Typing tool
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Typing tool
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Complete norovirus genomes
| MH218706 | GII.4 Sydney | |
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| GII.P31 |
ORF1: 5..5104
ORF2: 5085..6707
ORF3: 6707..7513
LOCUS MH218706 7568 bp RNA linear VRL 11-JUN-2018
DEFINITION Norovirus GII isolate NORO_48-1_01_07_2014, complete genome.
ACCESSION MH218706
VERSION MH218706.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7568)
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 7568)
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..7568
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="NORO_48-1_01_07_2014"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="United Kingdom"
/collection_date="01-Jul-2014"
/note="genotype: GII.Pe_GII.4"
gene 5..5104
/gene="ORF1"
CDS 5..5104
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="AWR17776.1"
/translation="MKMASNDASAAAVANSNNDIAKSSSDGVLSNMAVTFKRALGARP
KQPPPREIPPRPPRPPTPELVKKIPPPPPNGEDELVVSYSAKDGVSGLPELTTVRQPE
ETNTAFSVPPLNQRESRDAKEPLTGTIIEMWDGEIYHYGLYVERGLILGVHKPPAAIS
LAKVELTPLSLFWRPVYTPQYLISPDTLRRLHGESFPYTAFDNNCYAFCCWVLDLNDS
WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCTLSSLFTRPIKDIIGK
LKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED
LAVELVPIVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
KKEEANELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST
KSASPDIVGTINSLLARIAAARSLVHRAKEELSSRPRPVVVMISGRPGIGKTHLAREL
AKKIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC
PLTLNCDRIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK
AKRDFPGQPDMWKNAFSPDFSHIKLSLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA
SGLLHERLDEYELQGPALTTFNFDRNKILAFRQLAAENKYGLMDTMRVGKQLKDVKTM
SDLKQALKNIAIKKCQIVYSGSTYTLEADGKGSVKVDKVQSATVQTNNELAGALHHLR
CARIRYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQNLWSKPQVEDTEEMANKDGC
LKPKDDEEFVVSSDDIKTEGKKGKNKSGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
KYSIEEYLQDRDRYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV
TGSEIRKRNPEDFKPKGKLWADDDRSVDYNEKLNFEAPPSIWSRIVNFGSGWGFWVSP
SLFITSTHVIPQGAKEFFGVPIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG
TVATLLIKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDSKGTYCGAPILG
PGSAPKLSTKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP
RGKPPRPNVLEAAKKTIINVLEQTIDPPQKWSFAQACASLDKTTSSGHPHHMRKNDCW
NGESFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKVYGKVKKRLLWGSDL
ATMIRCARAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFEKHSRYRYHYDADYSRWD
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="AWR17777.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKVIFAAVPPNFPTEGLSPSQVTMFPHIVVDVRQLEPVLIPLPD
VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHTTGSHNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGVL
TQTTRTNGSTRGHKATVYTGSADFAPKLGRVQFKTDTDNDFEANQNTKFTPVGVIQDG
DTTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
VPPNGYFRFDSWVNQFHTLAPMGNGTGRRRAV"
gene 6707..7513
/gene="ORF3"
CDS 6707..7513
/gene="ORF3"
/codon_start=1
/product="VP2"
/protein_id="AWR17778.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQT
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGMLPGRANLRDTVPARGPSSKSS
NSSTATSVYSNQTTSTRLGSTAGSGTSVSSFPSTARTRSWVEGQSRNLSPFMRGAHDI
SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRRRGESRA"
ORIGIN
1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgct gttgccaaca gcaacaacga
61 catcgcaaaa tcttcaagtg acggtgtgct ttctaacatg gctgtcactt ttaagcgggc
121 cctcggggcg cggcctaaac agccgccccc gagggaaata ccacccagac ccccgcgacc
181 acccacacca gaattggtta aaaagatccc tcctccccca cccaacgggg aggatgaact
241 agtggtctct tacagcgcca aagatggcgt ttccggattg cctgagctca ccactgtcag
301 gcaaccggaa gaaaccaaca cggcattcag tgtcccccca ctcaaccaaa gggagagcag
361 ggacgccaag gagccattaa ctggaacaat tattgaaatg tgggatggag aaatctacca
421 ttacggcctg tacgtggaac gaggtcttat acttggtgtg cacaagccac cggcagctat
481 tagccttgcc aaggtcgagc taacaccgct ctctttgttc tggagacctg tatacacccc
541 ccagtatctc atctctccag acactcttag gaggttacac ggagagtcat tcccctacac
601 tgcatttgac aacaattgct atgccttttg ttgttgggtg ttagacctaa acgactcatg
661 gctaagcagg agaatgattc agagaacaac aggtttcttc aggccgtacc aggattggaa
721 caggaaaccc ctccccacta tggatgattc caaattaaag aaggtagcca acatattctt
781 gtgcactttg tcttcactat tcaccagacc cattaaggac ataataggga agttgaaacc
841 tcttaacatc ctcaacattc tggctacatg tgattggacc ttcgcaggca tagtggaatc
901 cttaatactc ttggcagaac tctttggagt tttctggaca cccccagatg tgtctgcgat
961 gatcgccccc ttgctaggtg attatgagct gcaaggacct gaggaccttg cagtggaact
1021 ggtcccaata gtgatggggg ggataggttt ggtgctagga tttaccaaag agaaaatcgg
1081 aaagatgcta tcatccgctg catccacttt aagagcttgt aaagaccttg gtgcatacgg
1141 actggaaatc ttaaaattgg tcatgaagtg gttcttccca aagaaagagg aagcaaatga
1201 actggctatg gtgagatcca tcgaggatgc agtactagac ctcgaggcaa ttgaaaacaa
1261 ccacatgacc accctactca aagacaaaga cagcttggca acctacatga gaacccttga
1321 ccttgaggag gagaaagcca gaaaactctc aaccaaatct gcttcacccg acattgtggg
1381 cacaatcaac tctcttctgg caagaattgc tgctgcacgc tccctagtgc atcgggcgaa
1441 ggaagaactc tccagcaggc cgagacccgt cgttgtgatg atatcgggaa ggccagggat
1501 agggaaaact caccttgcca gagagctggc caagaagatc gcggcctccc tcacagggga
1561 ccagcgcgtg ggtcttatcc cacgcaatgg tgtcgaccac tgggacgcat acaagggcga
1621 aagagttgtc ctatgggacg actatggaat gagcaacccc atccatgatg ccctcaggtt
1681 gcaggagctt gctgacacct gccccctcac gctaaattgt gacagaattg agaacaaagg
1741 gaaagtcttt gacagtgatg ccataattat caccaccaat ctggccaacc cagcaccact
1801 ggattatgtc aactttgaag cgtgctcgag acgcattgac ttcctcgtgt acgcagaagc
1861 ccctgaggtg gagaaagcaa agcgcgactt cccaggtcaa cctgacatgt ggaagaacgc
1921 tttcagtcct gacttctcac acataaaact atcattggct ccacagggtg gctttgacaa
1981 gaacggcaac accccgcatg gaaaaggggt catgaagacc ctcaccactg gctccctcat
2041 cgcccgagca tcagggttgc tccatgagag gctagatgaa tatgaactgc aaggcccagc
