Typing tool
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Typing tool
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Complete norovirus genomes
| MT537941 | GII.4 Sydney | |
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| GII.P16 |
ORF1: 1..5092
ORF2: 5073..6695
ORF3: 6695..7501
LOCUS MT537941 7512 bp RNA linear VRL 31-JUL-2020
DEFINITION Norovirus GII isolate 259-2 nonstructural polyprotein (ORF1) gene,
partial cds; and VP1 (ORF2) and VP2 (ORF3) genes, complete cds.
ACCESSION MT537941
VERSION MT537941.1
DBLINK BioProject: PRJNA604000
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norovirus norwalkense.
REFERENCE 1 (bases 1 to 7512)
AUTHORS Silva,A., Wolfe,J., Ruelle,S., Hirneisen,K. 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JOURNAL Unpublished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 7512)
AUTHORS Silva,A., Wolfe,J., Ruelle,S., Hirneisen,K. 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..7512
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="259-2"
/isolation_source="stool"
/host="Homo sapiens"
/db_xref="taxon:122929"
/geo_loc_name="USA"
/collection_date="17-Dec-2018"
/note="genotype: GII.4[P16]"
gene <1..5092
/gene="ORF1"
CDS <1..5092
/gene="ORF1"
/codon_start=2
/product="nonstructural polyprotein"
/protein_id="QKE61148.1"
/translation="ASNDATVAVACNNNNDKEKSSGEGLFTNMSFTLKKALGARPKQP
APRDEPQKPPRPPTPELVKRIPPPPPNGEGEEEPVIRYEVKSGISGLPELTTVPQPDV
ANTAFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAAISM
ARVELTPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLNDSW
LSRRMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLIGKI
KPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDL
AVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPK
KEEANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRLSTK
SASPDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAREVA
RKVASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELADTCP
LTLNCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKA
KRDFPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARAS
GLLHERMDEFELQGPTITTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVKTME
ELKQAIRNVTIKRCRIIYGGSTYDLESDGKGKVLVEKVKNTSVQTNNELAGALHHLKH
ARIRYYVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEEAPK
SEDDEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYS
IEEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLVTGS
EIRKRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSPSLF
ITSTHVIPAGITEAFGVPIKQIQIHKSGEFCRFRFPRPIRPDVTGMILEEGAPEGTVA
TVLIKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDCGC
PYIYKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGYDKGTYCGAPILGPGG
APKLSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPRGK
PPRPSVLEAAKQTVINVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFWNGE
TFTGKLADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYRKIKKRLLWGSDLSTM
IRCARSFGGLMDEMKAHCISLPVRVGMNVNEDGPIIFEKHSRYKYHYDADYSRWDSTQ
QRAVLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCTSQW
NSIAHWLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLKEYG
LKPTRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGPNHE
DPNETMIPHSQRPIQLMALLGEASLHGPSFYSRISKLVITELKEGGMDFYVPRQEPMF
RWMRFSDLSTWEGDRNLAPNFVNEDGVE"
mat_peptide <1..988
/gene="ORF1"
