Typing tool

Complete norovirus genomes

MH218625  GII.4 New Orleans
 GII.P31

Length: 7,560 | 3 CDS

ORF1: 5..5104
ORF2: 5085..6707
ORF3: 6707..7513
LOCUS       MH218625                7560 bp    RNA     linear   VRL 11-JUN-2018
DEFINITION  Norovirus GII isolate NORO_154_02_03_2015, complete genome.
ACCESSION   MH218625
VERSION     MH218625.1
KEYWORDS    .
SOURCE      Norovirus GII
  ORGANISM  Norovirus GII
            Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
            Picornavirales; Caliciviridae; Norovirus.
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_154_02_03_2015"
                     /host="Homo sapiens"
                     /db_xref="taxon:122929"
                     /country="United Kingdom"
                     /collection_date="02-Mar-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="AWR17533.1"
                     /translation="MKMASNDASAAAVANSNNDIAKSSSDGVLSNMAVTFKRALGARP
                     KQPPPKEIPPRPPRPPTPELVKKIPPPPPNGEDELVVSYSAKDGVSGLPELTTVRQPE
                     ETNTAFSVPPLNQRESRDAKEPLTGTIIEMWDGEIYHYGLYVERGLILGVHKPPAAIS
                     LAKVELIPLSLFWRPVYTPQYLISPDTLRRLHGESFPYTAFDNNCYAFCCWVLDLNDS
                     WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCTLSSLFTRPIKDIIGK
                     LKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED
                     LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
                     KREETNELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST
                     KSASPDIVGTINSLLARIAAARSLVHRAKEELSSRPRPVVVMISGRPGIGKTHLAREL
                     AKKIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC
                     PLTLNCDRIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK
                     AKRDFPGQPDMWKNAFSPDFSHIKLSLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA
                     SGLLHERLDEYELQGPALTTFNFDRNKILAFRQLAAENKYGLMDTMRVGKQLKDVKTM
                     SDLKQALKNIAIKKCQIVYNGSTYTLEADGKGSVKVDKVQSATVQTNNELAGALHHLR
                     CARIRYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQNLWSKPQVEDTEEMTNKDGC
                     LKPKDDEEFVVSSDDVKTEGKKGKNKSGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
                     KYSIEEYLQDRDRYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV
                     TGSEIRKRNPEDFKPKGKLWADDDRSVDYNEKLNFEAPPSIWSRIVNFGSGWGFWVSP
                     SLFITSTHVILQGAKEFFGVPIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG
                     TVATLLIKRPTGELMPLAVRMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
                     CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDSKGTYCGAPILG
                     PGSAPKLSTKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP
                     RGKPPRPNVLEAAKKTIINVLEQTIDPPQKWSFAQACASLDKTTSSGHPHHMRKNDCW
                     NGESFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKVYGKIKKRLLWGSDL
                     ATMIRCARAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFEKHSRYRYHYDADYSRWD
                     STQQRDVLAAALEIMVKFSPEPHLAQIVAEDLLSPSVMDVGDFQISISEGLPSGVPCT
                     SQWNSIAHWLLTLCALSEVTDLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLK
                     EYGLKPTRPDKTEGPLVISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP
                     NHEDPSETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQE
                     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"
                     /codon_start=1
                     /product="VP1"
                     /protein_id="AWR17534.1"
