Typing tool
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Typing tool
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Complete norovirus genomes
| MT537634 | GII.4 Sydney | |
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| GII.P16 |
ORF1: 1..5097
ORF2: 5078..6700
ORF3: 6700..7506
LOCUS MT537634 7515 bp RNA linear VRL 31-JUL-2020
DEFINITION Norovirus GII isolate 259-3 nonstructural polyprotein (ORF1) gene,
partial cds; and VP1 (ORF2) and VP2 (ORF3) genes, complete cds.
ACCESSION MT537634
VERSION MT537634.1
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 7515)
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JOURNAL Unpublished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 7515)
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..7515
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="259-3"
/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..5097
/gene="ORF1"
CDS <1..5097
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="QKE61145.1"
/translation="KMASNDATVAVACNNNNDKEKSSGEGLFTNMSFTLKKALGARPK
QPAPRDEPQKPPRPPTPELVKRIPPPPPNGEGEEEPVIRYEVKSGISGLPELTTVPQP
DVANTAFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAAI
SMARVELTPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLND
SWLSRRMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLIG
KIKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPE
DLAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFF
PKKEEANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRLS
TKSASPDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLARE
VARKVASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELADT
CPLTLNCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVE
KAKRDFPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIAR
ASGLLHERMDEFELQGPTITTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVKT
MEELKQAIRNVTIKRCRIIYGGSTYDLESDGKGKVLVEKVKNTSVQTNNELAGALHHL
KHARIRYYVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEEA
PKSEDDEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGK
YSIEEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLVT
GSEIRKRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSPS
LFITSTHVIPAGITEAFGVPIKQIQIHKSGEFCRFRFPRPIRPDVTGMILEEGAPEGT
VATVLIKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDC
GCPYIYKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGYDKGTYCGAPILGP
GGAPKLSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPR
GKPPRPSVLEAAKQTVINVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFWN
GETFTGKLADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYRKIKKRLLWGSDLS
TMIRCARSFGGLMDEMKAHCISLPVRVGMNVNEDGPIIFEKHSRYKYHYDADYSRWDS
TQQRAVLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCTS
QWNSIAHWLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLKE
YGLKPTRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGPN
HEDPNETMIPHSQRPIQLMALLGEASLHGPSFYSRISKLVITELKEGGMDFYVPRQEP
MFRWMRFSDLSTWEGDRNLAPNFVNEDGVE"
mat_peptide <1..993
/gene="ORF1"
/product="p48"
mat_peptide 994..2091
/gene="ORF1"
/product="NTPase"
mat_peptide 2092..2622
/gene="ORF1"
/product="p22"
mat_peptide 2623..3021
/gene="ORF1"
/product="VPg"
mat_peptide 3022..3564
/gene="ORF1"
/product="Pro"
