Typing tool
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Typing tool
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Complete norovirus genomes
| MT537605 | GII.4 Sydney | |
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| GII.P16 |
ORF1: 1..5090
ORF2: 5071..6693
ORF3: 6693..7499
LOCUS MT537605 7508 bp RNA linear VRL 31-JUL-2020
DEFINITION Norovirus GII isolate 259-1 nonstructural polyprotein (ORF1) gene,
partial cds; and VP1 (ORF2) and VP2 (ORF3) genes, complete cds.
ACCESSION MT537605
VERSION MT537605.1
DBLINK BioProject: PRJNA604000
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7508)
AUTHORS Silva,A., Wolfe,J., Hirneisen,K., Ruelle,S. and Yang,Z.
TITLE Application of whole-genome sequencing for Norovirus outbreak
tracking and surveillance efforts in Orange County, CA
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 7508)
AUTHORS Silva,A., Wolfe,J., Hirneisen,K., Ruelle,S. and Yang,Z.
TITLE Direct Submission
JOURNAL Submitted (29-MAY-2020) Schmid College of Science and Technology,
Chapman University, 1 University Drive, Orange, CA 94526, USA
COMMENT ##Assembly-Data-START##
Assembly Method :: CLC Genomics Workbench v. 11
Sequencing Technology :: Illumina
##Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..7508
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="259-1"
/isolation_source="stool"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="USA"
/collection_date="17-Dec-2018"
/note="genotype: GII.4[P16]"
gene <1..5090
/gene="ORF1"
CDS <1..5090
/gene="ORF1"
/codon_start=3
/product="nonstructural polyprotein"
/protein_id="QKE61139.1"
/translation="SNDATVAVACNNNNDKEKSSGEGLFTNMSFTLKKALGARPKQPA
PRDEPQKPPRPPTPELVKRIPPPPPNGEGEEEPVIRYEVKSGISGLPELTTVPQPDVA
NTAFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAAISMA
RVELTPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLNDSWL
SRRMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLIGKIK
PLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLA
VELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKK
EEANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRLSTKS
ASPDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAREVAR
KVASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELADTCPL
TLNCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAK
RDFPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASG
LLHERMDEFELQGPTITTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVKTMEE
LKQAIRNVTIKRCRIIYGGSTYDLESDGKGKVLVEKVKNTSVQTNNELAGALHHLKHA
RIRYYVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEEAPKS
EDDEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSI
EEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLVTGSE
IRKRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSPSLFI
TSTHVIPAGITEAFGVPIKQIQIHKSGEFCRFRFPRPIRPDVTGMILEEGAPEGTVAT
VLIKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDCGCP
YIYKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGYDKGTYCGAPILGPGGA
PKLSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPRGKP
PRPSVLEAAKQTVINVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFWNGET
FTGKLADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYRKIKKRLLWGSDLSTMI
RCARSFGGLMDEMKAHCISLPVRVGMNVNEDGPIIFEKHSRYKYHYDADYSRWDSTQQ
RAVLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCTSQWN
SIAHWLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLKEYGL
KPTRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGPNHED
PNETMIPHSQRPIQLMALLGEASLHGPSFYSRISKLVITELKEGGMDFYVPRQEPMFR
WMRFSDLSTWEGDRNLAPNFVNEDGVE"
mat_peptide <1..986
/gene="ORF1"
/product="p48"
mat_peptide 987..2084
/gene="ORF1"
/product="NTPase"
mat_peptide 2085..2615
/gene="ORF1"
/product="p22"
mat_peptide 2616..3014
/gene="ORF1"
/product="VPg"
mat_peptide 3015..3557
/gene="ORF1"
/product="Pro"
mat_peptide 3558..5087
/gene="ORF1"
/product="RdRp"
gene 5071..6693
/gene="ORF2"
CDS 5071..6693
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="QKE61140.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML
TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG
STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRVV"
gene 6693..7499
/gene="ORF3"
CDS 6693..7499
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="QKE61141.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRDAVPARGPSNKSS
NSSTATSVYSNQTISTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRV"
ORIGIN
1 cgtctaacga cgctaccgtt gccgttgctt gcaacaacaa caacgacaag gaaaaatctt
61 caggtgaagg cttattcaca aatatgtctt tcaccttaaa gaaagccctc ggggctaggc
121 ccaaacagcc tgccccgaga gacgaaccac aaaagccccc aagaccacca acccccgagt
181 tggtcaagag gataccccct cctccaccta atggcgaagg agaagaagaa ccagtcatta
241 ggtatgaggt taagagtggg atctctggcc tgcccgagct cacaacagtc ccccaaccgg
301 acgtggccaa cacagcattc agtgttccac cactgagctt gagagaaaac agggaggcca
361 aggaaccgct aacaggggca atattagaga tgtgggatgg agagatatac cactatggcc
421 tgtacgtgga gaaaggctta gtgttgggtg tgcacaaacc acctgcagcc ataagcatgg
481 caagagtgga gctgacgccg ctgtcattgt actggcgtgt ggtgtacact ccccaatacc
541 tcatctcccc tgaaactctc aggaggctca acggagaggc gttcccttac accgccttcg
601 acaacaactg ctacgccttt tgctgctggg tgttagacct caatgactca tggcttagca
661 ggaggatggt gcaaagaaca acgggcttct tcagacctta ccaagagtgg aacagaaagc
721 ccctgcctac catggatgac tccaaaatta agaaggtagc aaatatattc ctatgttcat
781 tgtccacatt attcaccaga cccataaaag acctcatagg gaaaattaaa ccattaaaca
841 tattgaacat cctggcaacg tgtgactgga cgtttgccgg aatagtggag tctctgatat
901 tacttgctga actcttcgga gttttctgga cgcccccaga tgtgtctgct atgatcgctc
961 ccttactcgg ggactacgag ttgcaagggc cagaagacct cgccgttgaa ctcgtacctg
1021 tggtaatggg agggattggt ttggtgttgg gattcaccaa agagaaaatt ggcaaaatgt
1081 tgtcctcagc agcatcaaca ctcagggctt gcaaagatct tggtgcctat ggcttagaga
1141 tactcaagtt ggtcatgaag tggttcttcc caaagaaaga ggaggccaat gagctagcca
1201 tggtgagggc catagaggat gccgtgctag atcttgaggc aatagaaaat aaccacatga
1261 caaccctgtt gaaagacaaa gacagcttag caacatacat gaaaacactg gacatggagg
1321 aggagaaagc cagaaggttg tccacaaaat ctgcatcccc tgacatagtt gggacaatca
1381 acgccctgct ggctcgaata gcagcggcca ggtcattagt ccacagggcc aaggaagagc
1441 tatctagcag gataaggcca gtagttgtta tgatatctgg caaaccagga ataggcaaaa
1501 ctcatctggc cagggaggtg gcaagaaagg tggcatccac tctcacaggg gaccaaagag
1561 tcggactcat accaagaaac ggtgtggacc attgggatgc atacaaaggt gagagagtcg
1621 tgctgtggga cgactatggc atgagtaacc ccatccatga tgctcttcgc atacaagaat
1681 tggctgatac gtgtcccctt accttaaatt gtgacagaat tgaaaataag ggaaaagttt
1741 ttgacagtga agtcataata attacaacaa accttgccaa tccagcccca cttgattatg
1801 tcaactttga ggcctgttcc aggagaattg atttcctggt gtacgctgag gcaccagaag
1861 tagaaaaggc aaaacgggac tttcctggtc agccagatat gtggaaggac gccttcaagc
