Typing tool
|
|
|
|
|
|
Typing tool
|
Complete norovirus genomes
| MH218727 | GI.3 | |
|
|---|---|---|---|
| GI.P3 |
ORF1: 5..5404
ORF2: 5388..7025
ORF3: 7025..7672
LOCUS MH218727 7745 bp RNA linear VRL 11-JUN-2018
DEFINITION Norovirus GI isolate NORO_87_18_02_2015, complete genome.
ACCESSION MH218727
VERSION MH218727.1
KEYWORDS .
SOURCE Norovirus GI
ORGANISM Norovirus GI
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7745)
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 7745)
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..7745
/organism="Norovirus GI"
/mol_type="genomic RNA"
/isolate="NORO_87_18_02_2015"
/host="Homo sapiens"
/db_xref="taxon:122928"
/country="United Kingdom"
/collection_date="18-Feb-2015"
/note="genotype: GI.P3_GI.3"
gene 5..5404
/gene="ORF1"
CDS 5..5404
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="AWR17839.1"
/translation="MMMASNDAIAVADVSNNNANTNNDNIGSRLMARIRGRMGPQRGE
TTTKITDANMALNLLRRSQTPSPSRQESPPKSQRDRPPRTASEVKKVLGWDVEPEHQE
STAKAWCDLTQEEKEEIMRNNEKLFDAGGITPSTLPSTFERADPVDSPIEQQPVTWSA
SGGVDIGVNDLTTVSGPFWNMCPLPPLDARNNGPAKEPLIGDMIEFYEGHIFHYAIYI
GQGKTIGVHSPQAAFSIPRITIHPLVAWWRVCYVPTNQQRLTYDQLKELENEPWPYAS
ITNNCYEFCCRVMALDDTWLERRLVSTGKFNHPTQDWSQDTPDFHQDSKLEMVRDAVL
SAINGLVSQPFKNILSKIKPLNVLNLLSNCDWTFMGVVELIVLLAELFDVFWTPPDIS
SFIASLLPEFHLQGPEDLARDLVPLILGGIGLAIGFTRDKVTKVMKSAVDGLRSATQL
GQYGLEIFSIIKKYFFGGDQTEKTLRGIEDAVIDMEVLSSTNVTQLVKDKKLARTYMN
VLDNEEEKARKLSVRSADPHIVTSVNNLISRISMARSALAKAQAEMTSRPRPVVIMMC
GPPGIGKTKAAEHLAGRLANEIRPGGKVGLVPRESIDHWDGYHGEDVLLWDDYGMSKI
TEDCNKLQAIADTAPLSLNCDRIENKGMQFSSDAIIITTNAPGPAPVDFVNLGPVCRR
VDFLVYCSAPEIEQMRRTHPGDANAIKDLYKRDYSHLKMELAPQGGFDSQGNTPFGKG
IMKPTTLNRLLIQATALAMERQDEFQLQGAVYNFDEDRVSAFTSLARANGLGLLSMAT
LGKRLRSVKSMEGLRNALVGYKIGECDIIWNTRVYSIKSDGSTVTIKEKQTPTSPQYQ
AISTATLALSRLRAARALAYASCLQSAVLSILQVAGSALVVSRAVKRMFGTRTEQPML
EGKHKEHNCRVHRAEAAGHGPIGHDGVIERYGLCESEQEEEGEQTVELPTANKEGKNK
GKTKKGRGRKSNFNAFSRRGLSDEEYEEYKKIREEKSGNYSIQEYLEDRQRYEEELAE
VQAGGDGGIGETEAEIRHRVFYKSKSGMRKQRQEERRQLGLVSGSEIRKRKPIDWTPP
KNDWSEDTRTVNYDEHISFEAPPSIWSRVVKFGSGWGFWVSSTVFITTTHVIPPGAKE
VFGEDLSNVAIHRVGEFTQFRFSKKMRPDLTGMVLEEGCPEGTVCTIMIKRDSGELLP
LAVRMGAVASMKIQGKLMHGQSGMLLTGANAKGMDLGTIPGDCGAPYVHKRGNDWVVC
GVHAAATKSGNTVVCAIQGGDGEATLEGGGQNKGHYAGHPILRYGNGPSLSTKTKFWK
STPQPLPPGTYEPAYLGGRDPRVEGGPSLQQVLRDQLKPFAEPRGRLPEAGLLEAAVE
TVTNAIEQVMDTPVAWSYSDACMSLDKTTSSGHPHHKKKNDDWNGNSFVRELGDQAAH
ANSMYELGKSMKPVYTAALKDELVKPDKVYTKIKKRLLWGADLGTVIRAARAFGPFCE
AIKPHVIKLPIKVGMNAIEDGPLIYAEHSKYKFHYDADYTAWDSTQNREIMMESFNIM
SKLTANPSLAAVVAQDLLSPSEMDVGDYVISVKDGLPSGFPCTSQVNSINHWILTLCA
LSEVTGLSPDVIQSQSYFSFYGDDEIVSTDIEFDPIRLTQILKEYGLKPTRPDKTDGP
IIIRQQVDGLVFLRRTISKDAIGYQGRLDRNSIERQLWWTRGPNHEDPFETLVPHSQR