2101 cctcaccact ttcaacttcg accgtaacaa gatacttgct tttagacagc ttgctgctga
2161 aaacaagtat gggctgatgg acacaatgag agtaggaaaa cagctcaagg atgtcaagac
2221 catgtcagac ctcaagcaag cactcaagaa catcgcgatc aagaagtgcc agatagtgta
2281 cagtggtagc acctatacac ttgaggccga tggcaagggt agtgtgaaag ttgacaaagt
2341 gcaaagtgcc actgtgcaga ccaacaatga actagccggt gccctacacc acctaaggtg
2401 cgccagaatc agatactacg ttaagtgcgt ccaggaggca ctgtattcca tcatccaaat
2461 cgctggggct gcattcgtca ccacgcgcat cgctaagcgc atgaatatac agaatctctg
2521 gtccaagcca caggtggaag acacagaaga gatggccaac aaagatggtt gcctaaaacc
2581 caaagatgat gaagagtttg tcgtctcatc cgacgacatc aaaactgagg gcaagaaagg
2641 gaagaacaag tccggccgtg gcaagaagca cacagccttt tcaagcaaag ggctcagtga
2701 tgaggagtac gatgagtaca agagaatcag agaagaaagg aatggtaagt actccataga
2761 agagtacctt caggatagag acaggtacta cgaggaggtg gccattgcca gggcaaccga
2821 agaggacttc tgtgaagaag aagaagccaa aatccggcag agaattttta gaccaacaag
2881 gaaacaacgt aaagaagaga gggcctctct 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 ggtgctaaag agttcttcgg agtccctatc aagcaaatcc agatacacaa
3181 atcaggtgaa ttctgccggt tgagattccc aaagccaatc agaactgacg tgacgggcat
3241 gattctagaa gaaggtgcgc ccgaggggac cgtggccaca ctgctcatta 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 agtaaaggga catactgtgg
3601 cgcaccaatc ttgggcccag ggagcgctcc gaagctcagt accaagacta agttctggag
3661 atcatccaca acgccactcc cacccggcac ctacgaacca gcctacctcg gtggcaaaga
3721 tcccagggtc aaaggtggcc cctcattgca acaagttatg agggaccagc tgaagccatt
3781 cacagaaccc agaggcaaac caccaagacc aaatgtgttg gaagctgcca agaaaaccat
3841 catcaatgtc cttgagcaaa caattgatcc accccaaaaa tggtcattcg cgcaagcttg
3901 cgcatccctt gacaaaacca cctccagcgg tcacccgcac cacatgcgga aaaacgattg
3961 ttggaatggg gagtccttca caggaaaatt ggctgatcaa gcctccaagg ccaacctaat
4021 gtttgaagag ggaaagaaca tgactccagt ctacacaggt gcacttaaag atgagttagt
4081 aaagaccgat aaagtttatg gtaaggtcaa gaagaggctt ctgtggggtt cagatctagc
4141 gaccatgata cggtgtgccc gagcttttgg aggccttatg gatgaactca aggcacactg
4201 tgtcacactt cctgtcagag ttggtatgaa catgaatgag gatggcccca tcatatttga
4261 gaagcactcc agatatagat atcactatga tgctgattat tcccggtggg attcaacaca
4321 acaaagggat gtgctagcag cagcactaga aatcatggtt aagttctctc cagaaccaca
4381 cctggcccag atagttgcag aagacctcct ttcccctagc gtaatggatg taggtgactt
4441 tcaaatatca ataagtgagg gtctcccctc tggggtacct tgtacctccc agtggaattc
4501 catcgcccac tggctcctca ctctttgtgc actctctgaa gtcacggacc tgtcccctga
4561 catcattcag gccaactccc ttttctcttt ctatggtgat gatgagattg taagcacaga
4621 cataaagttg gacccagaga agctgacagc aaaactcaag gagtacgggc tgaaaccaac
4681 ccgccccgat aaaactgaag gaccccttgt tatctctgaa gacctggatg gcctgacatt
4741 cctccggaga actgtaaccc gtgatccagc tggctggttt ggaaaattgg aacaaagttc
4801 aattctcagg caaatgtact ggaccagggg tcccaaccat gaagacccat ttgaaacaat
4861 gataccacac tcccaaagac ccatacaatt gatgtccttg ttgggcgagg ctgcactcca