1921 cggacttttc acacatcaag ctacagcttg cacctcaggg cggctttgac aagaatggca
1981 acaccccaca tgggaaagga gtgatgaaga ccctcactac cggttctctg attgcccgtg
2041 catcaggcct actacatgag aggatggatg aatttgaact ccaaggtccc acaatcacca
2101 ccttcaattt cgaccgaaac agaatcacag cattcagaca attggctgca gaaaacaagt
2161 atggattggt ggataccatg aaagttggca atcaattaaa aggagtgaaa accatggaag
2221 aactcaaaca agcaatcaga aatgtgacca tcaagaggtg ccggatcatc tacggtggct
2281 ccacgtatga ccttgaatct gatggcaagg gcaaagtttt ggtggaaaag gtcaagaaca
2341 cctctgtaca gaccaacaac gagttggccg gggccctgca ccatctcaaa cacgcccgaa
2401 tcaggtacta tgtcaaatgt gtgcaagaag cagtctattc catcatacaa attgccggcg
2461 ctgcgtttgt caccacgcgc attgcacgcc gcatgaacat acaagaactc tggtcgaagc
2521 cacaattaga tcaaaatgaa tcagagacta aggaagaggc ccccaaatca gaagatgacg
2581 agttcatcat atcttctaag gacatcaagg aggaaggaaa gaagggcaaa aacaaaactg
2641 gccgtggcaa gaaacacact gcattctcca gcaagggctt gagcgatgag gagtatgacg
2701 agtacaagag gataagagaa gagagaaatg ggaagtactc tatagaggag tatcttcaag
2761 acagagacag gtactatgag gagctcgcca ttgccaaggc cacggaagaa gacttctgtg
2821 aagaggagga gataaaaatc cgtcagagaa ttttccgtcc caccaggaaa caaagaaagg
2881 aagagagggc cacattagga ctggtaacag gttcagaaat cagaaaaaga aaccctgatg
2941 acttcaaacc caaagggaag ctgtgggccg atgacaacag aagtgttgac tataatgaga
3001 aactggactt tgaggccccc ccaagcatat ggtctaggat tgtgagcttt ggttctggct
3061 ggggcttctg ggtatcacca agcctgttca taacatcaac tcatgtaatc cccgcaggca
3121 taacagaagc atttggagtc cccatcaaac aaattcagat ccacaaatca ggtgaatttt
3181 gccgattcag attcccaaga ccaattagac cagacgtgac aggaatgatc ttggaagaag
3241 gtgcgcctga aggcaccgtg gcaactgtgc tcatcaaacg ccccaccgga gagctcatgc
3301 ctcttgcagc cagaatggga acacacgcaa ccatgaaaat tcaaggccgc atggttggcg
3361 gacagatggg tatgttgctc actggatcaa atgctaaagg aatggatttg ggaacaactc
3421 ctggtgactg tggctgtcct tacatctaca aaaggggcaa tgactatata gtcattgggg
3481 tgcacactgc agcagcccgt ggtggaaaca ccgtcatctg tgccacacag ggaagtgagg
3541 gtgaggcaac tcttgagggt ggatatgaca aaggaacata ctgtggggca cccattctag
3601 gccctggggg tgcaccaaag ttgagcacca aaaccaaatt ttggaggtca tcgaacacgc
3661 ccctcccacc agggacatat gagcctgcct acctcggtgg ccgtgatccg cgtgttaagg
3721 gtgggccctc cttgcagcag gtaatgagag accagttgaa gccattcact gaacccaggg
3781 gcaaacctcc aagaccaagt gtattggaag cagccaaaca aaccgttatc aatgtcctcg
3841 aacaaaccct ggatcctcca caaaaatgga catacgcaca ggcgtgtgcc tcacttgaca
3901 aaaccacttc cagcgggcat cctcatcacg tccgaaagaa tgaattctgg aatggtgaga
3961 ccttcaccgg caaattggca gaccaagcat caaaagcaaa cctaatgttt gaggaaggga
4021 aacacatgac accagtgtat acagcagcac tcaaggacga gctagtcaag actgagaaaa
4081 tctatagaaa gatcaagaag agactgctct ggggctctga cttgtccacc atgatccggt
4141 gcgctaggtc atttggtggg ctcatggacg agatgaaggc acactgcata tcactcccag
4201 tacgagttgg catgaatgtg aatgaagatg gcccaataat atttgagaaa cattccagat
4261 acaaatacca ctatgacgca gactactctc gttgggattc aacacaacag agggcagtac
4321 tagcagcagc cttggaaatc atggtcagat tctctgcaga accacaattg gcacaaatag
4381 tcgctgagga tcttctggcc cctagcgtag tagatgtagg agactttaaa atcactataa
4441 atgaagggct cccatctggt gtgccatgca cctcccaatg gaactccatc gcacactggc
4501 tgctaactct ctgtgccttg tctgaagtca ccaaactgtc ccctgacatt atacaagcaa
4561 attccatgtt ctcattttac ggtgatgacg agattgtcag caccgacata aaattggacc
4621 ctgaacagtt aaccgccaag ttgaaggagt atggcctgaa accaacccgc ccagacaaga
4681 ccgagggacc cctgatcatc agtgaagatt tgaacggact cactttcctc cgaaggacgg
