Typing tool

Complete norovirus genomes

MH218701  GII.4 Sydney
 GII.P31

Length: 7,546 | 3 CDS

ORF1: 5..5104
ORF2: 5085..6707
ORF3: 6707..7513
LOCUS       MH218701                7546 bp    RNA     linear   VRL 11-JUN-2018
DEFINITION  Norovirus GII isolate NORO_42_01_09_2014, complete genome.
ACCESSION   MH218701
VERSION     MH218701.1
KEYWORDS    .
SOURCE      Norovirus GII
  ORGANISM  Norovirus GII
            Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
            Picornavirales; Caliciviridae; Norovirus.
REFERENCE   1  (bases 1 to 7546)
  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 7546)
  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..7546
                     /organism="Norovirus GII"
                     /mol_type="genomic RNA"
                     /isolate="NORO_42_01_09_2014"
                     /host="Homo sapiens"
                     /db_xref="taxon:122929"
                     /country="United Kingdom"
                     /collection_date="01-Sep-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="AWR17761.1"
                     /translation="MKMASNDASAAAAAKSNNDIAKSSSDGVLSNMAVTFKRALGARP
                     KQPPPKEIPPRPPRPPTPELVKKIPPPPPNGEDELVVSYSAKDGVSGLPELTTVRQPE
                     ETNTAFSVPPLNQRENRDAKEPLTGTIIEMWDGEIYHYGLYVERGLILGVHKPPAAIS
                     LAKVELTPLSLFWRPVYTPQYLISPDTLRRLHGESFPYTAFDNNCYAFCCWVLDLNDS
                     WLSRRMIQRTTGFFRPFQDWNRKPLPTMDDSKLKKVANIFLCTLSSLFTRPIKDIIGK
                     LKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED
                     LAVELVPIVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
                     KKEEANELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST
                     KSASPDIVGTINSLLARIAAARSLVHRAKEELSSRPRPVVVMISGRPGIGKTHLAREL
                     AKKIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC
                     PLTLNCDRIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK
                     AKRDFPGQPDMWKNAFSPDFSHIKLSLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA
                     SGLLHERLDEYELQGPALTTFNFDRNKILAFRQLAAENKYGLMDTMRVGKQLKDVKTM
                     SDLKQALKNIAIKKCQIVYNGSTYTLEADGKGSVKVDKVQSATVQTNNELAGALHHLR
                     CARIRYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQNLWSKPQVEDTEEMTNKDGC
                     LKPKDDEEFVVSSDDIKTEGKKGKNKSGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
                     KYSIEEYLQDRDRYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV
                     TGSEIRKRNPEDFKPKGKLWADDDRSVDYNEKLNFEAPPSIWSRIVNFGSGWGFWVSP
                     SLFITSTHVIPQGAKEFFGVPIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG
                     TVATLLIKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
                     CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDSKGTYCGAPILG
                     PGSAPKLSTKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP
                     RGKPPRPNVLEAAKKTIINVLEQTIDPPQKWSFAQACASLDKTTSSGHPHHMRKNDCW
                     NGESFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKVYGKIKKRLLWGSDL
                     ATMIRCARAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFEKHSRYRYHYDADYSRWD
                     STQQRDVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVMDVGDFQISISEGLPSGVPCT
                     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="AWR17762.1"
                     /translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
                     QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
