Typing tool

Complete norovirus genomes

KY442320  GII.3
 GII.P41

Length: 7,527 | 3 CDS

ORF1: 5..5110
ORF2: 5091..6737
ORF3: 6737..7501
LOCUS       KY442320                7527 bp    RNA     linear   VRL 14-AUG-2017
DEFINITION  Norovirus GII.3 strain Hu/US/1972/GII.Pg_GII.3/ShippensburgC2,
            complete genome.
ACCESSION   KY442320
VERSION     KY442320.1
KEYWORDS    .
SOURCE      Norovirus GII.3
  ORGANISM  Norovirus GII.3
            Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
            Picornavirales; Caliciviridae; Norovirus.
REFERENCE   1  (bases 1 to 7527)
  AUTHORS   Johnson,J.A., Parra,G.I., Levenson,E.A. and Green,K.Y.
  TITLE     A large outbreak of acute gastroenteritis in Shippensburg,
            Pennsylvania, 1972 revisited: evidence for common source exposure
            to a recombinant GII.Pg/GII.3 norovirus
  JOURNAL   Epidemiol. Infect. 145 (8), 1591-1596 (2017)
   PUBMED   28294087
REFERENCE   2  (bases 1 to 7527)
  AUTHORS   Johnson,J.A., Parra,G.I., Levenson,E.A. and Green,K.Y.
  TITLE     Direct Submission
  JOURNAL   Submitted (10-JAN-2017) LID/NIAID, NIH, 50 South Drive-MSC8026,
            Bethesda, MD 20892, USA
COMMENT     ##Assembly-Data-START##
            Assembly Method       :: SAMtools v. 1.3
            Assembly Name         :: Shippensburg norovirus
            Coverage              :: 3,367 median depth
            Sequencing Technology :: Generated consensus from Ion Torrent NGS
                                     data; IonTorrent; Sanger dideoxy
                                     sequencing
            ##Assembly-Data-END##
FEATURES             Location/Qualifiers
     source          1..7527
                     /organism="Norovirus GII.3"
                     /mol_type="genomic RNA"
                     /strain="Hu/US/1972/GII.Pg_GII.3/ShippensburgC2"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:490041"
                     /country="USA"
                     /collection_date="1972"
     gene            5..5110
                     /gene="ORF1"
     CDS             5..5110
                     /gene="ORF1"
                     /codon_start=1
                     /product="nonstructural polyprotein"
                     /protein_id="ARA95793.1"
                     /translation="MKMASNDASAAAAATSNNDNAKSSSDGVLTSMAVTFKRALGARP
                     KQPSPRETTQKQKPPRPPTPELVKKIPPPPPNGEDELVVSYSVKDGVSGLPELSTVSQ
                     PNEANTAFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAA
                     ISLAKVELTPLSLYWRPVYTPQYLIAPDTLRKLHGESFPYTAFDNNCYAFCCWVLDLN
                     DSWLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKLKKMANIILCALSSLFTRPIKDII
                     GKLRPLNILNILASCDWTFAGVVESLILMAELFGVFWTPPDVSAMIAPLLSDYELQGP
                     EDIAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWF
                     FPKKDEANELAMVRSIEDAVLDLEAIENNHMTSLLKDKDSLATYMRTLDLEEEKARRL
                     STKSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVVMISGKPGIGKTHLAR
                     ELAKKIAATLTGDQRVGLVPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELAD
                     TCPLTLNCDRIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYADAPDV
