Typing tool
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Typing tool
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Complete norovirus genomes
| MH279825 | GII.4 Sydney | |
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| GII.P16 |
ORF1: 1..5093
ORF2: 5074..6696
ORF3: 6696..7502
LOCUS MH279825 7525 bp RNA linear VRL 01-JUL-2018
DEFINITION Norovirus GII strain ST90 nonstructural polyprotein (ORF1) gene,
partial cds; and VP1 (ORF2) and VP2 (ORF3) genes, complete cds.
ACCESSION MH279825
VERSION MH279825.1
DBLINK BioProject: PRJNA338014
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norovirus norwalkense.
REFERENCE 1 (bases 1 to 7525)
AUTHORS Casto,A.M., Adler,A., Huang,M.-L., Makhsous,N., Xie,H., Zerr,D. and
Greninger,A.
TITLE The limits of epidemiology: Real-time metagenomic sequencing during
norovirus outbreak reveals discrete transmission clusters and
elucidates long-term sequelae of hospital acquired infections
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 7525)
AUTHORS Casto,A.M., Adler,A., Huang,M.-L., Makhsous,N., Xie,H., Zerr,D. and
Greninger,A.
TITLE Direct Submission
JOURNAL Submitted (30-APR-2018) Department of Laboratory Medicine,
University of Washington, 1100 Fairview Ave. N, E5-110, PO Box
19024, Seattle, WA 98109, USA
FEATURES Location/Qualifiers
source 1..7525
/organism="Norovirus GII"
/mol_type="genomic RNA"
/strain="ST90"
/host="Homo sapiens"
/db_xref="taxon:122929"
/geo_loc_name="USA"
/collection_date="2017"
gene <1..5093
/gene="ORF1"
CDS <1..5093
/gene="ORF1"
/codon_start=3
/product="nonstructural polyprotein"
/protein_id="AWX06075.1"
/translation="ASNDATVAVACNNNNDKEKSSGEGLFTNMSSTLKKALGARPKQP
APRDEPQKPPRPPTPELVKRIPPPPPNGEGEEEPVIRYEVKSGISGLPELTTVPQPDV
ANTAFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAAISM
ARVELTPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLNDSW
LSRRMVQRTTGFFRPYQDWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLIGKI
KPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDL
AVELVPVVMGGVGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPK
KEEANELAMVRAIEDAVLDLEAIENNHMTALLKDKDSLATYMKTLDMEEEKARRLSTK
SASPDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAREVA
RKVASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELADTCP
LTLNCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKA
KRDFPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARAS
GLLHERMDEFELQGPTITTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVKTME
ELKQAIRNVTIKRCRIIYGGSTYDLESDGKGKVLVEKVKNTSVQTNNELVGALHHLKH
ARIRYYVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEEAPK
SEDDEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYS
IEEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLVTGS
EIRKRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSPSLF
ITSTHVIPAGITEAFGVPVKQIQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEGTVA
TVLIKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDCGC
PYIYKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILGPGG
APKLSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPRGK
PPRPSVLEAAKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFWNGE
TFTGKLADQASKANLMYEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDLSTM
IRCARSFGGLMDEMKAHCISLPVRVGMNMNEDGPIVFEKHSRYKYHYDADYSRWDSTQ
QRAVLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCTSQW
NSIAHWLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLKEYG
LKPTRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGPNHE
DPNETMIPHSQRPIQLMALLGEASLHGPSFYSRISKLVITELKEGGMDFYVPRQEPMF
RWMRFSDLSTWEGDRNLAPNFVNEDGVE"
mat_peptide <1..989
/gene="ORF1"
/product="p48"
mat_peptide 990..2087
/gene="ORF1"
/product="NTPase"
mat_peptide 2088..2618
/gene="ORF1"
/product="p22"
mat_peptide 2619..3017
/gene="ORF1"
/product="VPg"
mat_peptide 3018..3560
/gene="ORF1"
/product="Pro"
mat_peptide 3561..5090
/gene="ORF1"
/product="RdRp"
gene 5074..6696
/gene="ORF2"
CDS 5074..6696
/gene="ORF2"
/codon_start=1
/product="VP1"
/protein_id="AWX06073.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSSVNVCTFRGGVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML
TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG
STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRVV"
gene 6696..7502
/gene="ORF3"
CDS 6696..7502
/gene="ORF3"
/codon_start=1
/product="VP2"
/protein_id="AWX06074.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARITTYNAGHFSTPQPSRALPGRANLRDAVPARGPSNKSS
NSSIATSVYSNQTISTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRV"
ORIGIN
1 tggcgtctaa cgacgctacc gttgccgttg cttgcaacaa caacaacgac aaggaaaaat
61 cttcaggtga aggcttattc acaaatatgt cttccacctt aaagaaagcc ctcggggcta
121 ggcccaaaca gcctgccccg agagacgaac cacaaaagcc cccaagacca ccaactcccg
181 agttggtcaa gaggataccc cctcctccac ctaatggcga aggagaagaa gaaccagtca
241 ttaggtatga ggttaagagt gggatctctg gcctgcccga gctcacaaca gtcccccagc
301 cggacgtggc caacacagca ttcagtgttc caccactgag cttgagagaa aacagggagg
361 ccaaggaacc gctaacaggg gcaatattag agatgtggga cggagagata taccactatg
421 gcctgtacgt ggagaaaggc ttagtgttgg gtgtgcacaa accacctgca gccataagca
481 tggcaagagt ggagctgacg ccgttgtcat tgtactggcg tgtggtgtac actccccaat
541 acctcatctc ccctgaaact ctcaggaggc tcaacggaga ggcgttccct tacaccgcct
601 tcgacaacaa ctgctatgcc ttttgctgct gggtgttaga cctcaatgac tcatggctta
661 gcaggaggat ggtgcaaaga acaacgggct tcttcagacc ttaccaagat tggaacagaa
721 aacccctgcc taccatggat gactccaaaa taaagaaggt agcaaatata ttcctatgtt
781 cattgtccac attgtttacc agacccataa aagacctcat aggaaaaatt aaaccattaa
841 acatattgaa catcctggca acgtgtgact ggacgtttgc cggaatagtg gagtctctga
901 tattacttgc tgaactcttc ggagttttct ggacaccccc agatgtgtct gctatgatcg
961 ctcccttact cggggactac gagttgcaag ggccagaaga cctcgccgtt gaactcgtac
1021 ctgtggtaat gggaggggtt ggtttggtgt tgggattcac caaagagaaa attggcaaaa
1081 tgttgtcctc agcagcatca acactcaggg cttgcaaaga tcttggtgcc tatggcttag
1141 agatactcaa attggtcatg aagtggttct tcccaaagaa agaggaggcc aatgaactag
1201 ccatggtgag ggccatagag gatgccgtac tagatcttga ggcgatagaa aataaccaca
1261 tgacagccct gttgaaagac aaagacagct tagcaacata catgaaaaca ctggacatgg
1321 aggaggagaa agccagaagg ttgtccacaa aatctgcatc ccctgacata gttgggacaa
1381 tcaacgccct gctggctcga atagcagcgg ccaggtcatt agtccacagg gccaaggaag
1441 agctatctag caggataaga ccagtagttg ttatgatatc tggcaaacca ggaataggca
1501 aaactcatct ggccagggag gtggcaagaa aggtggcatc cactctcaca ggggatcaaa
1561 gagtcggact cataccaaga aacggtgtgg accactggga tgcatacaaa ggtgagagag
1621 tcgtgctgtg ggacgactat ggcatgagta accccattca tgatgctctt cgcatacagg
1681 aattggctga tacgtgcccc cttaccttaa attgtgacag aattgaaaat aagggaaaag
1741 tttttgacag tgaagtcata ataattacaa caaaccttgc caacccagcc ccacttgatt
1801 atgtcaactt tgaggcctgt tccaggagaa ttgatttcct ggtgtacgct gaggcaccag