KVQLISLLGEAALHGEKFYRKIAGRVIQEVKEGGLEIYIPGWQAMFRWMRFHDLSLWT
GDRDLLPDYVNDDGV"
mat_peptide 5..1219
/gene="ORF1"
/product="p48"
mat_peptide 1220..2308
/gene="ORF1"
/product="NTPase"
mat_peptide 2309..2908
/gene="ORF1"
/product="p22"
mat_peptide 2909..3328
/gene="ORF1"
/product="VPg"
mat_peptide 3329..3871
/gene="ORF1"
/product="Pro"
mat_peptide 3872..5401
/gene="ORF1"
/product="RdRp"
gene 5388..7025
/gene="ORF2"
CDS 5388..7025
/gene="ORF2"
/codon_start=1
/product="VP1"
/protein_id="AWR17840.1"
/translation="MMMASKDAPTNMDGTSGAGQLVPEANTAEPISMEPVAGAATAAA
TAGQVNMIDPWIMNNYVQAPQGEFTISPNNTPGDILFDLQLGPHLNPFLSHLAQMYNG
WVGNMKVKVLLAGNAFTAGKIIISCIPPGFAAQNISIAQATMFPHVIADVRVLEPIEV
PLEDVRNVLFHNNDNTPTMRLVCMLYTPLRASGSSSGTDPFVIAGRVLTCPSPDFSFL
FLVPPNVEQKTKPFSVPNLPLNTLSNSRVPSLIKSMMVSRDHGQMVQFQNGRVTLDGQ
LQGTTPTSASQLCKIRGSVFHANGGNGYNLTELDGSPYHAFESPAPIGFPDLGECDWH
MEASPTTQFNTGDVIKQINVKQESAFAPHLGTVQVDGLSDVSVNTNMIAKLGWVSPVS
DGHKGDVDPWVIPRYGSTLTEAAQLAPPIYPPGFGEAIVFFMSDFPIAHGTNGLSVPC
TIPQEFVTHFVNEQAPTRGEAALLHYLDPDTNRNLGEFKLYPDGFMTCVPNSSGTGPQ
TLPINGVFVFVSWVSRFYQLKPVGTAGPARRLGIRRS"
gene 7025..7672
/gene="ORF3"
CDS 7025..7672
/gene="ORF3"
/codon_start=1
/product="VP2"
/protein_id="AWR17841.1"
/translation="MAQAILGAIAATAAGSAVGAGIQAGTEAALQHQRFQQDLTLQKN
SFIHDKEMMGLQVEASTALLQNSLGTRYNMLTKAGMTSADAARMVVGAPATRVVDWNG
TRIAAPMSTATTLRSGGFMTVPTVYRGSKNKQSIGGGFSNVNYDPSVSSSRTSQWVSS
QNSMRSTLEPFHPGALRTTWVTPPGSTSTSTISTVSTVPKFFNTERLPLFANRGK"
ORIGIN
1 gtgaatgatg atggcgtcca acgacgctat tgccgttgct gatgtcagca ataacaatgc
61 taacaccaac aatgataaca ttggatcccg cctcatggcg aggatccgtg ggcgcatggg
121 cccacaacgt ggtgaaacaa ccacaaaaat aacagacgcc aatatggcgc ttaatctgct
181 acgccggtca caaacacctt ccccatcccg gcaagagagc cctcctaaga gccagagaga
241 tcgcccccct cggactgctt ctgaggtgaa gaaagtgttg gggtgggatg ttgaaccaga
301 acaccaggaa agcacggcca aggcatggtg cgacctcacg caagaagaga aggaggagat
361 aatgcgcaat aatgaaaagc tcttcgatgc tgggggaatc accccatcaa ctttgcctag
421 cacgtttgaa agggccgacc cagtcgatag ccccattgaa cagcaacctg tgacatggtc
481 tgctagtggt ggggtcgata ttggtgtcaa tgatttgacc accgtcagtg gcccattttg
541 gaatatgtgc cccctcccgc cactggatgc tcggaataat ggccccgcta aggagcccct
601 cataggagac atgatagagt tctatgaggg tcatatattc cattatgcca tctatattgg
661 acaaggtaag accattgggg tccactcacc gcaagcagct ttctccatac caaggataac
721 catccatcct ctggtagcct ggtggcgcgt gtgctacgtt ccaactaacc agcagcgcct
781 cacttatgac cagctcaaag agttggagaa tgagccatgg ccctacgctt ccattacaaa
841 caattgctat gagttttgct gcagagtgat ggcacttgac gacacatggc ttgagaggag
901 gttagtcagc actggaaaat tcaatcaccc cacacaagat tggtcacagg ataccccgga
961 ttttcaccag gactcgaaac ttgagatggt aagagatgcc gtgctatcag ctattaatgg
1021 ccttgtgtca cagcccttta aaaacatttt gtcaaagatc aaaccattaa acgttctcaa