                     /translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
                     QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
                     FEVQVILAGNAFTAGKVIFAAVPPNFPTEGLSPSQVTMFPHIVVDVRQLEPVLIPLPD
                     VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
                     TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
                     QLSPVNICTFRGDVTHITGSHNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGVL
                     TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDLEANQNTKFTPVGVIQDG
                     GTTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
                     CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
                     IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRVV"
     gene            6707..7513
                     /gene="ORF3"
     CDS             6707..7513
                     /gene="ORF3"
                     /codon_start=1
                     /product="VP2"
                     /protein_id="AWR17535.1"
                     /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
                     SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
                     APMTKALDWSGTRYWAPDARTITYNAGRFSTPQPSGALPGRANLRDAVPARGSSSKSS
                     NSSTAISVYSNQTTSTRLGSTAGSGTSVSSLPPAARTRSWVEDQSRNLSPFMRGAHNI
                     SFVTPPSSRSSSQGTVSTVPKEVLNSWTGAFNTHRQPLFAHIRKRGESRA"
ORIGIN      
        1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgct gttgccaaca gcaacaacga
       61 catcgcaaaa tcttcaagtg acggtgtgct ttctaacatg gctgtcactt ttaagcgggc
      121 cctcggggcg cggcctaaac agccgccccc gaaggaaata ccacccagac ccccgcgacc
      181 acccacacca gaattggtca aaaagatccc tcctccccca cccaacgggg aggatgaact
      241 agtggtctct tacagcgcca aagatggcgt ttccgggctg cctgagctca ccactgtcag
      301 acaaccggaa gaaaccaaca cggcgttcag tgtcccccca ctcaaccaaa gggagagcag
      361 ggacgccaag gagccactaa ctggaacaat tattgaaatg tgggatggag aaatctacca
      421 ttacggcctg tacgtggaac gaggtcttat acttggtgtg cacaagccac cggcagccat
      481 cagccttgcc aaggtcgagc taataccgct ctctttgttc tggagacctg tatacacccc
      541 ccaatacctc atctctccag acactcttag gagactacat ggagagtcat tcccctacac
      601 tgcatttgac aacaattgct acgccttttg ttgttgggtg ttagacctaa atgactcatg
      661 gctaagcagg agaatgattc agagaacaac aggtttcttc aggccgtacc aggattggaa
      721 caggaaaccc ctccccacta tggacgattc caaattaaag aaggtagcca acatattctt
      781 gtgcactttg tcttcactat tcaccagacc catcaaggac ataataggga agttgaagcc
      841 tcttaacatc cttaacattc tggctacatg tgattggacc ttcgcaggca tagtggaatc
      901 cttaatactc ttggcagaac tctttggagt tttctggaca cccccagatg tgtctgcgat
      961 gatcgccccc ttgctaggtg attatgaact gcaaggacct gaggaccttg cagtggaact
     1021 ggtcccagta gtgatggggg ggataggtct ggtgctagga tttaccaaag agaaaattgg
     1081 aaagatgcta tcatccgctg catccacttt aagagcttgt aaagatcttg gtgcatacgg
     1141 actggaaatc ttgaaattgg tcatgaagtg gttctttcca aagagagagg aaacaaatga
     1201 actggctatg gtgagatcca tcgaggatgc agtgctagac ctcgaggcaa ttgagaacaa
     1261 ccacatgacc accctactca aagacaaaga cagcttggca acctacatga gaacccttga
     1321 ccttgaggag gagaaagcca gaaaactctc aaccaaatcc gcttcacccg atattgtggg
     1381 cacaattaac tctcttctgg caagaatcgc tgctgcacgc tccctagtgc atcgggcaaa
     1441 agaagagctc tccagcaggc cgagacctgt cgttgtgatg atatcgggaa gaccagggat
     1501 agggaaaact caccttgcca gggagctggc caagaagatc gcggcctccc tcacagggga
     1561 ccagcgtgtg ggtcttatcc cgcgcaatgg cgtcgaccac tgggacgcat acaagggcga
     1621 aagagttgtc ctatgggacg attatgggat gagcaacccc atccatgatg ccctcaggtt