mat_peptide 3565..5094
/gene="ORF1"
/product="RdRp"
gene 5078..6700
/gene="ORF2"
CDS 5078..6700
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="QKE61146.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML
TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG
STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRVV"
gene 6700..7506
/gene="ORF3"
CDS 6700..7506
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="QKE61147.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRDAVPARGPSNKSS
NSSTATSVYSNQTISTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRV"
ORIGIN
1 aagatggcgt ctaacgacgc taccgttgcc gttgcttgca acaacaacaa cgacaaggaa
61 aaatcttcag gtgaaggctt attcacaaat atgtctttca ccttaaagaa agccctcggg
121 gctaggccca aacagcctgc cccgagagac gaaccacaaa agcccccaag accaccaacc
181 cccgagttgg tcaagaggat accccctcct ccacctaatg gcgaaggaga agaagaacca
241 gtcattaggt atgaggttaa gagtgggatc tctggcctgc ccgagctcac aacagtcccc
301 caaccggacg tggccaacac agcattcagt gttccaccac tgagcttgag agaaaacagg
361 gaggccaagg aaccgctaac aggggcaata ttagagatgt gggatggaga gatataccac
421 tatggcctgt acgtggagaa aggcttagtg ttgggtgtgc acaaaccacc tgcagccata
481 agcatggcaa gagtggagct gacgccgctg tcattgtact ggcgtgtggt gtacactccc
541 caatacctca tctcccctga aactctcagg aggctcaacg gagaggcgtt cccttacacc
601 gccttcgaca acaactgcta cgccttttgc tgctgggtgt tagacctcaa tgactcatgg
661 cttagcagga ggatggtgca aagaacaacg ggcttcttca gaccttacca agagtggaac
721 agaaagcccc tgcctaccat ggatgactcc aaaattaaga aggtagcaaa tatattccta
781 tgttcattgt ccacattatt caccagaccc ataaaagacc tcatagggaa aattaaacca
841 ttaaacatat tgaacatcct ggcaacgtgt gactggacgt ttgccggaat agtggagtct
901 ctgatattac ttgctgaact cttcggagtt ttctggacgc ccccagatgt gtctgctatg
961 atcgctccct tactcgggga ctacgagttg caagggccag aagacctcgc cgttgaactc
1021 gtacctgtgg taatgggagg gattggtttg gtgttgggat tcaccaaaga gaaaattggc
1081 aaaatgttgt cctcagcagc atcaacactc agggcttgca aagatcttgg tgcctatggc
1141 ttagagatac tcaagttggt catgaagtgg ttcttcccaa agaaagagga ggccaatgag
1201 ctagccatgg tgagggccat agaggatgcc gtgctagatc ttgaggcaat agaaaataac
1261 cacatgacaa ccctgttgaa agacaaagac agcttagcaa catacatgaa aacactggac
1321 atggaggagg agaaagccag aaggttgtcc acaaaatctg catcccctga catagttggg
1381 acaatcaacg ccctgctggc tcgaatagca gcggccaggt cattagtcca cagggccaag
1441 gaagagctat ctagcaggat aaggccagta gttgttatga tatctggcaa accaggaata
1501 ggcaaaactc atctggccag ggaggtggca agaaaggtgg catccactct cacaggggac
1561 caaagagtcg gactcatacc aagaaacggt gtggaccatt gggatgcata caaaggtgag
1621 agagtcgtgc tgtgggacga ctatggcatg agtaacccca tccatgatgc tcttcgcata
1681 caagaattgg ctgatacgtg tccccttacc ttaaattgtg acagaattga aaataaggga
1741 aaagtttttg acagtgaagt cataataatt acaacaaacc ttgccaatcc agccccactt
1801 gattatgtca actttgaggc ctgttccagg agaattgatt tcctggtgta cgctgaggca
1861 ccagaagtag aaaaggcaaa acgggacttt cctggtcagc cagatatgtg gaaggacgcc
1921 ttcaagccgg acttttcaca catcaagcta cagcttgcac ctcagggcgg ctttgacaag
1981 aatggcaaca ccccacatgg gaaaggagtg atgaagaccc tcactaccgg ttctctgatt
2041 gcccgtgcat caggcctact acatgagagg atggatgaat ttgaactcca aggtcccaca
2101 atcaccacct tcaatttcga ccgaaacaga atcacagcat tcagacaatt ggctgcagaa
