Typing tool
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Typing tool
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Complete norovirus genomes
| MH218720 | GI.2 | |
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| GI.P2 |
ORF1: 5..5371
ORF2: 5355..6995
ORF3: 6995..7630
LOCUS MH218720 7710 bp RNA linear VRL 11-JUN-2018
DEFINITION Norovirus GI isolate NORO_79_05_07_2014, complete genome.
ACCESSION MH218720
VERSION MH218720.1
KEYWORDS .
SOURCE Norovirus GI
ORGANISM Norovirus GI
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norovirus norwalkense.
REFERENCE 1 (bases 1 to 7710)
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 7710)
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..7710
/organism="Norovirus GI"
/mol_type="genomic RNA"
/isolate="NORO_79_05_07_2014"
/host="Homo sapiens"
/db_xref="taxon:122928"
/geo_loc_name="United Kingdom"
/collection_date="05-Jul-2014"
/note="genotype: GI.P2_GI.2"
gene 5..5371
/gene="ORF1"
CDS 5..5371
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="AWR17820.1"
/translation="MMMASKDVVATNVASNNNANNTSATSRFLSRFKGLGGGASPPSP
IKIKSTEMALGLIGRTTPESTGTAGPPPKQQRDRPPRTQEEVQYGMGWSDRPIDQNVK
SWEELDTTVKEEILDNHKEWFDAGGLGPCTMPPTYERVRDDSPPGEQVKWSARDGVNI
GVERLTTVSGPEWNLCPLPPIDLRNMEPASEPTIGDMIEFYEGHIYHYSIYIGQGKTV
GVHSPQAAFSVARVTIQPIAAWWRVCYIPQPKHRLSYDQLKELENEPWPYAAITNNCF
EFCCQVMNLEDTWLQRRLVTSGRFHHPTQSWSQQTPEFQQDSKLELVRDAILAAVNGL
VSQPFKNFLGKLKPLNVLNILSNCDWTFMGVVEMVILLLELFGVFWNPPDVSNFIASL
LPDFHLQGPEDLARDLVPVILGGIGLAIGFTRDKVTKIMKSAVDGLRAATQLGQYGLE
IFSLLKKYFFGGDQTERTLKGIEAAVIDMEVLSSTSVTQLVRDKQAAKAYMNILDNEE
EKARKLSAKNADPHVISSTNALISRISMARSALAKAQAEMTSRMRPVVIMMCGPPGIG
KTKAAEHLAKRLANEIRPGGKVGLVPREAVDHWDGYHGEEVMLWDDYGMTKIQDDCNK
LQAIADSAPLTLNCDRIENKGMQFVSDAIVITTNAPGPAPVDFVNLGPVCRRVDFLVY
CSAPEVEQIRRVSPGDTSALKDCFKPDFSHLKMELAPQGGFDNQGNTPFGRGTMKPTT
INRLLIQAVALTMERQDEFQLQGKMYDFDDDRVSAFTTMARDNGLGILSMAGLGKKLR
GVTTMEGLKNALKGYKISACTIKWQAKVYSLESDGNSVNIKEERNILTQQQQSVCAAS
VALTRLRAARAVAYASCIQSAITSILQIAGSALVVNRAVKRMFGTRTATLSLEGPPRE
HKCRVHMAKAAGKGPIGHDDVVEKYGLCETEEDEEVAHTEIPSATMEGKNKGKNKKGR
GRKNNYNAFSRRGLNDEEYEEYKKIREEKGGNYSIQEYLEDRQRYEEELAEVQAGGDG
GIGETEMEIRHRVFYKSKSRKHHQEERRQLGLVTGSDIRKRKPIDWTPPKSAWADDER
EVDYNEKISFEAPPTLWSRVTKFGSGWGFWVSSTVFITTTHVIPTSAKEFFGEPLTSI
AIHRAGEFTLFRFSKKIRPDLTGMILEEGCPEGTVCSVLIKRDSGELLPLAVRMGAIA
SMRIQGRLVHGQSGMLLTGANAKGMDLGTIPGDCGAPYVYKRANDWVVCGVHAAATKS
GNTVVCAVQASEGETTLEGGDKGHYAGHEIIKHGCGPALSTKTKFWKSSPEPLPPGVY
EPAYLGGRDPRVTGGPSLQQVLRDQLKPFAEPRGRMPEPGLLEAAVETVTSSLEQVMD
TPVPWSYSDACQSLDKTTSSGFPYHRRKNDDWNGTTFIRELGEQAAHANNMYEQAKSM
KPMYTAALKDELVKPEKVYQKVKKRLLWGADLGTVVRAARAFGPFCDAIKSHTIKLPI
KVGMNSIEDGPLIYAEHSKYKYHFDADYTAWDSTQNRQIMTESFSIMCRLTASPELAS
