Typing tool
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Typing tool
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Complete norovirus genomes
| KY442319 | GII.3 | |
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| GII.P41 |
ORF1: 5..5110
ORF2: 5091..6737
ORF3: 6737..7501
LOCUS KY442319 7527 bp RNA linear VRL 14-AUG-2017
DEFINITION Norovirus GII.3 strain Hu/US/1972/GII.Pg_GII.3/ShippensburgB24,
complete genome.
ACCESSION KY442319
VERSION KY442319.1
KEYWORDS .
SOURCE Norovirus GII.3
ORGANISM Norovirus GII.3
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
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/ShippensburgB24"
/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="ARA95790.1"
/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="ARA95791.1"
/translation="MKMASNDATPSNDGAAGLVPEINNEAMALEPVAGAAIAAPLTGQ
QNIIDPWIMNNFVQAPGGEFTVSPRNSPGEVLLNLELGPEINPYLAHLARMYNGYAGG
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="ARA95792.1"
/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 acctaggaac 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
//