                     FEVQVILAGNAFTAGKVIFAAVPPNFPTEGLSPSQVTMFPHIVVDVRQLEPVLIPLPD
                     VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
                     TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
                     QLSPVNICTFRGDVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGVL
                     TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG
                     STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
                     CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
                     IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAV"
     gene            6707..7513
                     /gene="ORF3"
     CDS             6707..7513
                     /gene="ORF3"
                     /codon_start=1
                     /product="VP2"
                     /protein_id="AWR17763.1"
                     /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
                     SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
                     APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRDAVPARGSSSKSS
                     NSSAATSVYSNQTTSTRLGSTAGSGTSVSSLPSTARTRSWVEDQSRNLSPFMRGAHNI
                     SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTHRQPLFAHIRKRGESRA"
ORIGIN      
        1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgct gctgccaaaa gcaacaacga
       61 catcgcaaaa tcttcaagtg acggtgtgct ctctaacatg gctgtcactt ttaagcgggc
      121 cctcggggcg cggcctaaac agccgccccc gaaggagata ccacccaggc ccccgcgacc
      181 acccacacca gaattggtca aaaagatccc tcctccccca cccaacgggg aggatgaact
      241 agtggtctct tacagcgcca aagatggcgt ttccgggttg cctgagctca ccactgtcag
      301 acaaccggag gaaaccaaca cggcgttcag tgtcccccca ctcaaccaaa gggagaacag
      361 ggacgccaag gagccactaa ctggaacaat tattgaaatg tgggatggag aaatctacca
      421 ttacggcctg tacgtggaac gaggtcttat acttggtgtg cacaagccac cggcagccat
      481 cagccttgcc aaggtcgagc taacaccgct ctctttgttc tggagacctg tatacacccc
      541 ccagtatctc atctctccag acactcttag gaggttacat ggagagtcat tcccctacac
      601 tgcatttgac aacaattgct acgccttttg ttgttgggta ttagacctaa acgactcatg
      661 gctaagcagg agaatgattc aaagaacaac aggtttcttc aggccgttcc aggattggaa
      721 caggaaaccc ctccccacta tggatgattc caaattaaag aaggtagcca acatattctt
      781 gtgcactttg tcttcactat tcactaggcc catcaaggac ataataggga agttgaaacc
      841 tcttaacatc cttaacattc tggctacatg tgattggacc ttcgcaggca tagtggaatc
      901 tttaatactc ttagcagaac tctttggagt tttctggaca cccccagatg tgtctgcgat
      961 gatcgccccc ttgctaggtg attatgaact gcaaggacct gaggaccttg cagtggaact
     1021 ggtcccaata gtgatggggg ggataggttt ggtgctagga tttaccaaag agaaaattgg
     1081 aaagatgcta tcatccgctg catccacttt aagagcttgt aaagaccttg gtgcatacgg
     1141 actggaaatt ttgaaactgg tcatgaagtg gttcttccca aagaaagagg aagcaaatga
     1201 actggctatg gtgagatcca tcgaggatgc agtgctagac ctcgaggcaa ttgaaaacaa
     1261 ccacatgacc accctactca aagacaaaga cagcttggca acctacatga gaacccttga
     1321 ccttgaagag gagaaagcca gaaaactctc aaccaaatct gcttcacccg atattgtggg
     1381 cacaatcaac tctcttctgg caagaatcgc tgctgcacgc tccctagtgc atcgggcgaa
     1441 agaagagctc tccagcaggc cgagacctgt cgttgtgatg atatcgggaa gaccagggat
     1501 agggaaaact caccttgcca gggagctggc caagaagatc gcggcctccc tcacagggga
     1561 ccagcgtgtg ggtcttatcc cacgcaatgg tgtcgatcac tgggacgcat ataagggcga
     1621 aagagttgtc ctatgggacg actatggaat gagcaacccc atccatgatg ccctcaggtt
     1681 gcaggagctt gctgacacct gccccctcac gctaaattgt gacagaattg agaataaagg
     1741 gaaagtcttt gacagtgatg ctataattat caccaccaat ttggccaacc cagcaccact
     1801 ggattatgtc aactttgaag cgtgctcgag acgtattgac ttcctcgtgt acgcagaagc