                     EKAKRDFPGQPDMWKDAFRSDFSHIKLMLAPQGGFDKNGNTPHGKGIMKTLTSGSLIA
                     RASGLLHERLDEYELQGPTPTTFNFDQNKVFAFRQLAAENKYGLMDTMRVGSQLKGVK
                     TVSELKQALKNIAIKRCQIVYGGLTYSLESDGKGNVKVERVQSTTVQTNNELSGALHH
                     LKCARIRYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQNLWSRPQVEDAEEVINRD
                     GCPKPKDDEEFVISSEDIKAEGKKGKNKSGRGKKHTAFSSKGLSDEEYDEYKRIREER
                     NGKYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLG
                     LVTGSEIRRRNPDDFKPKGKLWADDDRSVDYNERLSFEAPPSIWSRIVNFGSGWGFWV
                     SPSLFITSTHVIPQGSQEFFGVSIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAP
                     EGTVATLLIKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTP
                     GDCGCPYIYKRGNDYIVIGVHTAAARGGNTVICATQGNEGEAILEGGDNKGTYCGAPI
                     LGPGSAPKLSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFT
                     EPRGKPPNPSVLEAAKKTIINVLEQTIDPPQKWSFAQACASLDKTTSSGHPHHMRKNE
                     CWNGESFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGKIKKRLLWGS
                     DLATMIRCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFEKHSRYKYHYDADYSR
                     WDSTQQRAVLAAALEIMVKFSSEPHLAQIVAEDLLSPSVMDVGDFKISITEGLPSGVP
                     CTSQWNSIAHWLLTLCALSEVTNLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAK
                     LKEYGLKPTRPDKTEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTR
                     GPNHEDPSETMIPHSQRPIQLMSLLGEAALHGPSFYSKISKLVIAELKEGGMDFYVPR
                     QEPMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE"
     gene            5091..6737
                     /gene="ORF2"
     CDS             5091..6737
                     /gene="ORF2"
                     /codon_start=1
                     /product="major capsid protein VP1"
                     /protein_id="ARA95794.1"
                     /translation="MKMASNDATPSNDGAAGLVPEINNEAMALEPVAGAAIAAPLTGQ
                     QNIIDPWIMNNFVQAPGGEFTVSARNSPGEVLLNLELGPEINPYLAHLARMYNGYAGG
                     FEVQVVLAGNAFTAGKVIFAAIPPNFPIDNLSAAQITMCPHVIVDVRQLEPINLPMPD
                     VRNNFFHYNQGSDSRLRLIAMLYTPLRANNSGDDVFTVSCRVLTRPSPDFSFNFLVPP
                     TVESKTKPFTLPILTISEMSNSRFPVPIDSLHTSPTENIVVQCQNGRVTLDGELMGTT
                     QLLPSQICALRGTLTRSTSRASDQADTATPRLFNYYWHIQLDNLNGTPYDPAEDIPAP
                     LGTPDFRGKVFGVASQRNPDSTTRAHEAKVDTTSGRFAPKLGSLEISTESSDFDSNQP
                     TRFTPVGIGVDNEADFQQWSLPDYSGQFTHNMNLAPAVAPNFPGEQLLFFRSQLPSSG
                     GRSNGILDCLVPQEWVQHFYQESAPAQTQVALVRYVNPDTGRVLFEAKLHKLGFMTIA
                     KNGDSPITVPPNGYFRFESWVNPFYTLAPMGTGNGRRRIQ"
     gene            6737..7501
                     /gene="ORF3"
     CDS             6737..7501
                     /gene="ORF3"
                     /codon_start=1
                     /product="minor capsid protein VP2"
                     /protein_id="ARA95795.1"
                     /translation="MAGAFIAGLAGDMLTNTVGSLVNSGASAINQKVDFENNKYLQNA
                     SFAHDKEMLNAQIEATKRLQADMIAIKQGVLTAGGFSPTDAARGAINAPMTKVLDWSG
                     TRYWAPNATSTTSMSGGFTSQTVHRTAPNFKTNQAPKSTPSSGSSVRSNSTQLTSLSS