/product="p48"
mat_peptide 989..2086
/gene="ORF1"
/product="NTPase"
mat_peptide 2087..2617
/gene="ORF1"
/product="p22"
mat_peptide 2618..3016
/gene="ORF1"
/product="VPg"
mat_peptide 3017..3559
/gene="ORF1"
/product="Pro"
mat_peptide 3560..5089
/gene="ORF1"
/product="RdRp"
gene 5073..6695
/gene="ORF2"
CDS 5073..6695
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="QKE61149.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML
TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG
STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRVV"
gene 6695..7501
/gene="ORF3"
CDS 6695..7501
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="QKE61150.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRDAVPARGPSNKSS
NSSTATSVYSNQTISTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRV"
ORIGIN
1 ggcgtctaac gacgctaccg ttgccgttgc ttgcaacaac aacaacgaca aggaaaaatc
61 ttcaggtgaa ggcttattca caaatatgtc tttcacctta aagaaagccc tcggggctag
121 gcccaaacag cctgccccga gagacgaacc acaaaagccc ccaagaccac caacccccga
181 gttggtcaag aggatacccc ctcctccacc taatggcgaa ggagaagaag aaccagtcat
241 taggtatgag gttaagagtg ggatctctgg cctgcccgag ctcacaacag tcccccaacc
301 ggacgtggcc aacacagcat tcagtgttcc accactgagc ttgagagaaa acagggaggc
361 caaggaaccg ctaacagggg caatattaga gatgtgggat ggagagatat accactatgg
421 cctgtacgtg gagaaaggct tagtgttggg tgtgcacaaa ccacctgcag ccataagcat
481 ggcaagagtg gagctgacgc cgctgtcatt gtactggcgt gtggtgtaca ctccccaata
541 cctcatctcc cctgaaactc tcaggaggct caacggagag gcgttccctt acaccgcctt
601 cgacaacaac tgctacgcct tttgctgctg ggtgttagac ctcaatgact catggcttag
661 caggaggatg gtgcaaagaa caacgggctt cttcagacct taccaagagt ggaacagaaa
721 gcccctgcct accatggatg actccaaaat taagaaggta gcaaatatat tcctatgttc
781 attgtccaca ttattcacca gacccataaa agacctcata gggaaaatta aaccattaaa
841 catattgaac atcctggcaa cgtgtgactg gacgtttgcc ggaatagtgg agtctctgat
901 attacttgct gaactcttcg gagttttctg gacgccccca gatgtgtctg ctatgatcgc
961 tcccttactc ggggactacg agttgcaagg gccagaagac ctcgccgttg aactcgtacc
1021 tgtggtaatg ggagggattg gtttggtgtt gggattcacc aaagagaaaa ttggcaaaat
1081 gttgtcctca gcagcatcaa cactcagggc ttgcaaagat cttggtgcct atggcttaga
1141 gatactcaag ttggtcatga agtggttctt cccaaagaaa gaggaggcca atgagctagc
1201 catggtgagg gccatagagg atgccgtgct agatcttgag gcaatagaaa ataaccacat
1261 gacaaccctg ttgaaagaca aagacagctt agcaacatac atgaaaacac tggacatgga
1321 ggaggagaaa gccagaaggt tgtccacaaa atctgcatcc cctgacatag ttgggacaat
1381 caacgccctg ctggctcgaa tagcagcggc caggtcatta gtccacaggg ccaaggaaga
1441 gctatctagc aggataaggc cagtagttgt tatgatatct ggcaaaccag gaataggcaa
1501 aactcatctg gccagggagg tggcaagaaa ggtggcatcc actctcacag gggaccaaag
1561 agtcggactc ataccaagaa acggtgtgga ccattgggat gcatacaaag gtgagagagt
1621 cgtgctgtgg gacgactatg gcatgagtaa ccccatccat gatgctcttc gcatacaaga
1681 attggctgat acgtgtcccc ttaccttaaa ttgtgacaga attgaaaata agggaaaagt
1741 ttttgacagt gaagtcataa taattacaac aaaccttgcc aatccagccc cacttgatta
1801 tgtcaacttt gaggcctgtt ccaggagaat tgatttcctg gtgtacgctg aggcaccaga
1861 agtagaaaag gcaaaacggg actttcctgg tcagccagat atgtggaagg acgccttcaa
1921 gccggacttt tcacacatca agctacagct tgcacctcag ggcggctttg acaagaatgg
1981 caacacccca catgggaaag gagtgatgaa gaccctcact accggttctc tgattgcccg