     1861 ccctgaggtg gagaaggcaa agcgcgactt cccaggtcaa cctgatatgt ggaagaacgc
     1921 tttcagtcct gacttctcac acataaaact gtcattggct ccacagggtg gttttgacaa
     1981 gaacggcaac accccgcatg gaaaaggggt catgaagacc ctcaccactg gctccctcat
     2041 cgcccgagca tcagggttac tccatgagag gctagatgaa tatgaactgc aaggcccagc
     2101 cctcaccact ttcaactttg accgcaacaa gatacttgct tttagacagc ttgctgctga
     2161 aaacaagtat gggctgatgg acacaatgag agttggaaaa cagctcaagg atgtcaagac
     2221 catgtcagac ctcaaacaag cactcaagaa tatcgcgatt aagaagtgcc agatagtgta
     2281 caatggtagc acctacacac ttgaggccga tggcaagggt agtgtgaaag ttgacaaagt
     2341 gcaaagtgcc actgtgcaga ccaacaatga actagccggt gccctacacc acctaaggtg
     2401 cgctagaatc agatactatg ttaagtgcgt ccaggaggca ctgtattcca tcatccaaat
     2461 cgctggggct gcattcgtca ccacgcgcat cgctaagcgc atgaatatac agaatctctg
     2521 gtccaagcca caggtggaag acacagaaga gatgaccaac aaagatggtt gcctaaaacc
     2581 caaagatgat gaagagtttg tcgtctcatc cgacgacatc aaaactgagg gcaagaaagg
     2641 taagaacaag tccggccgtg gcaagaagca cacagccttt tcaagcaaag gactcagtga
     2701 tgaggagtac gatgagtaca agagaatcag agaagaaagg aatggtaaat actccataga
     2761 agagtacctt caggacagag acaggtacta cgaggaggtg gccattgcca gggcaaccga
     2821 agaggacttc tgtgaagaag aagaggccaa aatccggcag agaattttca gaccaacaag
     2881 gaaacaacgc aaagaagaga gggcctctct cggcttggtc acaggctctg aaatcaggaa
     2941 gagaaaccca gaagacttca aacccaaggg aaagctgtgg gctgatgatg acagaagtgt
     3001 tgactacaat gaaaaactca actttgaggc cccaccaagc atctggtcgc ggatagttaa
     3061 ctttggttca ggctggggct tctgggtttc ccccagtcta tttataacat caacccatgt
     3121 catacctcaa ggtgcaaaag agttcttcgg agtccctatc aagcaaatcc agatacacaa
     3181 atcaggtgaa ttctgccggt tgagattccc aaagccaatc agaactgatg tgacgggcat
     3241 gattctagaa gaaggtgcgc ccgaggggac cgtggccaca ctactcatca agagaccaac
     3301 tggagagctc atgcctctgg cagccagaat ggggacccat gcaaccatga aaattcaggg
     3361 gcgcacagtt ggagggcaaa tgggtatgct cctgacagga tccaacgcca agagtatgga
     3421 cctaggcaca acaccaggcg actgcggctg cccctacatc tacaagaggg ggaatgacta
     3481 cgtggtcata ggagtccata cggccgctgc ccgtggagga aacactgtca tatgtgccac
     3541 ccaggggagt gagggagaag ccacacttga aggaggtgac agtaaaggga catactgtgg
     3601 cgcaccaatc ttgggcccag ggagcgctcc gaagctcagc accaagacta agttttggag
     3661 atcatccaca acaccactcc cacctggcac ctacgaacca gcctacctcg gtggcaaaga
     3721 ccccagagtt aaaggtggcc cttcattgca acaagttatg agggaccagc taaagccatt
     3781 cacagaaccc agaggcaaac caccaaggcc aaatgtgttg gaagctgcca agaaaaccat
     3841 catcaatgtc cttgagcaaa caattgatcc accccaaaaa tggtcatttg cgcaagcttg
     3901 cgcatccctt gacaaaacca cctccagcgg ccacccgcac cacatgcgga aaaacgattg
     3961 ttggaatggg gagtccttca caggaaaatt ggctgatcaa gcctccaagg ccaacctaat
     4021 gtttgaagag ggaaagaaca tgaccccagt ctacacaggt gcacttaaag atgagttggt
     4081 gaagaccgat aaagtttatg gtaagatcaa gaagaggctt ctgtggggtt cagatctggc
     4141 gaccatgata cggtgcgccc gagcttttgg aggcctcatg gatgaactca aggcgcactg
     4201 tgtcacactt cctgtcagag ttggtatgaa catgaatgag gatggcccca tcatctttga
     4261 aaagcactcc agatatagat atcactatga tgctgattat tcccggtggg actcaacaca
     4321 acaaagggat gtgctagcag cagcactaga aatcatggtt aagttctctc cagaaccaca
     4381 cctagcccag gtagttgcag aagacctcct ttcccctagc gtaatggatg taggtgactt
     4441 tcaaatatca ataagtgagg gtcttccctc tggggtgcct tgtacctccc agtggaattc
     4501 catcgcccac tggctcctca ctctttgtgc actctctgaa gtcacggatc tgtcccctga
     4561 catcattcag gccaactccc ttttctcctt ctatggtgat gatgagattg taagcacaga
     4621 cataaagttg gacccagaga agctgacagc aaaactcaag gagtacgggc tgaaaccaac