4921 cggcccggca ttctatagca aaattagcaa attagtcatt gcagagttga aggaaggtgg
4981 catggatttt tacgtgccca gacaagagcc aatgttcaga tggatgagat tctcagacct
5041 gagcacgtgg gagggcgatc gcaatctggc tcccagtttt gtgaatgaag atggcgtcga
5101 gtgacgccaa cccatctgat gggtccgcag ccaacctcgt cccagaggtc aacaatgagg
5161 ttatggctct ggagcccgtt gttggtgccg ccatcgcggc acctgtggcg ggccaacaaa
5221 atgtaattga cccctggatt agaaataatt ttgtacaagc ccctggtgga gagtttacag
5281 tatcccctag aaacgctcca ggtgaaatac tatggagtgc gcccctgggc cctgatctaa
5341 atccctacct atcccatttg gccagaatgt acaatggtta tgctggtggt tttgaagtgc
5401 aggtaattct cgcggggaat gcgttcaccg ccgggaaggt catatttgca gcagtcccac
5461 caaattttcc aactgaaggc ttgagcccca gccaggtcac tatgttcccc catatagtag
5521 tagatgttag gcaattagaa cctgtgttga ttcccttacc cgatgttagg aataatttct
5581 atcattacaa tcaatcaaat gaccccacca ttaagttgat agcaatgttg tatacaccac
5641 ttagggctaa taacgctggg gatgatgtct tcacagtttc ttgccgagtt ctcacgagac
5701 catcccccga ttttgatttc atatttctag tgccacctac agttgagtca agaactaaac
5761 cattctctgt cccagtttta actgttgagg agatgaccaa ttcaagattc cccattcctt
5821 tggaaaagtt gttcacgggt cccagtagtg cttttgttgt ccaaccacaa aacggcaggt
5881 gcacgactga cggcgtgctc ctaggcacca cccaactgtc tcctgtcaac atctgcacct
5941 tcagaggaga tgtcacccat accacaggta gtcataacta cacaatgaat ttggcttctc
6001 aaaattggaa caattatgac ccaacagaag aaatcccagc ccctctggga actccagatt
6061 ttgtggggaa gattcaaggc gtgctcaccc aaaccacaag gacaaatggc tcaacacgcg
6121 gccacaaagc tacagtgtac actgggagcg ccgactttgc tccaaaactg ggtagagttc
6181 aatttaaaac tgacacagac aatgattttg aagctaacca aaacacaaag ttcaccccag
6241 tcggtgtcat ccaagatggt gacaccaccc accgaaatga accccagcag tgggtgctcc
6301 caagttactc aggcaggaat actcataatg tgcatctggc ccccgctgta gcccccactt
6361 ttccgggtga gcaactcctt ttcttcagat ccaccatgcc cggatgcagc gggtacccca
6421 acatggattt ggactgtctg ctcccccagg aatgggtgca gcacttctat caagaggcag
6481 ccccagcaca atctgacgtg gctctgctaa gatttgtgaa tccagacaca ggtagggttt
6541 tgtttgagtg taagcttcat aaatcaggct atgttacagt ggcccacact ggccaacatg
6601 atttagttgt ccccccaaat ggttatttta ggtttgattc ctgggtcaac cagtttcaca
6661 cgcttgcccc catgggaaat ggaacggggc gtagacgtgc agtataatgg ctggagcttt
6721 ctttgctgga ttggcatctg atgtccttgg ctctggactt ggttccctta tcaatgctgg
6781 ggctggggcc atcaaccaaa aagttgagtt tgaaaataac agaaaattgc aacaaacatc
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 ggaccacaac
7081 atacaatgca ggccgctttt ccacccctca accatcgggg atgctgccag gaagagctaa
7141 tcttagggat actgtccctg ctcggggtcc ctccagcaaa tcttctaact cttctactgc
7201 cacttctgtg tactcaaatc aaactacttc aacgagactt ggttctacag ctggttctgg
7261 caccagtgtc tcgagcttcc cgtcaactgc aaggactagg agctgggttg agggtcaaag
7321 taggaatttg tcacctttca tgaggggggc ccacgacata tcgtttgtca ccccaccatc
7381 tagcagatcc tctagccaag gcacagtctc aaccgtgcct aaagagattt tggactcctg
7441 gactggcgct ttcaacacgc gcaggcagcc actcttcgct cacattcgta ggcgagggga
7501 gtcacgggcg taatgtgaaa agacaaaatt gattatcttt ctttttcttt agtgtctttt
7561 aaaaaaaa
//