1081 tctcttgtca aattgtgatt ggaccttcat gggggttgtg gaactgattg tgctcctagc
1141 ggagttgttt gatgtgttct ggaccccacc agacatctca agtttcattg cctcactact
1201 acctgaattt cacctgcagg gcccagaaga cctagctagg gacttggtcc ctctcatcct
1261 aggtggtata ggcctggcta ttggctttac aagagacaaa gtgacgaaag tgatgaagag
1321 tgccgtcgat gggttgagat cggcgacaca gctcgggcag tacggactgg aaatattctc
1381 aatcatcaag aaatatttct ttggtgggga tcaaacggaa aagaccttac ggggtattga
1441 ggatgcagtg atagacatgg aggtgttatc tagcaccaat gtgacacaat tggttaaaga
1501 taagaaattg gccagaacct acatgaatgt gctagacaat gaagaggaaa aagcaaggaa
1561 actctcagtc cgtagtgctg atccgcacat agtgacctca gttaacaatc tgatatcacg
1621 aatatctatg gcaagatcag ccttggccaa agcccaggct gagatgacat ctcgcccacg
1681 ccctgtggtc ataatgatgt gtggcccccc cggcatcgga aaaaccaagg ccgccgaaca
1741 cctggctggc cgattggcaa acgagattag accaggaggt aaggttggac ttgtgccccg
1801 ggaatccata gatcactggg acggatacca tggcgaggat gtcctactat gggatgacta
1861 tggcatgtca aagataacag aggactgtaa taagctacaa gccatagctg acactgcacc
1921 cctatcactt aattgtgaca ggatagagaa caaaggcatg caattctcct cagatgcaat
1981 aatcataacc accaatgccc ctggcccggc cccggtggac tttgtcaacc taggccctgt
2041 gtgcaggcga gtggactttt tagtttactg ttctgcccct gaaattgagc aaatgagaag
2101 gacccaccct ggtgatgcca atgccatcaa agacctatac aaaagggact actcacactt
2161 aaagatggaa ttggccccac aaggtggttt tgatagtcag ggtaacacac catttgggaa
2221 gggcatcatg aaacccacga ccctcaatag gctactcatt caggcaacag cattagctat
2281 ggagcggcaa gacgagttcc agctccaagg tgctgtctac aactttgatg aagacagggt
2341 gtccgccttc acaagcctgg cccgagctaa cggcttgggg cttttaagca tggcaacatt
2401 gggtaaaagg ctcagaagtg tcaaatctat ggagggcctg cgtaacgcat tggtgggcta
2461 caaaatagga gagtgtgata taatctggaa cactagagtg tattcaatta aaagtgatgg
2521 tagtactgtc acaatcaagg aaaaacaaac cccaacttca ccccaatacc aagccattag
2581 cacagccact cttgcactct ctaggttgcg ggccgctaga gctctcgcgt acgcctcctg
2641 cctgcagagt gcagtgctgt caatacttca agtagctggc tctgccctgg tggtgagtag
2701 agccgttaag cgcatgtttg gcacgcgcac tgaacaacct atgttggaag gcaagcacaa
2761 agaacacaac tgtagagtgc accgcgcaga ggcagctggc catggtccta ttgggcacga
2821 tggagtcatc gaacgctatg gcctctgtga gagtgagcaa gaagaagaag gcgagcaaac
2881 agttgagcta cccactgcca ataaagaagg caaaaacaag ggcaagacca aaaagggccg
2941 tggacgaaaa tccaatttta atgctttctc aagacgaggc ctcagtgatg aagaatatga
3001 agaatacaag aagatcagag aagaaaagag tggcaattac agcatccagg agtacctcga
3061 ggaccgccag cgatatgagg aagaacttgc tgaagtgcaa gctggtgggg atggtggaat
3121 tggtgagact gaagcagaga ttcgccatcg ggttttctat aaatcaaaat ccggcatgag
3181 aaagcaacgc caagaagaac ggcgtcagtt gggtctcgtt agcggttctg agatccgcaa
3241 acgcaagccc atagactgga ccccccctaa gaacgattgg tcagaagaca ccaggactgt
