDVLAAALEIMVKFSPEPHLAQIVAEDLLSPSVMDVGDFQISISEGLPSGVPCT
SQWNSIAHWLLTLCALSEVTDLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLK
EYGLKPTRPDKTEGPLVISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP
NHEDPFETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQE
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="AWR17519.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKVIFAAVPPNFPTEGLSPSQVTMFPHIVVDVRQLEPVLIPLPD
VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHITGSHNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGVL
TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTNHDFEANQNTKFTPVGVIQDG
STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTIPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAV"
gene 6707..7513
/gene="ORF3"
CDS 6707..7513
/gene="ORF3"
/codon_start=1
/product="VP2"
/protein_id="AWR17520.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARTTTYNAGRLSTPQPLGTLPGRANLRDIVPARGSSSKSS
NSSTATSVYSNQTTSTRLGSTAGSGTSVSSFPSTARTRSWVEDQSRNMSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRA"
ORIGIN
1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgct gttgccaaca gcaacaacga
61 catcgcaaaa tcttcaagtg acggtgtgtt ttctaacatg gctgacactt ttaagcgggc
121 cctcggggcg cggcctaaac agccgccccc gagggaaata ccacccagac ccccgcgacc
181 acccacacca gaattggtca aaaagatccc tcctccccca cccaacgggg aggatgaact
241 agtggtctct tatagcgcca aagatggcgt ttccggactg cctgagctca ccactgtcag
301 acaaccggaa gaaaccaaca cggcgttcag tgtcccccca ctcaaccaaa gggagagcag
361 ggacgccaag gagccactaa ctggaacaat tattgaaatg tgggatggag aaatctacca
421 ttacggcctg tacgtggaac gaggtcttat acttggtgtg cacaagccac cggcagctat
481 tagccttgcc aaggtcgagc tagcaccgct ctctttgttc tggagacctg tatacacccc
541 ccagtatctc atctctccag acactcttag gagattacat ggagagtcat tcccctacac
601 tgcatttgac aacaattgct acgccttttg ttgttgggtg ttagacctaa acgactcatg
661 gctaagcagg agaatgattc agagaacaac aggtttcttc aggccgtacc aggattggaa
721 caggaaaccc ctccccacta tggacgattc caaattaaag aaggtagcca acatattctt
781 gtgcaccttg tcttcactgt tcaccagacc tattaaggac ataataggga agttgaaacc
841 tcttaacatc cttaacattc tggctacatg tgattggact ttcgcaggca tagtggaatc
901 cttaatactc ttggcagaac tctttggagt tttctggaca cccccagatg tgtctgcgat
961 gatcgccccc ttgctaggtg attatgaact gcaaggacct gaggaccttg cagtggaact
1021 agtcccaata gtgatggggg ggataggttt ggtgctagga tttaccaaag agaaaatcgg
1081 aaagatgtta tcatccgctg catccacttt aagagcttgt aaagaccttg gtgcatacgg
1141 actggaaatc ttaaaattgg tcatgaagtg gttcttccca aagaaagagg aagcaaatga
1201 gctggctatg gtgagatcca tcgaggatgc agtgctagac ctcgaggcaa ttgaaaacaa
1261 ccacatgacc accctactca aagacaaaga cagcttggca acatacatga gaacccttga
1321 ccttgaggag gagaaagcca gaaaactctc aaccaaatct gcttcacccg acattgtggg
1381 cacaatcaac tctcttctgg caagaattgc tgctgcacgc tccctagtgc atcgggcgaa
1441 ggaagagctc tccagcaggc cgagacctgt cgttgtgatg atatcgggaa gaccagggat
1501 agggaaaact caccttgcca gggagctggc caagaagatc gcggcctccc tcacagggga
1561 ccagcgtgtg ggtcttatcc cacgcaatgg tgtcgaccac tgggacgcat acaagggcga
1621 gagagttgtc ctatgggacg actatggaat gagcaacccc atccacgatg ccctcaggtt
1681 gcaggagctt gctgacactt gccccctcac gctaaattgt gacagaattg agaacaaagg
1741 gaaagtcttt gacagtgatg ccataattat caccaccaat ctggccaacc cagcaccact
1801 ggattatgtc aactttgaag cgtgctcgag acgcattgac ttcctcgtgt acgcagaagc