VVAQDLLAPSEMDVGDYVIRVKEGLPSGFPCTSQVNSINHWLITLCALSEVTGLSPDV
IQSMSYFSFYGDDEIVSTDIEFDPAKLTQVLREYGLKPTRPDKSEGPIIVRKSVDGLV
FLRRTISRDAAGFQGRLDRASIERQIYWTRGPNHSDPFETLVPHQQRKVQLISLLGEA
SLHGEKFYRKISSKVIQEIKTGGLEMYVPGWQAMFRWMRFHDLGLWTGDRNLLPEFVN
DDGV"
gene 5355..6995
/gene="ORF2"
CDS 5355..6995
/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) [ATA
ending at position 6992 on + strand];first in-frame stop
codon exists 3' of stop position predicted by homology to
reference [homology search predicted 5355..6992 revised to
5355..6995 (stop shifted 3 nt)]"
/codon_start=1
/product="VP1"
/protein_id="AWR17818.1"
/translation="MMMASKDAPQSADGASGAGQLVPEVNTADPLPMEPVAGPTTAVA
TAGQVNMIDPWIVNNFVQSPQGEFTISPNNTPGDILFDLQLGPHLNPFLSHLSQMYNG
WVGNMRVRILLAGNAFSAGKIIVCCVPPGFTSSSLTIAQATLFPHVIADVRTLEPIEM
PLEDVRNVLYHTNDNQPTMRLVCMLYTPLRTGGGSGNSDSFVVAGRVLTAPSSDFSFL
FLVPPTIEQKTRAFTVPNIPLQTLSNSRFPSLIQGMILSPDASQVVQFQNGRCLIDGQ
LLGTTPATSGQLFRVRGKINQGARTLNLTEVDGKPFMAFDSPAPVGFPDFGKCDWHMR
ISKTPNNTSSGDPMRSVSVQTNVQGFVPHLGSIQFDEVFNHPTGDYIGTIEWISQPST
PPGTDIDLWEIPDYGSSLSQAANLAPPVFPPGFGEALVYFVSAFPGPNNRSAPNDVPC
LLPQEYITHFVSEQAPTMGDAALLHYVDPDTNRNLGEFKLYPGGYLTCVPNGVGAGPQ
QLPLNGVFLFVSWVSRFYQLKPVGTASTARGRLGVRRI"
gene 6995..7630
/gene="ORF3"
CDS 6995..7630
/gene="ORF3"
/codon_start=1
/product="VP2"
/protein_id="AWR17819.1"
/translation="MAQAIIGAIAASAAGSALGAGIQAGAEAALQSQRYQQDLALQRN
TFEHDKDMLSYQVQASNALLAKNLNTRYSMLVAGGLSSADASRAVAGAPVTQLIDWNG
TRVAAPRSSATTLRSGGFMAVPMPVQSKSKALQSSGFSNPAYDTSTVSSRTSSWVQSQ
NSLRSVSPFHRQALQTVWVTPPGSTSSSSVSSTPYGVFNTDRMPLFANLRR"
ORIGIN
1 gtgaatgatg atggcgtcga aagacgtcgt tgcaactaat gttgcaagca acaacaatgc
61 taacaacact agtgctacat ctcggttctt atcgagattt aagggcttag gaggcggcgc
121 aagcccccct agccctataa aaattaaaag tacagaaatg gctctggggt taattggcag
181 aacgacccca gaatcaacgg ggaccgctgg cccaccgccc aaacaacaga gagaccgacc
241 tcctagaact caggaggagg tccagtacgg tatggggtgg tctgacaggc ccattgacca
301 gaacgtcaaa tcatgggaag agcttgacac cacagttaag gaagagatcc tagacaacca
361 caaagaatgg tttgacgctg gtggtttggg tccttgcaca atgcctccaa catatgaacg
421 ggtcagggat gacagtccgc ctggtgaaca ggttaaatgg tccgcacgtg atggagtcaa
481 cattggagtg gaacgcctca caacagtgag tgggcctgag tggaatcttt gccccttacc
541 ccccattgat ttgaggaaca tggaaccagc tagtgaaccc actattggag atatgataga
601 attctacgaa ggccacatct atcattactc catatacatt gggcaaggta agacagtcgg
661 cgtccattct ccacaggcgg cattttcagt ggctagagtg accatccagc ccatagccgc
721 ttggtggaga gtttgttaca taccccaacc caagcataga ctgagttacg accaactcaa
781 ggaactagag aatgagccat ggccatacgc ggccataact aataattgtt ttgaattctg
841 ctgtcaagtc atgaaccttg aggacacgtg gttgcaaagg cgactggtca cgtcgggcag
901 attccaccac cccacccagt cgtggtcaca gcagacccct gagttccaac aagatagcaa