2041 tgcatcaggc ctactacatg agaggatgga tgaatttgaa ctccaaggtc ccacaatcac
2101 caccttcaat ttcgaccgaa acagaatcac agcattcaga caattggctg cagaaaacaa
2161 gtatggattg gtggatacca tgaaagttgg caatcaatta aaaggagtga aaaccatgga
2221 agaactcaaa caagcaatca gaaatgtgac catcaagagg tgccggatca tctacggtgg
2281 ctccacgtat gaccttgaat ctgatggcaa gggcaaagtt ttggtggaaa aggtcaagaa
2341 cacctctgta cagaccaaca acgagttggc cggggccctg caccatctca aacacgcccg
2401 aatcaggtac tatgtcaaat gtgtgcaaga agcagtctat tccatcatac aaattgccgg
2461 cgctgcgttt gtcaccacgc gcattgcacg ccgcatgaac atacaagaac tctggtcgaa
2521 gccacaatta gatcaaaatg aatcagagac taaggaagag gcccccaaat cagaagatga
2581 cgagttcatc atatcttcta aggacatcaa ggaggaagga aagaagggca aaaacaaaac
2641 tggccgtggc aagaaacaca ctgcattctc cagcaagggc ttgagcgatg aggagtatga
2701 cgagtacaag aggataagag aagagagaaa tgggaagtac tctatagagg agtatcttca
2761 agacagagac aggtactatg aggagctcgc cattgccaag gccacggaag aagacttctg
2821 tgaagaggag gagataaaaa tccgtcagag aattttccgt cccaccagga aacaaagaaa
2881 ggaagagagg gccacattag gactggtaac aggttcagaa atcagaaaaa gaaaccctga
2941 tgacttcaaa cccaaaggga agctgtgggc cgatgacaac agaagtgttg actataatga
3001 gaaactggac tttgaggccc ccccaagcat atggtctagg attgtgagct ttggttctgg
3061 ctggggcttc tgggtatcac caagcctgtt cataacatca actcatgtaa tccccgcagg
3121 cataacagaa gcatttggag tccccatcaa acaaattcag atccacaaat caggtgaatt
3181 ttgccgattc agattcccaa gaccaattag accagacgtg acaggaatga tcttggaaga
3241 aggtgcgcct gaaggcaccg tggcaactgt gctcatcaaa cgccccaccg gagagctcat
3301 gcctcttgca gccagaatgg gaacacacgc aaccatgaaa attcaaggcc gcatggttgg
3361 cggacagatg ggtatgttgc tcactggatc aaatgctaaa ggaatggatt tgggaacaac
3421 tcctggtgac tgtggctgtc cttacatcta caaaaggggc aatgactata tagtcattgg
3481 ggtgcacact gcagcagccc gtggtggaaa caccgtcatc tgtgccacac agggaagtga
3541 gggtgaggca actcttgagg gtggatatga caaaggaaca tactgtgggg cacccattct
3601 aggccctggg ggtgcaccaa agttgagcac caaaaccaaa ttttggaggt catcgaacac
3661 gcccctccca ccagggacat atgagcctgc ctacctcggt ggccgtgatc cgcgtgttaa
3721 gggtgggccc tccttgcagc aggtaatgag agaccagttg aagccattca ctgaacccag
3781 gggcaaacct ccaagaccaa gtgtattgga agcagccaaa caaaccgtta tcaatgtcct
3841 cgaacaaacc ctggatcctc cacaaaaatg gacatacgca caggcgtgtg cctcacttga
3901 caaaaccact tccagcgggc atcctcatca cgtccgaaag aatgaattct ggaatggtga
3961 gaccttcacc ggcaaattgg cagaccaagc atcaaaagca aacctaatgt ttgaggaagg
4021 gaaacacatg acaccagtgt atacagcagc actcaaggac gagctagtca agactgagaa
4081 aatctataga aagatcaaga agagactgct ctggggctct gacttgtcca ccatgatccg
4141 gtgcgctagg tcatttggtg ggctcatgga cgagatgaag gcacactgca tatcactccc
4201 agtacgagtt ggcatgaatg tgaatgaaga tggcccaata atatttgaga aacattccag
4261 atacaaatac cactatgacg cagactactc tcgttgggat tcaacacaac agagggcagt
4321 actagcagca gccttggaaa tcatggtcag attctctgca gaaccacaat tggcacaaat
4381 agtcgctgag gatcttctgg cccctagcgt agtagatgta ggagacttta aaatcactat
4441 aaatgaaggg ctcccatctg gtgtgccatg cacctcccaa tggaactcca tcgcacactg
4501 gctgctaact ctctgtgcct tgtctgaagt caccaaactg tcccctgaca ttatacaagc
4561 aaattccatg ttctcatttt acggtgatga cgagattgtc agcaccgaca taaaattgga
4621 ccctgaacag ttaaccgcca agttgaagga gtatggcctg aaaccaaccc gcccagacaa
4681 gaccgaggga cccctgatca tcagtgaaga tttgaacgga ctcactttcc tccgaaggac
4741 ggtgactcgt gacccagctg gctggtttgg aaaactggac caaagttcaa ttttgaggca