                     HSSGSSRSSGSTVVSSLPSSNRTRDWVNQQNLNLEPHMPGSLRTAFVTPPSSTASSSG
                     TVSTVPKSVLDSWTSAFNTRRQPLFAHLRRRGESNV"
ORIGIN      
        1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgct gctgctacca gcaacaacga
       61 caacgcaaaa tcttcaagtg acggagtact aactagtatg gctgtcactt ttaaacgggc
      121 cctcggggcc cggcctaaac agccgtcccc gagggaaaca acacaaaaac aaaagccccc
      181 acgaccgccc actccggagt tggtcaaaaa gatcccgcct cccccaccaa acggggagga
      241 cgaactagtg gtctcctata gtgttaaaga cggcgtctcc ggtttgcccg aactttctac
      301 cgtcagtcag ccgaacgagg ccaacacagc attcagtgtc cccccactca atcagaggga
      361 gaacagggac gctaaagagc cactaactgg caccattctg gaaatgtggg acggggagat
      421 ctaccattat ggcctgtacg tggaacgggg cctggtgctc ggagtacaca aaccaccagc
      481 ggctatcagt cttgccaagg ttgagttgac accactgtct ctatactgga gaccagtgta
      541 caccccccag taccttatag ctccagacac tctcagaaag ctacatggag agtcatttcc
      601 ttacacggcc tttgacaaca actgttatgc cttctgttgc tgggtcctag acctgaacga
      661 ctcttggctt agcaggagaa tgatacagag aacaactggc tttttcaggc cctaccagga
      721 ctggaacaga aagcccctcc ctaccatgga tgactccaaa ttgaaaaaga tggccaatat
      781 aatcctgtgt gctttgtcat cactgttcac caggcccatc aaggatataa ttggaaaatt
      841 aagaccttta aacatcctta acatattggc ttcctgcgat tggacttttg caggcgtagt
      901 ggaatcctta atcctcatgg cagagctctt tggagttttc tggacacccc cagatgtgtc
      961 tgcgatgatc gcccccttac taagtgacta tgagctacag ggacctgaag acattgctgt
     1021 agaactcgta ccagtagtga tgggggggat aggcttggtt ctaggtttca ccaaagaaaa
     1081 gattggcaaa atgctatcat ctgctgcgtc cacgcttaga gcgtgtaaag accttggagc
     1141 atacggattg gaaattctaa aactggtcat gaaatggttc ttcccgaaga aagatgaggc
     1201 aaacgaactt gcaatggtga gatccattga ggacgcagtg ttggacctag aagcaattga
     1261 aaacaaccac atgacttctt tgctcaaaga caaggacagc ctggcaacct acatgagaac
     1321 cctagatctt gaagaggaga aggccaggag actctccaca aaatctgcct cacctgacat
     1381 cgtaggcaca atcaacgccc tgctagcaag gatcgcggcc gctcgttccc tggtgcatcg
     1441 ggcaaaagag gagctttcta gcagaccaag gcccgttgtt gtgatgatat caggtaagcc
     1501 aggaatagga aagacccacc ttgctagaga attggcaaag aagatcgcag ccaccctcac
     1561 aggagatcag agggtgggcc tcgtcccacg taacggcgtc gaccactggg atgcatacaa
     1621 aggtgaaaga gttgtccttt gggatgacta tgggatgagc aaccccattc acgacgccct
     1681 taggctgcaa gaacttgctg acacttgccc cctaacacta aactgtgata gaattgagaa
     1741 caagggaaaa gtctttgaca gtgatgctat aattattaca actaatctgg ccaacccagc
     1801 accactggac tatgttaact ttgaagcatg ctcaaggcgt attgacttcc tcgtgtatgc
     1861 tgatgcccct gatgttgaga aggcaaagcg cgacttccca gggcagcctg acatgtggaa
     1921 ggatgccttt agatctgact tctcacatat aaagctgatg ttggctcctc agggtggttt
     1981 tgataagaac ggcaacactc cacatgggaa gggtatcatg aaaaccctta catctggctc
     2041 tctcattgct cgtgcgtcag ggctcctcca tgaaagactg gacgaatacg agttgcaagg
     2101 cccaacaccc acaacattca acttcgacca gaataaggtt tttgctttca ggcaactcgc
     2161 tgctgaaaat aaatacgggc tgatggacac tatgagagtg ggaagtcagc tcaagggtgt
     2221 caaaaccgtg tcagagctca agcaggcgct caagaacatc gcaatcaaaa gatgccagat
     2281 agtctacggt ggtctcacat actcacttga atctgatggc aaaggcaatg tgaaggttga
     2341 gagagtgcag agtacaactg tacaaaccaa caatgagcta tctggcgctc tacaccatct
     2401 caagtgcgcc aggatcaggt actatgttaa gtgtgtccag gaggccctgt attctatcat