     1681 gcaggagctt gctgacactt gccccctcac gctaaattgt gacagaattg aaaacaaagg
     1741 gaaagtcttt gacagtgatg ccataattat caccaccaac ctggccaacc cagcaccact
     1801 ggattatgtc aactttgaag cgtgctcgag acgcattgac ttcctcgtgt acgcagaagc
     1861 ccctgaagtg gaaaaggcaa agcgcgactt cccaggtcaa cctgacatgt ggaagaacgc
     1921 tttcagccct gacttctcac acataaaact atcattggct ccacagggtg gttttgacaa
     1981 gaacggcaac accccgcatg gaaaaggggt catgaagacc ctcaccactg gttccctcat
     2041 cgcccgagcg tcagggttac tccatgagag actagatgaa tatgaactgc aaggcccagc
     2101 cctcaccact ttcaactttg accgtaacaa gatacttgct tttagacagc ttgctgctga
     2161 aaacaagtac gggctgatgg acacaatgag agttggaaaa cagctcaagg atgtcaagac
     2221 catgtcagac ctcaaacaag cactcaagaa catcgcgatc aagaagtgcc agatagtgta
     2281 taatggtagc acctacacac ttgaggccga tggcaagggt agtgtgaaag ttgacaaagt
     2341 gcaaagtgcc actgtgcaga ccaacaatga gctagccggt gccctacacc acctaaggtg
     2401 cgctagaatc agatactatg ttaagtgcgt ccaggaggca ctgtattcta tcatccaaat
     2461 cgctggggct gcatttgtta ccacgcgcat cgctaagcgc atgaacatac agaatctctg
     2521 gtccaagcca caggtggaag acacagaaga gatgaccaac aaagatggtt gcctaaaacc
     2581 taaagatgat gaagagtttg tcgtctcatc cgacgacgtc aaaactgagg gcaagaaagg
     2641 gaagaacaag tccggccgtg gcaagaagca cacagccttt tcaagcaaag ggcttagtga
     2701 tgaggagtac gatgagtaca agagaatcag agaggaaagg aatggtaagt actccataga
     2761 agagtacctt caggacagag acaggtacta cgaggaggtg gccattgcca gggcaaccga
     2821 agaagacttc tgtgaagaag aagaggccaa aatccggcag aggatcttta gaccaacaag
     2881 gaaacaacgc aaagaagaga gggcctctct cggcttggtc acaggttctg aaatcaggaa
     2941 gagaaaccca gaagacttca aacccaaggg aaagctgtgg gctgatgatg acagaagtgt
     3001 tgactacaat gagaaactca actttgaggc cccaccaagc atctggtcgc ggatagtcaa
     3061 ctttggttca ggttggggct tctgggtctc ccccagtctg tttataacat caacccatgt
     3121 catactccaa ggtgcaaaag agttcttcgg ggtccctatc aagcaaattc aaatacacaa
     3181 atcaggtgaa ttctgccggt tgagattccc aaagccaatc agaactgatg tgacgggcat
     3241 gattctagaa gaaggtgcgc ccgaggggac cgtggccaca ctgctcatca aaaggccaac
     3301 tggagagctt atgcctctgg cagtcagaat ggggacccat gcaaccatga aaattcaggg
     3361 gcgcacagtt ggagggcaaa tgggtatgct cctgacagga tccaacgcca agagcatgga
     3421 cctaggcaca acaccaggcg actgcggctg cccctacatc tacaagaggg gaaatgacta
     3481 cgtggtcata ggagtccata cggccgctgc ccgtggagga aacactgtca tatgtgccac
     3541 ccaggggagt gagggagaag ccacacttga aggaggagac agtaaaggga catactgtgg
     3601 cgcaccaatc ttgggcccag ggagcgctcc gaagctcagt accaagacta agttttggag
     3661 atcatccaca acaccactcc cacctggcac ctatgaacca gcctacctcg gtggcaaaga
     3721 ccccagagtc aaaggtggcc cttcattaca acaagttatg agggaccagc taaaaccatt
     3781 cacagaaccc agaggcaaac caccaagacc aaatgtgttg gaagctgcca agaaaaccat
     3841 catcaacgtc cttgagcaaa caattgatcc accccaaaaa tggtcatttg cgcaagcttg
     3901 cgcatccctt gacaaaacca cctccagcgg ccacccgcac cacatgcgga aaaacgattg
     3961 ttggaacggg gagtccttca caggaaaatt ggctgatcaa gcctctaagg ccaacctaat
     4021 gtttgaagag ggaaagaaca tgactccagt ctacacaggt gcacttaaag atgagttggt
     4081 aaagaccgac aaagtttatg gtaagatcaa gaagaggctt ctgtggggtt cagatctggc
     4141 gaccatgata cggtgcgccc gagcttttgg aggccttatg gacgaactca aggcacactg
     4201 tgtcacactt cccgtcagag ttggtatgaa catgaatgag gatggcccca tcatctttga
     4261 gaagcactcc agatacagat atcactatga tgctgattat tcccggtggg actcaacaca
     4321 acaaagggat gtactagcag cagcactaga aatcatggtt aagttctctc cagaaccaca
     4381 cctggcccag atagttgcag aagacctcct ttcccctagc gtgatggatg taggtgactt
     4441 tcaaatatca ataagtgagg gtctcccctc tggggtacct tgtacctccc agtggaattc
     4501 catcgcccac tggctcctca ctctctgtgc actctctgaa gtcacagact tgtcccctga