4801 gatgtactgg actagaggac caaatcacga agatcccaat gagacaatga taccccattc
4861 tcaaagaccc atacagctca tggcactgct tggtgaagcc tctcttcacg gaccctcttt
4921 ctacagtaga atcagtaaat tggtcataac tgaactcaaa gaaggtggga tggactttta
4981 cgtgccaagg caggaaccca tgttcaggtg gatgaggttt tctgacttga gcacgtggga
5041 gggcgatcgc aatctggctc ccaattttgt gaatgaagat ggcgtcgagt gacgccaacc
5101 catctgatgg gtccgcagcc aacctcgtac cagaggtcaa caatgaggtt atggctttgg
5161 agcccgttgt cggtgccgct attgcggcac ctgtagcggg ccaacaaaat gtaattgacc
5221 cctggattag aaataatttt gtacaagccc ctggtgggga gtttacagta tcccccagaa
5281 acgctccagg tgaaatacta tggagcgcgc ccctaggccc tgacctaaat ccctacctat
5341 cccatttggc cagaatgtac aatggttatg caggtggttt tgaagtgcag gtaattctcg
5401 cggggaacgc gttcaccgcc gggaagatca tatttgcagc agtcccacca aattttccaa
5461 ctgaaggctt aagtcctagc caggtcacta tgttccccca tataatagta gatgttagac
5521 agttagaacc tgtgctgatt cctttacccg atgttaggaa taatttctat cattacaatc
5581 agtcaaatga ctccactatt aagttgatag caatgttgta cacaccactt agggctaata
5641 atgctgggga tgatgttttc acagtttcgt gccgagttct cacgagacca tcccccgatt
5701 ttgatttcat atttttagtg ccacccacag ttgagtcaag aactaaacca ttctctgtcc
5761 cagttttaac tgttgaggag atgaccaatt caagattccc catccctttg gaaaagctgt
5821 tcacaggccc cagcagtgcc tttgttgttc aaccacaaaa cggcaggtgc acaactgatg
5881 gcgtgctcct aggcaccacc caactttctc ctgtcaacat ctgcaccttc agaggggatg
5941 tcacccacat cacaggtagt cgcaactaca caatgaattt ggcttctcaa aattggaaca
6001 actatgaccc aacagaagaa atcccagccc ctctaggaac tccagatttt gtggggaaga
6061 ttcaaggcat gctcacccaa accacaagga cagatggttc aacacgcggc cacaaagcta
6121 cagtgtacac tgggagcgcc gactttgctc caaaactggg tagagttcaa tttgaaactg
6181 acacagacca tgattttgaa gctaatcaaa acacaaagtt caccccagtc ggtgtcatcc
6241 aagatggtag caccacccat cgaaacgaac cccaacagtg ggtgctccca agttactcag
6301 gcagaaatac tcacaatgta catctggccc ccgctgtagc ccccaccttt ccgggtgagc
6361 aacttctctt cttcagatcc accatgcccg gatgcagcgg gtaccccaac atggatttgg
6421 actgtctgct cccccaggaa tgggtgcagt acttctatca agaggcagcc ccagcacaat
6481 ctgatgtggc tctgctaaga tttgtgaatc cagacacagg tagggttttg tttgagtgca
6541 agcttcacaa atcaggctat gttacagtgg ctcacactgg ccaacatgat ttggttatcc
6601 cccccaatgg ctactttaga tttgattcct gggtcaacca gttctatacg cttgccccca
6661 tgggaaatgg aacggggcgt agacgtgtag tataatggct ggagctttct ttgctggatt
6721 ggcatctgat gtccttggct ctggacttgg ttccctcatc aatgctgggg ctggggccat
6781 caaccaaaaa gttgagtttg aaaataacag aaaattgcaa caagcatcct tccaatttag
6841 cagcaatctg caacaggctt cctttcaaca tgataaagag atgctccaag cacaaattga
6901 ggccactaaa aagctacaac aggaaatgat gaaagttaag caggcaatgc tcctagaggg
6961 tgggttctct gagacagatg cagcccgcgg ggcaattaac gcccccatga caaaagcttt
7021 ggactggagt gggacaaggt actgggctcc cgatgctagg actacaacat acaatgcagg
7081 ccgcttttcc acccctcaac catcgggggc actgccagga agagctaatc ttagggatgc
7141 tgtccctgct cggggaccct ccaacaaatc ttctaactct tctactgcca cctctgtgta
7201 ttcaaatcaa actatttcaa cgagacttgg ttctacagct ggttctggaa ccagtgtctc
7261 gagcctcccg tcaactgcaa ggactaggag ctgggttgag gatcaaaata ggaatttgtc
7321 acctttcatg aggggggccc acaacatatc atttgtcacc ccaccatcta gcagatcctc
7381 tagccaaggc acagtctcaa ccgtgcctaa agagattttg gactcctgga ctggcgcttt
7441 caacacgcgc aggcagcctc tcttcgctca cattcgtaag cgaggggagt cacgggtgta
7501 atgtgaaaag ac
//