     2461 ccagattgct ggggctgcat ttgtcaccac gcgcattgca aaacgcatga acatacaaaa
     2521 tctttggtct aggccacagg tagaggatgc agaagaggtc atcaatagag acgggtgtcc
     2581 aaaaccaaaa gatgatgagg agtttgtcat ctcatctgaa gacatcaaag ctgagggcaa
     2641 gaaaggaaag aacaagtccg gtcgtggcaa gaaacacaca gccttctcaa gcaagggtct
     2701 cagtgatgag gagtacgatg aatacaaaag aattagggaa gaaaggaatg gtaagtactc
     2761 tatagaagaa tacctccagg acagagacaa gtattatgaa gaggtggcca tagccagggc
     2821 tactgaagag gacttctgtg aagaagagga agccaagatc cgacagagga tttttagacc
     2881 aacgaggaaa caacgtaaag aggagagggc ttctcttggc ctggtcacag gctcagaaat
     2941 cagaaggagg aacccagatg acttcaaacc caagggaaaa ttgtgggctg atgacgacag
     3001 aagtgtcgat tacaacgaaa gacttagttt tgaagctccc ccaagcattt ggtcgagaat
     3061 agtcaacttt ggttcaggtt ggggtttctg ggtttcacct agtctgttca taacatccac
     3121 tcatgtcata cctcaaggat cacaggagtt cttcggggtt tccattaagc aaatccaaat
     3181 ccacaaatcg ggtgagttct gccgcctaag attcccaaaa ccaatcagaa ctgatgtgac
     3241 aggcatgatc ttggaagaag gggcccctga aggaacagtg gccacactac tcataaagag
     3301 accaactggg gaactcatgc cactggcagc taggatgggc acccatgcaa ccatgaagat
     3361 ccagggtcgc actgttgggg gccagatggg aatgctcttg acaggatcta atgctaagag
     3421 catggatctg ggcaccacac caggtgactg tgggtgtccc tacatctaca aaagaggaaa
     3481 tgactacata gtcattggag tccacacggc cgctgctcgc ggagggaata ctgtcatctg
     3541 tgcaacccag ggaaacgagg gtgaggccat acttgaaggt ggtgataaca aaggcaccta
     3601 ctgcggtgcc ccaatcctag gcccaggaag tgcccccaag ctcagcacca agaccaaatt
     3661 ctggaggtcc tcaacagcac cactcccacc tggaacatat gagccagcct accttggagg
     3721 taaggacccc agagttaaag gtggcccctc actacaacaa gtaatgagag accaattaaa
     3781 accattcaca gagcccaggg gcaaaccacc aaacccgagt gtgctagagg ctgccaaaaa
     3841 gaccatcatc aatgtcctcg aacagacaat agacccaccc caaaaatggt cgtttgcgca
     3901 agcttgcgca tctcttgata agaccacctc tagtggccat ccgcaccaca tgcggaagaa
     3961 tgaatgctgg aacggagagt ccttcacagg gaaattggca gaccaagcct caaaagccaa
     4021 cctaatgttt gaggaaggga aaaacatgac cccagtctac acaggtgccc tcaaggatga
     4081 gctagttaaa actgataaaa tatatggtaa aattaagaag aggctcctct ggggatcgga
     4141 tctggcaacc atgatccgtt gtgctcgagc attcggaggg ctaatggatg aactcaaggc
     4201 tcactgtgtc acactcccta ttagagttgg aatgaacatg aatgaggatg gccctattat
     4261 ctttgagaaa cactctagat acaaatacca ttatgatgca gactactctc ggtgggattc
     4321 aacacagcag agagctgtac tggctgcagc cctagaaatc atggtcaaat tttcttcaga
     4381 accacaccta gcccagatag tcgcagaaga ccttctgtct cccagtgtga tggacgtggg
     4441 cgacttcaaa atatcaatca ctgaaggact cccttctggg gtgccttgca cctcacaatg
     4501 gaattctatt gcccattggc tcctcacact ctgtgcactc tccgaggtga caaacttatc
     4561 ccctgatatt atccaagcca attctctttt ctctttctat ggtgatgatg aaattgtgag
     4621 tacagatatt aaattggatc cagaaaaact gacagctaaa ctgaaagagt atgggctaaa
     4681 accaacacgc cctgataaga ctgaagggcc tctggtcatc tctgaggacc tgaatggtct
     4741 gaccttcctg cggaggactg tgacccgcga tccagctggt tggtttggaa aattggaaca
     4801 gagttcaata cttagacaaa tgtattggac caggggtcca aatcatgagg acccctctga
     4861 aacaatgata ccacattccc agagacctat acagctaatg tccctgctag gtgaagctgc
     4921 actgcatggc ccatcattct acagcaagat cagcaagcta gtcattgcag agttgaagga