     4561 catcattcag gccaactccc ttttctcctt ctatggtgat gatgagattg taagcacaga
     4621 cataaagttg gacccagaga agctgacagc aaaactcaag gagtacgggc tgaaaccaac
     4681 ccgccccgat aaaactgaag gaccccttgt tatctctgag gacttggatg gcctgacatt
     4741 cctccggagg actgtgaccc gtgatccagc tggttggttt ggaaaattgg aacaaagttc
     4801 aattctcagg caaatgtact ggaccagggg tcccaaccat gaagatccat ccgaaacaat
     4861 gataccacac tcccaaagac ccatacaatt gatgtccttg ctaggcgagg ctgcactcca
     4921 cggcccggca ttttatagca 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 tcatggctct ggagcccgtt gtaggtgccg ccattgcggc acctgtagcg ggccaacaaa
     5221 atgtaattga cccctggatt agaaacaatt ttgtgcaagc ccctggtgga gagtttacag
     5281 tatcccctag gaacgctcca ggtgaaatac tatggagcgc gcccttaggc cctgatctaa
     5341 atccctacct atcccatttg gccaggatgt acaatggtta tgcaggtggt tttgaagtgc
     5401 aggttattct cgcggggaac gcgttcaccg ccgggaaggt catatttgca gcagtcccac
     5461 caaattttcc aactgaaggc ttgagcccca gccaggtcac tatgtttccc catatagtag
     5521 tagatgttag gcaactagaa cctgtgttga ttcccttacc cgatgttagg aataatttct
     5581 atcactacaa tcaatcaaat gatcccacca ttaagttgat agcaatgttg tatacaccac
     5641 ttagggctaa taatgctggg gatgatgtct tcacagtttc ttgccgagtt ctcacgagac
     5701 catcccctga ttttgatttc atatttctag tgccacctac agttgagtca agaactaaac
     5761 cattctctgt cccagtttta actgttgagg agatgaccaa ttcaagattc cccattcctt
     5821 tggaaaagtt gttcacgggg cccagcagtg cctttgttgt tcaaccacaa aacggcaggt
     5881 gcacgactga tggcgtgctt ctaggcacca cccaactgtc tcctgtcaac atctgcacct
     5941 tcagagggga tgtcacccat atcacaggta gtcacaacta cacaatgaat ttggcttctc
     6001 aaaattggaa caattatgac ccaacagaag aaatcccagc ccctctagga actccagatt
     6061 ttgtggggaa gattcaaggc gtgctcaccc aaaccacaag gacagatggc tcaacacgcg
     6121 gccacaaagc tacagtgtac actgggagcg ccgactttgc tccaaaactg ggtagagttc
     6181 agtttgaaac tgacacagat catgatcttg aagctaacca aaacacaaag ttcaccccag
     6241 tcggtgttat ccaagatggt ggcaccaccc accgaaatga accccaacag tgggtgcttc
     6301 caagttactc aggtagaaac acccataatg tgcatctggc ccccgctgta gctcccactt
     6361 ttccgggtga gcaacttctc ttcttcagat ccacgatgcc cggatgcagc gggtacccca
     6421 acatggattt ggactgtctg cttccccagg aatgggtgca gtacttctac caagaggcag
     6481 ccccagcaca atctgacgtg gctctgctaa gatttgtgaa cccagacaca ggtagggttt
     6541 tgtttgagtg taagcttcat aaatcaggtt atgttacagt ggctcacact ggccaacatg
     6601 atttggttat cccccccaat ggttatttta gatttgattc ctgggtcaac cagttctaca
     6661 cgcttgcccc catgggaaat ggaacggggc gtagacgtgt agtataatgg ctggagcttt
     6721 ctttgctgga ttggcatctg atgtccttgg ctctggactt ggttccctta tcaatgctgg
     6781 ggctggggcc atcaatcaaa aagttgagtt tgaaaataac agaaaattgc aacaagcatc
     6841 cttccaattt agcagcaatc tacaacaggc ttccttccaa catgataaag agatgctcca
     6901 agcacaaatt gaggccacca agaagctaca acaggaaatg atgaaagtta agcaggcaat
     6961 gctcctagag ggtgggttct ctgagacaga tgcagcccgt ggggcaatca acgcccccat
     7021 gacaaaagct ttggactgga gcgggacaag gtactgggct cccgatgcta ggactataac
     7081 atacaatgca ggccgctttt ccacccctca accatcgggg gcactgccag gaagagctaa
     7141 tcttagggat gctgtccctg ctcggggttc ctccagcaaa tcttctaact cttctactgc
     7201 tatttctgtg tactcaaatc aaactacttc aacgagactt ggttctacag ctggttctgg
     7261 taccagtgtc tcgagtctcc cgccagctgc aaggactagg agttgggttg aggaccaaag
     7321 taggaatttg tcacctttta tgaggggggc ccacaacata tcgtttgtca ccccaccatc
     7381 tagcagatcc tctagccaag gcacagtctc aaccgtgcct aaagaggttt tgaactcctg
     7441 gactggcgct ttcaacacgc acaggcagcc actcttcgct cacattcgta agcgagggga
     7501 gtcacgggcg taatgtgaaa agacaaaatt gattatctct cttcttcttt aatgtctttt
//