2161 aacaagtatg gattggtgga taccatgaaa gttggcaatc aattaaaagg agtgaaaacc
2221 atggaagaac tcaaacaagc aatcagaaat gtgaccatca agaggtgccg gatcatctac
2281 ggtggctcca cgtatgacct tgaatctgat ggcaagggca aagttttggt ggaaaaggtc
2341 aagaacacct ctgtacagac caacaacgag ttggccgggg ccctgcacca tctcaaacac
2401 gcccgaatca ggtactatgt caaatgtgtg caagaagcag tctattccat catacaaatt
2461 gccggcgctg cgtttgtcac cacgcgcatt gcacgccgca tgaacataca agaactctgg
2521 tcgaagccac aattagatca aaatgaatca gagactaagg aagaggcccc caaatcagaa
2581 gatgacgagt tcatcatatc ttctaaggac atcaaggagg aaggaaagaa gggcaaaaac
2641 aaaactggcc gtggcaagaa acacactgca ttctccagca agggcttgag cgatgaggag
2701 tatgacgagt acaagaggat aagagaagag agaaatggga agtactctat agaggagtat
2761 cttcaagaca gagacaggta ctatgaggag ctcgccattg ccaaggccac ggaagaagac
2821 ttctgtgaag aggaggagat aaaaatccgt cagagaattt tccgtcccac caggaaacaa
2881 agaaaggaag agagggccac attaggactg gtaacaggtt cagaaatcag aaaaagaaac
2941 cctgatgact tcaaacccaa agggaagctg tgggccgatg acaacagaag tgttgactat
3001 aatgagaaac tggactttga ggccccccca agcatatggt ctaggattgt gagctttggt
3061 tctggctggg gcttctgggt atcaccaagc ctgttcataa catcaactca tgtaatcccc
3121 gcaggcataa cagaagcatt tggagtcccc atcaaacaaa ttcagatcca caaatcaggt
3181 gaattttgcc gattcagatt cccaagacca attagaccag acgtgacagg aatgatcttg
3241 gaagaaggtg cgcctgaagg caccgtggca actgtgctca tcaaacgccc caccggagag
3301 ctcatgcctc ttgcagccag aatgggaaca cacgcaacca tgaaaattca aggccgcatg
3361 gttggcggac agatgggtat gttgctcact ggatcaaatg ctaaaggaat ggatttggga
3421 acaactcctg gtgactgtgg ctgtccttac atctacaaaa ggggcaatga ctatatagtc
3481 attggggtgc acactgcagc agcccgtggt ggaaacaccg tcatctgtgc cacacaggga
3541 agtgagggtg aggcaactct tgagggtgga tatgacaaag gaacatactg tggggcaccc
3601 attctaggcc ctgggggtgc accaaagttg agcaccaaaa ccaaattttg gaggtcatcg
3661 aacacgcccc tcccaccagg gacatatgag cctgcctacc tcggtggccg tgatccgcgt
3721 gttaagggtg ggccctcctt gcagcaggta atgagagacc agttgaagcc attcactgaa
3781 cccaggggca aacctccaag accaagtgta ttggaagcag ccaaacaaac cgttatcaat
3841 gtcctcgaac aaaccctgga tcctccacaa aaatggacat acgcacaggc gtgtgcctca
3901 cttgacaaaa ccacttccag cgggcatcct catcacgtcc gaaagaatga attctggaat
3961 ggtgagacct tcaccggcaa attggcagac caagcatcaa aagcaaacct aatgtttgag
4021 gaagggaaac acatgacacc agtgtataca gcagcactca aggacgagct agtcaagact
4081 gagaaaatct atagaaagat caagaagaga ctgctctggg gctctgactt gtccaccatg
4141 atccggtgcg ctaggtcatt tggtgggctc atggacgaga tgaaggcaca ctgcatatca
4201 ctcccagtac gagttggcat gaatgtgaat gaagatggcc caataatatt tgagaaacat
4261 tccagataca aataccacta tgacgcagac tactctcgtt gggattcaac acaacagagg
4321 gcagtactag cagcagcctt ggaaatcatg gtcagattct ctgcagaacc acaattggca
4381 caaatagtcg ctgaggatct tctggcccct agcgtagtag atgtaggaga ctttaaaatc
4441 actataaatg aagggctccc atctggtgtg ccatgcacct cccaatggaa ctccatcgca
4501 cactggctgc taactctctg tgccttgtct gaagtcacca aactgtcccc tgacattata
4561 caagcaaatt ccatgttctc attttacggt gatgacgaga ttgtcagcac cgacataaaa
4621 ttggaccctg aacagttaac cgccaagttg aaggagtatg gcctgaaacc aacccgccca
4681 gacaagaccg agggacccct gatcatcagt gaagatttga acggactcac tttcctccga
4741 aggacggtga ctcgtgaccc agctggctgg tttggaaaac tggaccaaag ttcaattttg
4801 aggcagatgt actggactag aggaccaaat cacgaagatc ccaatgagac aatgataccc