3301 caactatgat gaacacatta gctttgaagc tcctccctca atttggagta gggtggtgaa
3361 gtttggcagt ggttggggtt tttgggtgag ctcaacagtg ttcataacca cgacccatgt
3421 cataccacct ggggccaaag aagtctttgg tgaagacctc agtaacgtgg ccatccatag
3481 agttggtgag ttcacccagt tccgtttctc caaaaagatg agacctgacc tcaccggtat
3541 ggttttagaa gaaggttgcc cagagggaac agtgtgcacc ataatgatca agagagattc
3601 tggtgagttg ctgccgctcg ccgttcggat gggggcagtg gcatcaatga agatccaagg
3661 caaacttatg catgggcaat caggaatgtt actcaccggt gctaatgcca aaggcatgga
3721 ccttgggact atacccggtg attgtggggc accctatgtc cacaagaggg gaaatgactg
3781 ggtggtctgt ggagtacatg cagccgccac aaaatcaggt aacactgtgg tgtgcgccat
3841 acaaggtggc gatggtgaag ccactctaga aggcggcggt caaaacaagg gccactatgc
3901 agggcatccg atactaaggt atgggaatgg cccttcacta tcaaccaaaa caaaattttg
3961 gaaatcaacc ccccagcctt tgcctcctgg tacatatgag ccagcttacc ttggaggcag
4021 agaccccaga gttgaggggg gcccatcctt acagcaggtg ttaagggacc agttaaaacc
4081 atttgccgag ccccgtggca gattacccga agcgggtttg ttggaagctg cagttgaaac
4141 ggtcaccaat gctattgaac aggtcatgga cacaccggtg gcatggagct atagtgatgc
4201 ttgcatgtca ctagataaga caaccagctc cggccacccc catcacaaga agaaaaatga
4261 tgattggaat gggaattcat ttgtgagaga attgggtgac caggcggcac acgctaacag
4321 catgtatgag cttggtaagt ccatgaagcc tgtgtataca gcagccctaa aggatgagct
4381 agtcaaacca gataaggtgt atacaaaaat caaaaagaga ctgctttggg gcgcggacct
4441 cggtaccgtc attcgcgctg ccagagcatt tggaccattt tgtgaggcca taaaacccca
4501 tgtaattaag ttgcctatca aggtgggtat gaatgccata gaggatggcc ccttgattta
4561 tgctgagcac tccaaatata aatttcatta tgatgctgac tatacagctt gggactcaac
4621 acaaaacaga gaaatcatga tggaatcttt caacattatg agcaagctta cagccaatcc
4681 ctccttggcc gcagtggtgg cacaggatct actctcccca tctgaaatgg atgttggtga
4741 ctatgtaatc agtgtcaaag atggtttacc atctggcttt ccatgcactt cacaggtgaa
4801 cagtatcaac cactggatac taaccctgtg tgcactgtca gaagtcactg gcttgtcccc
4861 agatgtgata cagtcacaat cctacttctc attttatggt gatgatgaaa tagtctcaac
4921 agatatagaa tttgacccaa tcagattgac acaaattctg aaggaatatg gtttgaagcc
4981 tacaagacct gacaaaactg atggcccaat tattattaga caacaggttg atggcctggt
5041 cttcctccgg cgcaccattt ctaaggatgc cattggatac cagggacgac tcgaccgtaa
5101 ctctattgaa aggcagcttt ggtggactcg tggaccaaac catgaggacc catttgagac
5161 actggtccca cattcacaga gaaaggtcca attaatatcc ttgctaggtg aagcagcact
5221 ccacggtgaa aagttctaca ggaagatagc tggtagggtc attcaagaag tcaaagaggg
5281 agggcttgaa atctacattc ctggttggca ggccatgttc cgctggatgc gattccatga
5341 tctaagtttg tggacaggag accgcgatct cctgcccgat tatgtaaatg atgatggcgt
5401 ctaaggacgc cccaacaaac atggatggca ccagtggtgc cggccagctg gtaccagagg
5461 caaacacagc tgagcctata tcaatggagc ccgtggctgg ggcagcaaca gctgccgcaa