4741 tgactcgtga cccagctggc tggtttggaa aactggacca aagttcaatt ttgaggcaga
4801 tgtactggac tagaggacca aatcacgaag atcccaatga gacaatgata ccccattctc
4861 aaagacccat acagctcatg gcactgcttg gtgaagcctc tcttcacgga ccctctttct
4921 acagtagaat cagtaaattg gtcataactg aactcaaaga aggtgggatg gacttttacg
4981 tgccaaggca ggaacccatg ttcaggtgga tgaggttttc tgacttgagc acgtgggagg
5041 gcgatcgcaa tctggctccc aattttgtga atgaagatgg cgtcgagtga cgccaaccca
5101 tctgatgggt ccgcagccaa cctcgtacca gaggtcaaca atgaggttat ggctttggag
5161 cccgttgtcg gtgccgctat tgcggcacct gtagcgggcc aacaaaatgt aattgacccc
5221 tggattagaa ataattttgt acaagcccct ggtggggagt ttacagtatc ccccagaaac
5281 gctccaggtg aaatactatg gagcgcgccc ctaggccctg acctaaatcc ctacctatcc
5341 catttggcca gaatgtacaa tggttatgca ggtggttttg aagtgcaggt aattctcgcg
5401 gggaacgcgt tcaccgccgg gaagatcata tttgcagcag tcccaccaaa ttttccaact
5461 gaaggcttaa gtcctagcca ggtcactatg ttcccccata taatagtaga tgttagacag
5521 ttagaacctg tgctgattcc tttacccgat gttaggaata atttctatca ttacaatcag
5581 tcaaatgact ccactattaa gttgatagca atgttgtaca caccacttag ggctaataat
5641 gctggggatg atgttttcac agtttcgtgc cgagttctca cgagaccatc ccccgatttt
5701 gatttcatat ttttagtgcc acccacagtt gagtcaagaa ctaaaccatt ctctgtccca
5761 gttttaactg ttgaggagat gaccaattca agattcccca tccctttgga aaagctgttc
5821 acaggcccca gcagtgcctt tgttgttcaa ccacaaaacg gcaggtgcac aactgatggc
5881 gtgctcctag gcaccaccca actttctcct gtcaacatct gcaccttcag aggggatgtc
5941 acccacatca caggtagtcg caactacaca atgaatttgg cttctcaaaa ttggaacaac
6001 tatgacccaa cagaagaaat cccagcccct ctaggaactc cagattttgt ggggaagatt
6061 caaggcatgc tcacccaaac cacaaggaca gatggttcaa cacgcggcca caaagctaca
6121 gtgtacactg ggagcgccga ctttgctcca aaactgggta gagttcaatt tgaaactgac
6181 acagaccatg attttgaagc taatcaaaac acaaagttca ccccagtcgg tgtcatccaa
6241 gatggtagca ccacccatcg aaacgaaccc caacagtggg tgctcccaag ttactcaggc
6301 agaaatactc acaatgtaca tctggccccc gctgtagccc ccacctttcc gggtgagcaa
6361 cttctcttct tcagatccac catgcccgga tgcagcgggt accccaacat ggatttggac
6421 tgtctgctcc cccaggaatg ggtgcagtac ttctatcaag aggcagcccc agcacaatct
6481 gatgtggctc tgctaagatt tgtgaatcca gacacaggta gggttttgtt tgagtgcaag
6541 cttcacaaat caggctatgt tacagtggct cacactggcc aacatgattt ggttatcccc
6601 cccaatggct actttagatt tgattcctgg gtcaaccagt tctatacgct tgcccccatg
6661 ggaaatggaa cggggcgtag acgtgtagta taatggctgg agctttcttt gctggattgg
6721 catctgatgt ccttggctct ggacttggtt ccctcatcaa tgctggggct ggggccatca
6781 accaaaaagt tgagtttgaa aataacagaa aattgcaaca agcatccttc caatttagca
6841 gcaatctgca acaggcttcc tttcaacatg ataaagagat gctccaagca caaattgagg
6901 ccactaaaaa gctacaacag gaaatgatga aagttaagca ggcaatgctc ctagagggtg
6961 ggttctctga gacagatgca gcccgcgggg caattaacgc ccccatgaca aaagctttgg
7021 actggagtgg gacaaggtac tgggctcccg atgctaggac tacaacatac aatgcaggcc
7081 gcttttccac ccctcaacca tcgggggcac tgccaggaag agctaatctt agggatgctg
7141 tccctgctcg gggaccctcc aacaaatctt ctaactcttc tactgccacc tctgtgtatt
7201 caaatcaaac tatttcaacg agacttggtt ctacagctgg ttctggaacc agtgtctcga
7261 gcctcccgtc aactgcaagg actaggagct gggttgagga tcaaaatagg aatttgtcac
7321 ctttcatgag gggggcccac aacatatcat ttgtcacccc accatctagc agatcctcta
7381 gccaaggcac agtctcaacc gtgcctaaag agattttgga ctcctggact ggcgctttca
7441 acacgcgcag gcagcctctc ttcgctcaca ttcgtaagcg aggggagtca cgggtgtaat
7501 gtgaaaag
//