1861 ccctgaagtg gagaaagcaa agcgcgactt cccaggtcaa cctgacatgt ggaagaacgc
1921 tttcagtcct gacttctcac acataaaact gtcattggct ccacagggtg gttttgacaa
1981 gaacggcaac accccgcatg gaaaaggggt catgaagacc ctcaccactg gctccctcat
2041 cgcccgagca tcagggttgc tccacgagag gctagatgaa tatgaactgc aaggcccaac
2101 cctcaccact tttaatttcg accgcaacaa gatacttgct tttagacagc ttgctgctga
2161 aaacaagtac gggctgatgg acacaatgag agttggaaaa cagctcaagg atgtcaagac
2221 catgtcagac ctcaagcaag cactcaagaa catcgcgatc aagaagtgcc agatagtgta
2281 caatggtagc acctatacac ttgaggccga tggcaagggt aatgtgaaag ttgacaaagt
2341 gcaaagtgcc actgtgcaga ccaacaatga actagccggt gccctacacc acctaaggtg
2401 cgccagaatc agatactacg ttaagtgcgt ccaggaggca ctgtattcta tcatccaaat
2461 cgctggggct gcattcgtca ccacgcgcat cgctaagcgc atgaatatac agaatctctg
2521 gtccaagcca caggtggaag acacagaaga gatggccaac aaagatggtt gcctaaaacc
2581 caaagatgat gaagagtttg tcgtctcatc cgacgacatc aaaactgagg gcaagaaagg
2641 gaagaacaag tccggtcgtg gcaagaagca cacagccttt tcaagcaaag ggctcagtga
2701 tgaggagtac gatgagtaca agagaatcag agaagaaagg aatggaaagt actccataga
2761 agagtacctt caggacagag acaggtacta cgaggaggtg gccattgcca gggcaaccga
2821 agaggacttc tgtgaggaag aagaagccaa aatccggcag agagttttta gaccaacaag
2881 gaaacaacgt aaagaagaga gggcctccct cggcttggtc acaggctctg aaatcaggaa
2941 gagaaaccca gaagacttca aacccaaggg aaagctgtgg gctgatgatg acagaagtgt
3001 tgactacaat gagaaactca actttgaggc cccaccaagc atctggtcgc gaatagtcaa
3061 ctttggttca ggctggggct tctgggtctc ccccagtctg tttataacat caacccatgt
3121 cataccccaa ggtgcaaaag agttcttcgg agtccctatc aagcaaatcc agatacacaa
3181 atcaggtgaa ttctgccggt tgagattccc aaagccaatc agaactgatg tgacgggcat
3241 gattctagaa gaaggtgcgc ccgaggggac cgtggccaca ctgctcatca agagaccaac
3301 tggagagctc atgcctctgg cagccagaat ggggacccat gcaaccatga aaatccaggg
3361 gcgcacagtt ggagggcaaa tgggtatgct cctgacagga tccaacgcca agagtatgga
3421 cctaggcaca acaccaggcg actgcggctg cccctacatc tacaagaggg ggaatgacta
3481 cgtggtcata ggagtccata cggccgctgc ccgcggagga aacactgtca tatgtgccac
3541 ccaggggagt gagggagaag ccacacttga aggaggtgac agcaaaggga catactgtgg
3601 cgcaccaatc ttgggcccag ggagcgctcc gaagctcagt accaagacca agttctggag
3661 atcatccaca acgccactcc cacccggcac ctacgaacca gcctacctcg gtggcaaaga
3721 ccccagggtc aaaggtggcc cttcgttgca acaagttatg agggaccagc tgaagccatt
3781 cacagaaccc agaggcaaac caccaagacc aaatgtgctg gaagctgcca agaaaaccat
3841 catcaatgtc cttgagcaaa caattgatcc accccaaaaa tggtcattcg cgcaagcttg
3901 cgcatccctt gacaaaacca cctccagcgg tcacccgcac cacatgcgga aaaacgattg
3961 ttggaatggg gagtccttca caggaaaatt ggctgatcaa gcctccaagg ccaacctaat
4021 gtttgaagaa ggaaagaaca tgactccagt ctacacaggt gcacttaaag atgagttagt
4081 aaagaccgat aaagtttatg gtaaggtcaa gaagaggctt ctgtggggtt cagatctggc
4141 gaccatgata cggtgcgccc gagcttttgg aggccttatg gaagaactca aggcacactg
4201 tgtcacactt cctgtcagag ttggtatgaa catgaatgag gatggcccca tcatatttga
4261 gaagcactcc agatatagat atcactatga tgctgattat tcccggtggg actcaacaca
4321 acaaagggat gtgctagcag cagcactaga aatcatggtt aagttctctc cagaaccaca
4381 cctggcccag atagttgcag aagacctcct ttcccctagc gtaatggatg taggtgactt
4441 tcaaatatca ataagtgagg gtctcccctc cggggtacct tgtacctccc agtggaattc
4501 catcgcccac tggctcctca ctctttgtgc actctctgaa gtcacggacc tgtcccctga
4561 catcattcag gccaactccc ttttctcttt ctatggtgat gatgagattg taagcacaga