     4681 ccgccccgac aaaactgaag gaccccttgt tatctctgaa gatctggatg gcctgacatt
     4741 ccttcggaga actgtgaccc gtgatccagc tggctggttt ggaaaattgg aacaaagttc
     4801 aattctcaga caaatgtact ggaccagggg tcctaaccat gaagatccat ttgaaacaat
     4861 gataccacac tcccaaagac ccatacaatt gatgtccttg ctgggtgagg ctgcgctcca
     4921 cggcccggca ttttatagca aaattagcaa attagtcatt gcagagttga aggaaggtgg
     4981 catggatttt tacgtgccca ggcaagagcc tatgttcaga tggatgagat tctcagacct
     5041 gagcacgtgg gagggcgatc gcaatctggc tcccagcttt gtgaatgaag atggcgtcga
     5101 gtgacgccaa cccatctgat gggtccgcag ccaacctcgt cccagaggtc aacaatgagg
     5161 ttatggctct ggagcccgtt gttggtgccg ctattgcggc acctgtagcg ggccaacaaa
     5221 atgtaattga cccctggatt agaaacaatt ttgtacaagc ccctggtgga gagtttacag
     5281 tatcccctag aaacgctcca ggtgaaatac tatggagcgc gcccttgggc cctgatctaa
     5341 atccctacct atcccatttg gccagaatgt acaatggtta tgcaggtggt tttgaagtgc
     5401 aggtaattct cgcggggaac gcgttcaccg ccgggaaggt catatttgca gcagtcccac
     5461 caaactttcc aactgaaggc ttgagcccca gccaggtcac tatgttcccc catatagtag
     5521 tagatgttag gcaactagaa cctgtgttga ttcccttacc cgatgttagg aataatttct
     5581 atcattataa tcaatcaaat gaccccacca ttaaattgat agcaatgttg tatacaccac
     5641 ttagggctaa taatgctgga gatgatgtct ttacagtttc ttgccgagtt ctcacgagac
     5701 catcccccga ttttgatttc atatttctag tgccacccac agttgagtca agaactaaac
     5761 cattctctgt cccagtttta actgttgagg agatgaccaa ttcaagattc cccattcctt
     5821 tggaaaagtt gttcacgggt cccagcagtg cctttgttgt ccaaccacaa aacggcaggt
     5881 gcacgactga tggcgtgctc ctaggcacca cccaactgtc tcctgtcaac atctgcacct
     5941 tcagaggaga tgtcacccac atcacaggta gccgtaacta cacaatgaat ttggcttctc
     6001 agaattggaa caattatgac ccaacagaag aaatcccagc ccctctagga actccagact
     6061 ttgtggggaa gattcaaggc gtgctcaccc aaaccacaag gacagatggc tcaacacgcg
     6121 gccacaaagc cacagtgtac actgggagcg ccgactttgc tccaaaactg ggtagagttc
     6181 aatttgaaac tgacacggac catgattttg aagctaacca aaacacaaag ttcaccccag
     6241 tcggtgtcat ccaagatggt agcaccaccc accgaaatga accccaacag tgggtgctcc
     6301 caagttactc aggcagaaat actcataatg tgcacctggc ccccgctgta gcccccactt
     6361 ttccgggtga gcaacttctc ttcttcagat ccaccatgcc cggatgcagc gggtacccca
     6421 acatggattt ggactgtctg ctcccccagg aatgggtgca gtacttctac caagaggcag
     6481 ccccagcaca atctgatgtg gctctgctaa ggtttgtgaa tccagacaca ggtagggttt
     6541 tgtttgagtg taagcttcat aaatcaggct atgttacagt ggctcacact ggccaacatg
     6601 atttggttat cccccccaat ggttatttca gatttgattc ctgggtcaac cagttctaca
     6661 cgcttgcccc catgggaaat ggaacggggc gtagacgtgc agtataatgg ctggagcttt
     6721 ctttgctgga ttggcatctg atgtccttgg ctctggactt ggttccctta tcaatgctgg
     6781 ggctggggcc atcaaccaaa aagttgagtt tgaaaataac agaaaattgc aacaagcatc
     6841 cttccaattt agcagcaatc tacaacaggc ttcctttcaa catgacaaag agatgctcca
     6901 agcacaaatt gaggccacca aaaagctaca acaggaaatg atgaaagtta agcaggcaat
     6961 gctcctggag ggtgggttct ctgagacaga tgcagcccgc ggggcaatca acgcccccat
     7021 gacaaaagct ttggactgga gcgggacaag gtactgggct cccgatgcta ggactacaac
     7081 atacaatgca ggccgctttt ccacccctca accatcgggg gcactgccag gaagagctaa
     7141 tcttagggat gctgtccctg ctcggggttc ctccagtaaa tcttctaact cttctgctgc
     7201 tacttctgtg tactcaaatc aaaccacttc aacgagactt ggttctacag ctggttctgg
     7261 caccagtgtc tcgagcctcc cgtcaactgc aaggactagg agttgggttg aggatcaaag
     7321 taggaatttg tcacctttca tgaggggggc ccacaacata tcgtttgtca ccccaccatc
     7381 tagcagatcc tctagccaag gcacagtctc aaccgtgcct aaagagattt tggactcctg
     7441 gactggtgct ttcaacacgc acaggcagcc actcttcgct cacattcgta agcgagggga
     7501 gtcacgggcg taatgtgaaa agacaaaatt gattatcttt cttttt
//