961 gttagagttg gttagggacg ccatattggc tgcagtgaat ggtcttgttt cgcagccctt
1021 taagaacttc ttgggtaaac tcaaacccct caatgtgctt aacatcctgt ctaactgtga
1081 ttggaccttc atgggggtgg tggaaatggt catactatta cttgaactct ttggtgtgtt
1141 ctggaacccg cctgatgtat ccaattttat agcgtccctt cttcctgatt tccatcttca
1201 gggacctgaa gacttggcac gagatctagt cccagtgatt cttggtggta taggattggc
1261 cattgggttc accagagaca aagttacaaa gatcatgaag agtgctgtgg atggtcttcg
1321 agctgctaca caactgggac agtatggatt agaaatattc tcactgctca agaagtactt
1381 ctttgggggg gaccagactg agcgcaccct caaaggcatt gaggcagcag tcatagatat
1441 ggaggtactg tcctccactt cagtgacaca gctagtgagg gacaaacagg cagcaaaggc
1501 ctatatgaac atcttggaca atgaagaaga gaaggccagg aagctctctg ctaaaaacgc
1561 tgacccacat gtgatatcct caacaaatgc cctaatatcg cgcatatcca tggcacgatc
1621 tgcattggcc aaggcccagg ctgagatgac cagtcgaatg cgaccagttg tcattatgat
1681 gtgtggtcca cctgggattg ggaagaccaa ggctgctgag cacctagcta agcgtctagc
1741 caatgagatc agaccaggtg gtaaggtggg gttggttccc cgtgaagctg tcgaccactg
1801 ggacggctat catggtgagg aagtgatgct gtgggatgac tatggcatga caaaaataca
1861 agacgactgt aataaactcc aggccattgc tgattcggcc cccctcacat taaattgtga
1921 taggattgaa aataaaggaa tgcagttcgt ttcagatgca atagtcatca ccaccaacgc
1981 cccaggcccc gcccctgtgg actttgtcaa ccttggacca gtgtgtagac gggtcgactt
2041 tttggtgtac tgctctgccc cagaggtgga gcagatacgg agagtcagcc ctggcgacac
2101 atcagcactg aaagactgct tcaagccaga tttctcacat ttaaaaatgg agctggctcc
2161 acaaggtggg ttcgataatc aagggaacac accgtttggc aggggcacca tgaagccaac
2221 aaccattaat agactcctca tacaagccgt ggcccttacc atggaaaggc aggatgagtt
2281 ccagttgcag ggaaagatgt atgactttga tgatgacagg gtgtcagcgt tcaccaccat
2341 ggcacgtgac aatggcctgg gcatcttgag catggcgggt ctaggtaaga agctacgcgg
2401 tgtcacaacg atggagggct tgaagaatgc cctgaaggga tacaaaatta gtgcgtgcac
2461 aataaaatgg caggctaaag tgtactcact agagtcagat ggcaacagtg tcaacattaa
2521 agaggagagg aacatcttaa ctcaacaaca acagtcagtg tgtgctgcct ctgttgcgct
2581 cactcgcctc cgggctgcgc gtgcggtggc atacgcgtca tgcatccaat cggctataac
2641 ctctatacta caaattgctg gctcggccct agtggtcaac agagcagtga agagaatgtt
2701 tggcacgcgt actgccaccc tgtcccttga gggccccccc agagaacaca agtgcagggt
2761 ccacatggcc aaggccgcag gaaaggggcc tattggccat gatgatgtgg tagaaaagta
2821 tgggctttgc gaaactgagg aggacgaaga agtggcccac actgaaatcc cttctgccac
2881 catggagggc aagaataaag ggaagaacaa gaaaggacgt ggtcggaaga acaactacaa
2941 cgccttctcc cgcaggggac tcaatgatga agagtacgaa gagtacaaga agatacgcga
3001 ggagaaaggt ggcaattata gcatacagga gtacctagag gataggcaaa ggtatgaaga
3061 agagctagca gaggttcaag caggtggaga tggaggaatc ggggaaactg aaatggaaat
3121 ccgccacaga gtgttctaca aatctaagag tagaaagcat caccaggaag agcgacgcca
3181 gctagggctg gtaacaggtt ccgacattcg gaagagaaaa ccaatcgact ggaccccacc
