Typing tool

Complete norovirus genomes

MH218720  GI.2
 GI.P2

Length: 7,710 | 3 CDS

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.
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"
                     /country="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
//