4621 cataaagttg gacccagaga agctgacagc aaaactcaag gagtacgggc tgaaaccaac
4681 ccgtcctgac aaaactgaag gaccccttgt aatctctgag gacctggatg gcctgacatt
4741 cctccggaga actgtgaccc gtgacccagc tggctggttt ggaaaattgg aacaaagttc
4801 aattctcagg caaatgtact ggaccagggg ccccaaccat gaagatccat ttgaaacaat
4861 gataccacac tcccaaagac ccatacaatt gatgtccttg cttggcgagg ctgcactcca
4921 cggtccggca ttctacagca aaattagcaa attagtcatt gcagagttga aggaaggtgg
4981 catggatttt 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 agaaataatt ttgtacaagc ccctggtgga gagtttacag
5281 tgtcccctag aaacgctcca ggtgaaatac tatggagcgc gcccttgggc cctgatctaa
5341 atccctacct atcccatttg gccagaatgt acaatggtta tgcaggtggt tttgaagtgc
5401 aggtaattct cgcggggaat gcgttcaccg ccgggaaggt catatttgca gcagtcccac
5461 caaattttcc aactgaaggc ttgagcccca gccaggtcac tatgttcccc catatagtag
5521 tagatgttag gcaattagaa cctgtgttga ttcccttacc cgatgttagg aataatttct
5581 accattacaa tcaatcaaat gaccccacca ttaagttgat agcaatgttg tatacaccac
5641 tcagggctaa taacgctggg gatgatgtct tcacagtttc ttgccgggtt ctcacgagac
5701 catcccccga ttttgatttc atatttctag tgccacccac agttgagtca agaactaaac
5761 cattctctgt cccagtttta actgttgagg agatgaccaa ctcaagattc cccattcctt
5821 tggaaaagtt gttcacgggt cccagcagtg cctttgttgt ccaaccacaa aacggcaggt
5881 gcacgactga tggcgtgctc ctaggcacca cccaactgtc tcctgtcaac atctgcacct
5941 tcagaggaga tgtcacccac atcacaggta gtcataacta cacaatgaat ttggcttctc
6001 aaaattggaa caattatgac ccaacagaag aaatcccagc ccctctggga actccagatt
6061 ttgtggggaa gattcaaggt gtgctcaccc aaaccacaag gacagatggc tcaacacgcg
6121 gccacaaagc tacagtgtac actgggagcg ccgactttgc tccaaaactg ggtagagttc
6181 aatttgaaac tgacacaaac catgattttg aagctaacca aaacacaaag ttcaccccag
6241 tcggtgtcat ccaagatggt agcaccaccc accgaaatga accccaacag tgggtgctcc
6301 caagttactc aggcagaaat actcataatg tgcatctggc ccccgctgta gcccccactt
6361 ttccgggtga gcaacttctc ttcttcagat ccaccatacc cggatgcagc gggtacccca
6421 acatggattt ggactgtctg ctcccccagg agtgggtgca gtacttctac caagaggcag
6481 ccccagcaca atctgacgtg gccctgctaa gatttgtgaa tccagacaca ggtagggttt
6541 tgtttgagtg taagcttcat aaatcaggct atgttacagt ggctcacact ggccaacatg
6601 atttggttat ccccccaaat ggttatttta ggtttgattc ctgggtcaac cagttttaca
6661 cgcttgcccc catgggaaat ggaacggggc gtagacgtgc agtataatgg ctggagcttt
6721 ctttgctgga ttggcatctg atgtccttgg ctctggactt ggttccctta tcaatgctgg
6781 agctggggcc atcaaccaaa aagttgagtt cgaaaataac agaaaactgc aacaagcatc
6841 cttccaattt agcagcaatc tacaacaggc ttcctttcaa catgacaaag agatgctcca
6901 agcgcaaatt gaggccacca aaaagctaca acaggaaatg atgaaagtta agcaggcaat
6961 gctcctagag ggtgggttct ctgagacaga tgcagcccgc ggggcaatca acgcccccat
7021 gacaaaagct ttggactgga gcgggacaag gtactgggct cccgatgcta ggactacaac
7081 atacaatgca ggccgccttt ccacccccca accattaggg acactgccag gaagagctaa
7141 tcttagggat attgtccctg ctcggggttc ctccagcaaa tcttctaact cttccactgc
7201 cacttctgtg tactcaaatc aaactacttc aacgagactt ggttctacag ctggttctgg
7261 caccagtgtc tcgagcttcc cgtcaactgc aaggactagg agctgggttg aggatcaaag
7321 taggaatatg tcacctttca tgaggggggc ccacaacata tcgtttgtca ccccaccatc
7381 tagcagatcc tctagccaag gcacagtctc aaccgtgcct aaagagattt tggactcctg
7441 gactggcgct tttaacacgc gcaggcagcc actcttcgct cacattcgta agcgagggga
7501 gtcacgggcg taatgtgaaa agacaaaatt gattattttt ctttttcttt agtgtctttt
//