3241 caagtcagca tgggcagatg atgagcgtga ggtggattac aatgagaaga tcagttttga
3301 ggcgcccccc actttatgga gcagagtgac aaagtttggg tctggatggg gtttctgggt
3361 cagctctaca gtcttcataa ccacaacgca cgtcatacca accagtgcga aggaattctt
3421 tggtgaaccc ctaaccagca tagccatcca cagggctggt gagttcactc tattcaggtt
3481 ctcaaagaaa attaggcctg acctcacagg tatgatcctt gaggagggtt gccccgaggg
3541 cacagtgtgt tcagtactaa taaaaaggga ctctggtgaa ctactgccat tggctgtaag
3601 aatgggcgca atagcatcaa tgcgtataca gggccgcctt gtccatgggc agtccggcat
3661 gttgctcacc ggggccaatg ctaagggcat ggaccttgga accatcccag gagactgtgg
3721 ggctccttat gtctataaga gagccaacga ctgggtggtc tgtggtgtac acgctgctgc
3781 caccaaatca ggcaacaccg ttgtgtgcgc cgttcaggcc agtgaaggag aaaccacgct
3841 tgaaggcggt gacaaaggtc attatgctgg acatgaaata attaagcatg gttgtggacc
3901 agccctgtca accaaaacca aattctggaa atcatccccc gaaccactac cccctggggt
3961 ctatgaaccc gcctacctcg ggggccggga ccctagggta actggcggtc cctcactcca
4021 acaggtgttg cgggaccagt taaagccatt tgctgagcca cgaggacgca tgccagagcc
4081 aggtctcttg gaggccgcag ttgagactgt gacttcatca ttagagcagg ttatggacac
4141 tcccgttcct tggagctata gtgatgcgtg ccagtccctt gataagacca ctagttctgg
4201 ttttccctac cacagaagga agaatgacga ctggaatggc accaccttta tcagggagtt
4261 aggggagcag gcagcacacg ctaataacat gtatgaacag gctaaaagta tgaaacccat
4321 gtacacggca gcacttaaag atgaactagt caaaccagag aaggtatacc aaaaagtgaa
4381 gaagcgcttg ttatgggggg cagacttggg cacggtggtt cgggccgcgc gggcttttgg
4441 tccattctgt gatgctataa aatcccacac aatcaaattg cccattaaag ttggaatgaa
4501 ttcaattgag gatgggccac tgatctatgc agaacattca aagtataagt accattttga
4561 tgcagattac acagcttggg attcaactca aaatagacaa atcatgacag agtcattctc
4621 aatcatgtgt cggctaactg catcacctga actagcttca gtggtggctc aagatttgct
4681 tgcaccctca gagatggatg ttggcgacta tgtcataaga gtgaaggaag gcctcccatc
4741 tggttttcca tgtacatcac aggttaatag tataaaccat tggttaataa ctctgtgtgc
4801 cctttctgaa gtaactggtc tgtcgccaga tgtcatccag tccatgtcat atttctcttt
4861 ctatggtgat gatgaaatag tgtcaactga catagaattt gatccagcaa aactgacaca
4921 agtcctcaga gagtatggac ttaaacccac ccgccccgac aaaagcgagg gcccaataat
4981 tgtgaggaag agtgtggatg gtttagtctt tttgcgtcgc actatctccc gcgacgccgc
5041 aggattccag gggcgactgg accgggcatc cattgaaagg caaatctact ggactagagg
5101 acccaaccac tcagaccctt ttgagaccct ggtgccacat caacaaagga aggtccaact
5161 aatatcatta ttgggtgagg cctcactgca tggtgaaaag ttttacagga agatttcaag
5221 taaagtcatc caggagatta aaacaggggg ccttgaaatg tatgtgccag gatggcaagc
5281 catgttccgt tggatgcggt tccatgacct tggtttgtgg acaggagatc gcaatctcct
5341 gcccgaattt gtaaatgatg atggcgtcta aggacgcccc tcaaagcgct gatggcgcaa
5401 gcggcgcagg tcaactggtg ccggaggtta atacagctga ccccttaccc atggaacctg