1861 aagtagaaaa ggcaaaacgg gactttcctg gtcagccaga tatgtggaag gacgccttca
1921 agccggactt ttcacacatc aagttacagc ttgcacctca gggcggcttt gacaagaatg
1981 gcaacacccc acatgggaaa ggagtgatga agaccctcac tactggttct ctgattgccc
2041 gtgcatcagg cctactgcat gagaggatgg atgaatttga actccaaggt cccacaatca
2101 ccaccttcaa tttcgaccgg aacagaatca cagcattcag acaattggct gcagaaaaca
2161 agtatggatt ggtggatacc atgaaagttg gcaatcaact aaaaggagtg aaaaccatgg
2221 aagaactcaa acaagcaatc aggaatgtga ccatcaagag gtgccgaatc atctatggtg
2281 gctccacgta tgaccttgaa tctgatggca agggcaaagt tttggtggaa aaggtcaaga
2341 acacctctgt acagaccaac aacgagttgg tcggggccct gcaccacctc aaacacgccc
2401 gaatcaggta ctatgtcaaa tgtgtgcaag aagcagtcta ttccatcata caaattgccg
2461 gcgctgcgtt tgtcaccacg cgcattgcac gccgcatgaa catacaagaa ctctggtcga
2521 agccacaatt agaccaaaat gaatcagaga ctaaggaaga ggcccccaag tcagaagatg
2581 acgagttcat catatcttct aaggacatca aggaggaagg aaagaagggc aaaaacaaaa
2641 ctggccgtgg caagaaacac actgcattct ccagcaaggg cttgagcgat gaagagtatg
2701 acgagtacaa gaggataaga gaagagagaa atgggaagta ctctatagag gagtatcttc
2761 aagacagaga caggtactat gaggagctcg ccattgccaa ggccacggag gaagacttct
2821 gtgaagagga ggagatcaaa atccgtcaga gaattttccg tcccaccagg aaacaaagaa
2881 aggaagagag ggccacatta gggctggtga caggttcaga aatcagaaaa agaaaccccg
2941 atgacttcaa acccaaaggg aagctgtggg ccgatgacaa cagaagtgtt gactacaatg
3001 agaaactgga ctttgaggcc cccccaagca tatggtctag gattgtgagc tttggttctg
3061 gctggggctt ctgggtatca ccaagcctgt tcataacatc aactcatgta atccccgcag
3121 gcataacaga agcatttgga gtccccgtca aacaaattca gatccacaaa tcaggtgaat
3181 tctgccgatt cagattccca aaaccaatta gaccagatgt gacagggatg atcttggaag
3241 aaggtgcgcc tgaaggcacc gtggcaactg tgctcatcaa acgccccacc ggagagctca
3301 tgcctcttgc agccagaatg ggaacacacg caaccatgaa aattcaaggc cgcatggttg
3361 gcggacagat gggtatgttg ctcactggat caaatgctaa aggaatggat ttgggaacaa
3421 ctcctggtga ctgtggctgt ccttacatct ataaaagggg caatgactat atagtcattg
3481 gggtgcacac tgcagcagcc cgtggtggaa acaccgtcat ctgtgccaca cagggaagtg
3541 agggtgaggc aactcttgag ggtggagatg acaaaggaac atactgtggg gcacccattc
3601 taggccctgg gggtgcacca aaattgagca ccaaaaccaa attttggagg tcatcgaaca
3661 cgccccttcc accagggaca tatgagcctg cctacctcgg tggccgtgat ccgcgtgtta
3721 agggtgggcc ctccttgcag caggtgatga gagaccagtt gaagccattc actgaaccca
3781 ggggcaaacc tccaagacca agtgtattgg aagcagccaa acaaaccatt atcaatgttc
3841 tcgaacaaac cctggaccct ccgcaaaagt ggacatacgc acaggcgtgt gcctcacttg
3901 acaaaaccac ctccagcggg catccccatc acgtccgaaa gaatgaattc tggaatggtg
3961 agaccttcac tggtaaactg gcagaccaag catcaaaagc aaacctaatg tatgaggaag
4021 ggaaacacat gacaccagtg tatacagcag cactcaagga cgagctagtc aagactgaga
4081 aaatctatgg aaagatcaag aagagactgc tctggggctc tgacttgtcc actatgatcc
4141 ggtgcgctag gtcatttggt gggctcatgg acgagatgaa ggcacactgc atatcactcc
4201 cagtacgagt tggcatgaat atgaatgaag atggcccaat agtatttgag aaacattcca
4261 gatacaaata ccactatgat gcagactact ctcgttggga ttcaacacaa cagagggcag
4321 tgctagcagc agccttggaa atcatggtca gattctctgc agaaccacaa ttggcacaaa
4381 tagtcgctga ggatctactg gcccctagtg tagtagatgt aggagacttt aaaatcacaa
4441 taaatgaagg gctcccatct ggtgtgccat gcacttctca atggaactcc atcgcacact
4501 ggctgctaac tctctgtgcc ttgtctgaag tcaccaaact gtcccctgac attatacaag
4561 caaattccat gttctcattt tacggtgatg acgagattgt cagcaccgac ataaaattgg
4621 accctgaaca gttaactgcc aagctgaagg agtacggcct gaaaccaacc cgcccagaca