4861 cattctcaaa gacccataca gctcatggca ctgcttggtg aagcctctct tcacggaccc
4921 tctttctaca gtagaatcag taaattggtc ataactgaac tcaaagaagg tgggatggac
4981 ttttacgtgc caaggcagga acccatgttc aggtggatga ggttttctga cttgagcacg
5041 tgggagggcg atcgcaatct ggctcccaat tttgtgaatg aagatggcgt cgagtgacgc
5101 caacccatct gatgggtccg cagccaacct cgtaccagag gtcaacaatg aggttatggc
5161 tttggagccc gttgtcggtg ccgctattgc ggcacctgta gcgggccaac aaaatgtaat
5221 tgacccctgg attagaaata attttgtaca agcccctggt ggggagttta cagtatcccc
5281 cagaaacgct ccaggtgaaa tactatggag cgcgccccta ggccctgacc taaatcccta
5341 cctatcccat ttggccagaa tgtacaatgg ttatgcaggt ggttttgaag tgcaggtaat
5401 tctcgcgggg aacgcgttca ccgccgggaa gatcatattt gcagcagtcc caccaaattt
5461 tccaactgaa ggcttaagtc ctagccaggt cactatgttc ccccatataa tagtagatgt
5521 tagacagtta gaacctgtgc tgattccttt acccgatgtt aggaataatt tctatcatta
5581 caatcagtca aatgactcca ctattaagtt gatagcaatg ttgtacacac cacttagggc
5641 taataatgct ggggatgatg ttttcacagt ttcgtgccga gttctcacga gaccatcccc
5701 cgattttgat ttcatatttt tagtgccacc cacagttgag tcaagaacta aaccattctc
5761 tgtcccagtt ttaactgttg aggagatgac caattcaaga ttccccatcc ctttggaaaa
5821 gctgttcaca ggccccagca gtgcctttgt tgttcaacca caaaacggca ggtgcacaac
5881 tgatggcgtg ctcctaggca ccacccaact ttctcctgtc aacatctgca ccttcagagg
5941 ggatgtcacc cacatcacag gtagtcgcaa ctacacaatg aatttggctt ctcaaaattg
6001 gaacaactat gacccaacag aagaaatccc agcccctcta ggaactccag attttgtggg
6061 gaagattcaa ggcatgctca cccaaaccac aaggacagat ggttcaacac gcggccacaa
6121 agctacagtg tacactggga gcgccgactt tgctccaaaa ctgggtagag ttcaatttga
6181 aactgacaca gaccatgatt ttgaagctaa tcaaaacaca aagttcaccc cagtcggtgt
6241 catccaagat ggtagcacca cccatcgaaa cgaaccccaa cagtgggtgc tcccaagtta
6301 ctcaggcaga aatactcaca atgtacatct ggcccccgct gtagccccca cctttccggg
6361 tgagcaactt ctcttcttca gatccaccat gcccggatgc agcgggtacc ccaacatgga
6421 tttggactgt ctgctccccc aggaatgggt gcagtacttc tatcaagagg cagccccagc
6481 acaatctgat gtggctctgc taagatttgt gaatccagac acaggtaggg ttttgtttga
6541 gtgcaagctt cacaaatcag gctatgttac agtggctcac actggccaac atgatttggt
6601 tatccccccc aatggctact ttagatttga ttcctgggtc aaccagttct atacgcttgc
6661 ccccatggga aatggaacgg ggcgtagacg tgtagtataa tggctggagc tttctttgct
6721 ggattggcat ctgatgtcct tggctctgga cttggttccc tcatcaatgc tggggctggg
6781 gccatcaacc aaaaagttga gtttgaaaat aacagaaaat tgcaacaagc atccttccaa
6841 tttagcagca atctgcaaca ggcttccttt caacatgata aagagatgct ccaagcacaa
6901 attgaggcca ctaaaaagct acaacaggaa atgatgaaag ttaagcaggc aatgctccta
6961 gagggtgggt tctctgagac agatgcagcc cgcggggcaa ttaacgcccc catgacaaaa
7021 gctttggact ggagtgggac aaggtactgg gctcccgatg ctaggactac aacatacaat
7081 gcaggccgct tttccacccc tcaaccatcg ggggcactgc caggaagagc taatcttagg
7141 gatgctgtcc ctgctcgggg accctccaac aaatcttcta actcttctac tgccacctct
7201 gtgtattcaa atcaaactat ttcaacgaga cttggttcta cagctggttc tggaaccagt
7261 gtctcgagcc tcccgtcaac tgcaaggact aggagctggg ttgaggatca aaataggaat
7321 ttgtcacctt tcatgagggg ggcccacaac atatcatttg tcaccccacc atctagcaga
7381 tcctctagcc aaggcacagt ctcaaccgtg cctaaagaga ttttggactc ctggactggc
7441 gctttcaaca cgcgcaggca gcctctcttc gctcacattc gtaagcgagg ggagtcacgg
7501 gtgtaatgtg aaaag
//