     4981 aggtggcatg gatttttacg tgcctagaca agagccaatg tttcggtgga tgaggttctc
     5041 agacttgagc acgtgggagg gcgatcgcaa tctggctccc agtttcgtga atgaagatgg
     5101 cgtcgaatga cgccactcca tctaacgatg gtgccgccgg cctcgtccca gagatcaaca
     5161 atgaggcaat ggcgctagag ccagtggcag gtgcagcaat agcagcaccc ctcactggcc
     5221 agcaaaatat aattgatccc tggattatga ataattttgt gcaagcacct ggtggtgagt
     5281 ttacagtgtc agctaggaac tcccctggtg aagtacttct taatttagaa ttaggtccag
     5341 aaataaaccc ctatttggct caccttgcta ggatgtacaa tggttatgca ggtgggtttg
     5401 aagtgcaggt agtcctggct ggaaatgcgt ttacagcagg aaaggtgatc tttgcagcta
     5461 taccccccaa ttttccaatt gacaatctga gcgcagcaca gattacaatg tgcccgcatg
     5521 tgatcgtgga tgtcaggcaa ttggaaccaa tcaaccttcc gatgcctgat gtccgtaata
     5581 atttctttca ttataatcaa gggtctgatt cgaggttacg cttaattgca atgttataca
     5641 cacctcttag ggcaaataat tcaggagatg atgttttcac tgtgtcttgt agagtattaa
     5701 ctaggcctag ccctgatttc tcattcaatt ttcttgttcc acccactgtg gaatcaaaga
     5761 caaagccttt caccctcccc attttgacta tctctgaaat gtctaattcc aggtttccag
     5821 tgccaattga ctctctgcac accagcccga ctgagaatat tgttgtccag tgccaaaatg
     5881 ggcgcgtcac ccttgacggt gagttaatgg gcaccaccca actcttgccg agtcaaatat
     5941 gtgctctcag gggcacgctc accagatcaa caagcagggc cagtgaccaa gccgacacgg
     6001 caacccctag gctgttcaat tattattggc acatacaatt ggataatcta aatggaaccc
     6061 cctacgaccc tgcagaagac ataccagccc ctttgggaac accagacttc cggggcaagg
     6121 tctttggcgt agctagccag agaaaccctg acagcacaac aagagcacat gaagcaaaag
     6181 tggacacaac atctggtcgc ttcgccccga aattgggttc cctagaaata tccactgaat
     6241 ccagtgactt tgactcaaat caaccaacaa ggttcacccc agttggcatt ggggttgaca
     6301 atgaggcaga ttttcagcaa tggtccttac ctgactactc cggtcagttc actcataaca
     6361 tgaacttagc cccagctgtc gcccccaatt tccctggtga gcagcttctt ttcttccgct
     6421 cacagttgcc atcttctggt gggcggtcta acgggattct agactgcctg gttccccagg
     6481 aatgggttca acacttctac caggaatcag cccctgccca aacacaggtg gccctggtta
     6541 ggtatgttaa ccctgacact ggtagagtgc tatttgaggc caagctacac aaattgggct
     6601 tcatgactat agctaagaat ggtgactctc caataactgt ccctccaaat gggtacttta
     6661 ggtttgaatc ttgggtgaac cccttttata cacttgcccc catgggaact ggaaatgggc
     6721 gtagaaggat tcaataatgg ctggagcttt tatagcagga ttggctggtg acatgctcac
     6781 aaatactgta ggatctttag ttaattcagg ggctagtgcc atcaatcaaa aagttgattt
     6841 tgaaaataat aaatatttac aaaatgcatc ttttgctcat gataaggaga tgttaaatgc
     6901 acaaattgag gcaacaaaga ggctacaggc tgacatgatt gctatcaaac aaggggtctt
     6961 gaccgctggc ggcttctccc ccactgatgc agcccgtggg gcaattaatg cccccatgac
     7021 aaaagttttg gattggagtg gaacgaggta ctgggcacca aacgccacct ccacaacctc
     7081 aatgtcaggt ggcttcacaa gccaaactgt gcacagaacc gcaccaaatt ttaaaacgaa
     7141 ccaggccccc aagtccacac ccagcagtgg gtcttcagtg aggtcaaatt caacccaact
     7201 cactagcttg agctcacact cctccgggtc gtctcgatcc agcgggtcta cggttgtcag
     7261 ctcattgcca tcttccaaca ggactaggga ttgggtcaat caacagaatc tcaatttgga
     7321 accacacatg cctggatctc ttaggacagc ttttgtcact ccaccatcta gtacagcctc
     7381 tagttcaggc acggtctcaa ccgtgcccaa aagtgttttg gactcctgga catctgcgtt
     7441 taatacgcgc agacaaccgc tattcgcaca ccttcgtaga aggggggagt caaatgttta
     7501 gtgaaaagat tattttaaat ttaattt
//