4681 agaccgaggg acccctgatc atcagtgaag atttaaacgg actcaccttc ctccgtagga
4741 cggtgactcg tgacccagct ggctggtttg gaaaactgga ccaaagttca atcttgaggc
4801 aaatgtactg gactagagga ccaaatcatg aagaccccaa tgaaacaatg ataccccact
4861 ctcaaagacc catacagctc atggcactgc ttggtgaagc ctctcttcac ggaccctctt
4921 tctatagtag aatcagtaaa ttggtcataa ctgaactcaa agaaggtggg atggactttt
4981 acgtgccaag gcaggaaccc atgttcaggt ggatgaggtt ttctgacttg agcacgtggg
5041 agggcgatcg caatctggct cccaattttg tgaatgaaga tggcgtcgag tgacgccaac
5101 ccatctgatg ggtccgcagc caacctcgta ccagaggtca acaatgaggt tatggctttg
5161 gagcccgttg ttggtgccgc tattgcggca cctgtagcgg gccaacaaaa tgtaattgac
5221 ccctggatta gaaataattt tgtacaagcc cctggtgggg agtttacagt atcccctaga
5281 aacgctccag gtgaaatact atggagcgcg cccctaggcc ctgacctaaa tccctaccta
5341 tcccatttgg ccagaatgta caatggttat gcaggtggtt ttgaagtgca ggtaattctc
5401 gcggggaacg cgttcaccgc cgggaagatt atatttgcag cagtcccacc aaattttcca
5461 actgaaggct taagtcctag ccaggttact atgttccccc atataatagt agatgttaga
5521 caattagaac ctgtgctgat tcccttaccc gatgttagga ataacttcta tcattacaat
5581 cagtcaaatg attccactat taagttgata gcaatgttgt atacaccact tagggctaat
5641 aatgctgggg atgatgtttt cacagtttcg tgtcgagtcc tcacgagacc atcccccgat
5701 tttgatttca tatttttggt gccacccacg gttgagtcaa gaactaagcc attctctgtc
5761 ccagttttaa ctgttgagga gatgaccaat tcaagattcc ccatcccttt ggaaaagttg
5821 ttcacaggcc ccagcagtgc ctttgttgtt caaccacaaa acggcaggtg cacaactgat
5881 ggcgtgctcc taggcaccac ccaactttct tctgtcaacg tctgcacctt cagagggggt
5941 gtcacccaca tcacaggtag tcgcaactac acaatgaatt tggcttctca aaattggaac
6001 aactatgacc caacagaaga aatcccagcc cctctaggaa ctccagattt tgtggggaag
6061 attcaaggca tgctcaccca aaccacaagg acagatggct caacacgcgg ccacaaagct
6121 acagtgtaca ctgggagcgc cgactttgct ccaaaactgg gtagagttca atttgaaact
6181 gacacagacc atgattttga agctaatcaa aacacaaagt tcaccccagt cggtgtcatc
6241 caagatggta gcaccaccca ccgaaacgaa ccccaacagt gggtgctccc aagttactca
6301 ggcagaaata ctcacaatgt acatttggcc cccgctgtag cccccacttt tccgggtgag
6361 caacttctct tcttcagatc caccatgccc ggatgcagcg ggtaccccaa catggatttg
6421 gactgtctgc tcccccagga atgggtgcag tatttctacc aagaggcagc cccagcacaa
6481 tctgatgtgg ctctgctaag atttgtgaat ccagacacag gtagggtttt gtttgagtgc
6541 aagcttcaca aatcaggcta tgttacagtg gctcacactg gccaacatga tttggttatc
6601 ccccccaatg gttactttag gtttgattcc tgggtcaacc agttctacac gcttgccccc
6661 atgggaaatg gaacggggcg tagacgtgta gtataatggc tggagctttc tttgctggat
6721 tggcatctga tgtccttggc tctggacttg gttcccttat caatgctggg gctggggcca
6781 tcaaccaaaa agttgagttt gaaaataaca gaaaattgca acaagcatcc ttccaattta
6841 gcagcaatct gcaacaggct tcttttcaac atgataaaga gatgctccaa gcacaaattg
6901 aggccaccaa aaagctacaa caggaaatga tgaaagttaa gcaggcaatg ctcctagagg
6961 gtgggttctc tgagacagat gcagcccgcg gggcaattaa cgcccccatg acaaaagctt
7021 tggactggag cgggacaagg tactgggctc cagatgctag gattacaaca tacaatgcag
7081 gccacttttc cacccctcaa ccatcgaggg cactgccagg aagagctaat cttagggatg
7141 ctgtccctgc acggggaccc tccaataaat cttctaactc ttctattgcc acctctgtgt
7201 actcaaatca aactatttca acgagacttg gttctacagc tggttctgga accagtgtct
7261 cgagcctccc gtcaactgca aggactagga gctgggttga ggatcaaaat aggaatttgt
7321 cacctttcat gaggggggcc cacaacatat cgtttgtcac cccaccatct agcagatcct
7381 ctagccaagg cacagtctca accgtgccta aagagatttt ggactcctgg actggcgctt
7441 tcaacacgcg caggcagcct ctcttcgctc acattcgtaa gcgaggggag tcacgggtgt
7501 aatgtgaaaa gacaaaactg attat
//