5521 ctgctggcca agttaatatg attgacccct ggataatgaa caattatgta caagcccccc
5581 aaggtgaatt taccatatcg cctaataaca caccaggtga tattttgttt gatttacaat
5641 taggccccca ccttaaccct ttcttatctc atttggccca aatgtataat ggctgggttg
5701 gcaatatgaa agtaaaggtt ctattggctg gtaatgcttt cacggctggt aaaataatta
5761 ttagttgcat accccctggc tttgccgcac aaaatatttc tattgcccag gccaccatgt
5821 tcccccatgt catagctgat gttagggttt tggaacccat tgaggtgcca ttggaagatg
5881 tgaggaatgt gctcttccac aacaatgaca acacgccaac tatgcggttg gtgtgcatgc
5941 tatacacccc cttgcgggcc agcggtagct cgtctggaac tgaccccttt gtgattgctg
6001 ggcgtgtttt gacatgccca agtcctgatt ttagcttttt gtttttggtc ccccccaatg
6061 tagagcaaaa gactaaacct ttcagtgtcc caaaccttcc attgaatacc ctttcaaatt
6121 cgagagtccc ttctctaatc aaatcaatga tggtgtccag ggaccatggg cagatggttc
6181 agtttcaaaa tggtagggtc accctagatg ggcagctgca aggcaccaca cccacatcag
6241 ctagtcagct gtgcaaaatc aggggcagtg tcttccatgc caatggtggg aatgggtata
6301 acttaacaga actggatggg agcccatacc acgcatttga gagccccgca ccaatagggt
6361 ttccagatct aggtgaatgt gattggcaca tggaggcttc tcctaccacc caatttaata
6421 ctggagatgt tataaaacaa atcaatgtta aacaagagtc agcatttgcc ccccaccttg
6481 gcaccgtaca ggtagacggc ctgagtgatg tgagtgtcaa caccaacatg atagctaaat
6541 taggatgggt gtctcccgtc agtgatggac acaaagggga tgtcgacccg tgggtcattc
6601 cacgctatgg ttcaactctg actgaggccg cccaattagc ccccccaata tatcccccag
6661 gctttggtga ggccattgtg tttttcatgt cagattttcc cattgcccat ggcaccaatg
6721 gtttgagtgt gccttgcact ataccccaag aatttgtcac ccattttgtc aatgaacagg
6781 cccctactag aggggaagca gccctgctac actatctgga ccctgatact aatagaaatc
6841 ttggtgagtt taaattatat cctgatggct tcatgacatg tgtgcctaac tccagtggca
6901 ctggtccaca aactcttcca atcaatggcg tctttgtctt tgtgtcctgg gtttctagat
6961 tttatcaatt aaagcctgtg ggaacagccg gcccggctcg taggcttggg attaggagat
7021 cataatggct caagccatac ttggagccat agcagcaaca gcagccggta gtgctgttgg
7081 tgctggtata caagctggaa ccgaagctgc cctacagcat caaagatttc agcaagattt
7141 gaccttacaa aagaattcct ttattcatga taaagagatg atgggcctac aggtagaggc
7201 ttcaactgca ctcctccaaa acagcttggg tacgaggtac aatatgttga ccaaagcagg
7261 gatgacatcc gcagatgcgg cacgtatggt agtgggggca cccgcgactc gtgtcgttga
7321 ctggaacggg actaggatcg ccgcacccat gtcaactgcg acgacactta ggtctggtgg
7381 tttcatgacc gtaccaactg tttatagggg tagtaaaaat aaacaatcaa ttggtggtgg
7441 tttttctaat gtaaattatg atccctcagt ctcctcttcc cgcacttctc aatgggtctc
7501 ttctcaaaat tcaatgcgtt ccactctgga accgtttcat ccaggtgctc tgagaaccac
7561 atgggtcacc ccacctgggt caacttctac ttctacaatt tctacagttt ctactgtgcc
7621 aaaattcttt aatacagaaa ggttaccctt attcgcaaat aggggtaagt gattttgtaa
7681 tatgaattag tgggcatcat attcaatttg gaatcaatta gatatttaga ttggcagatg
7741 atgtt
//