5461 tggctgggcc aacaacagcc gtagccactg ctgggcaagt taatatgatt gatccctgga
5521 ttgttaataa ttttgtccag tcacctcaag gtgagttcac aatctctcct aacaataccc
5581 ccggtgatat tttgtttgat ttacaattag gtccacatct aaaccctttc ttgtcacatt
5641 tgtcccaaat gtataatggc tgggttggga acatgagagt cagaattctc cttgctggga
5701 atgcattctc agctggaaag attatagttt gttgtgtccc ccctggcttt acatcttctt
5761 ctctcaccat agctcaggcc acattgtttc cccatgtaat tgctgatgtg agaacccttg
5821 agccaataga aatgcccctc gaggatgtac gcaatgtcct ctatcacacc aatgataatc
5881 aaccaacaat gcggttggtg tgtatgctat acacgccgct ccgcactggt ggggggtctg
5941 gtaattctga ttcctttgta gttgctggca gggttctcac agcccctagt agcgacttta
6001 gtttcttgtt ccttgtcccg cctaccatag agcagaagac tcgggctttc actgtgccta
6061 atatcccctt gcaaaccttg tccaattcta ggtttccttc cctcatccag gggatgattc
6121 tgtcccccga tgcatctcaa gtggtccaat tccaaaatgg gcgctgcctt atagatggtc
6181 aactcctagg cactacaccc gctacatcag gacagctgtt cagagtaaga ggaaagataa
6241 atcagggagc ccgcacactt aacctcacag aggtggatgg taaaccattc atggcatttg
6301 attcccctgc acctgtgggg ttccccgatt ttggaaaatg tgattggcat atgagaatca
6361 gcaaaacccc aaacaacaca agttcaggtg accccatgcg cagtgtcagc gtgcaaacca
6421 atgtgcaggg ttttgtgcca cacctgggaa gtatacaatt tgatgaagtg tttaaccatc
6481 ccacaggtga ctacattggc accattgaat ggatttccca gccatctaca ccccctggaa
6541 cagatattga tctgtgggag atccccgatt atggatcatc cctttcccaa gcagctaatc
6601 tggccccccc agtattcccc cctggatttg gtgaggccct tgtgtacttt gtttctgctt
6661 tcccgggccc caataaccgc tcagccccga atgatgtacc ctgtcttctc cctcaagagt
6721 acataaccca ctttgtcagt gaacaagccc caacgatggg tgacgcagcc ttactgcatt
6781 atgtcgaccc tgataccaac aggaaccttg gggagttcaa gctataccct ggaggttacc
6841 tcacctgtgt accaaatggg gtaggtgccg ggcctcaaca gcttcctctt aatggtgttt
6901 ttctctttgt ttcttgggtg tctcgttttt atcagcttaa gcctgtggga acagccagta
6961 cggcaagagg taggcttgga gtgcgccgta tataatggcc caagccatca taggagcaat
7021 tgccgcgtca gctgcaggct cagcattggg tgcgggcatc caggctggtg ccgaggctgc
7081 gcttcagagt caaagatacc aacaagactt agccctgcaa aggaatactt ttgaacatga
7141 caaggatatg ctttcctacc aggtccaggc aagtaatgca cttttggcaa agaatctcaa
7201 tacccgctat tctatgcttg ttgcaggggg tctttctagt gctgatgctt ctcgggctgt
7261 tgctggggcc cctgtaacac aattgattga ttggaacggc actcgggttg ccgcccccag
7321 atcaagtgca acaactctga ggtctggtgg tttcatggca gtccccatgc ctgttcaatc
7381 caaatctaag gccctgcaat cctctgggtt ttctaatcct gcttatgaca cgtccacagt
7441 ttcttctagg acttcttctt gggtgcagtc acagaattcc ctgcgaagtg tgtcaccctt
7501 tcataggcag gcccttcaaa ctgtatgggt tactccacct gggtctactt cctcttcttc
7561 tgtttcctca acaccttatg gtgtttttaa tacggatagg atgccgctat tcgcaaattt
7621 gcggcgttaa tgttgtaata taatgcagca gtgggcacta tattcaattt ggtttaatta
7681 gtgaataatt tggccattga ttagtgttaa
//