Typing tool
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Typing tool
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Complete norovirus genomes
| MH260491 | GII.4 Sydney | |
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| GII.P16 |
ORF1: 1..5063
ORF2: 5044..6666
ORF3: 6666..7472
LOCUS MH260491 7495 bp RNA linear VRL 16-JUN-2018
DEFINITION Norovirus GII isolate ST256 nonstructural polyprotein (ORF1) gene,
partial cds; and VP1 (ORF2) and VP2 (ORF3) genes, complete cds.
ACCESSION MH260491
VERSION MH260491.1
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 7495)
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JOURNAL Unpublished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 7495)
AUTHORS Casto,A.M., Adler,A., Huang,M.-L., Makhsous,N., Xie,H., Zerr,D. and
Greninger,A.
TITLE Direct Submission
JOURNAL Submitted (25-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..7495
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="ST256"
/host="Homo sapiens"
/db_xref="taxon:122929"
/geo_loc_name="USA"
/collection_date="2017"
/note="genotype: GII"
gene <1..5063
/gene="ORF1"
CDS <1..5063
/gene="ORF1"
/codon_start=3
/product="nonstructural polyprotein"
/protein_id="AWT08329.1"
/translation="CNNNNDKEKSSGEGLFTNMSSTLKKALGARPKQPAPRDEPQKPP
RPPTPELVKRIPPPPPNGEEEEEPVIRYEVKSGISGLPELTTVPQPDVANTAFSVPPL
SLRENREAKEPLTGAILEMWDGEIYHYGMYVEKGLVLGVHKPPAAISMARVELTPLSL
YWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLNDSWLSRRMVQRTT
GFFRPYQDWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLIGKIKPLNILNILA
TCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVELVPVVMG
GVGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEANELAMV
RAIEDAVLDLEAIENNHMTALLKDKDSLATYMKTLDMEEEKARRLSTKSASPDIVGTI
NALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAREVARKVASTLTGD
QRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELADTCPLTLNCDRIEN
KGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRDFPGQPDM
WKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLHERMDEF
ELQGPTITTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVKTMEELKQAIRNVT
IKRCRIIYGGSTYDLESDGKGKVLVEKVKNTSVQTNNELVGALHHLKHARIRYYVKCV
QEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEEAPKSEDDEFIISS
KDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEEYLQDRDR
YYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLVTGSEIRKRNPDDF
KPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSPSLFITSTHVIPAG
ITEAFGVPVKQIQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEGTVATVLIKRPTGE
LMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDCGCPYIYKRGNDY
IVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILGPGGAPKLSTKTKF
WRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPRGKPPRPSVLEAA
KQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFWNGETFTGKLADQA
SKANLMYEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDLSTMIRCARSFGGL
MDEMKAHCISLPVRVGMNMNEDGPIVFEKHSRYKYHYDADYSRWDSTQQRAVLAAALE
IMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCTSQWNSIAHWLLTL
CALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLKEYGLKPTRPDKTE
GPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGPNHEDPNETMIPHS
QRPIQLMALLGEASLHGPSFYSRISKLVITELKEGGMDFYVPRQEPMFRWMRFSDLST
WEGDRNLAPNFVNEDGVE"
mat_peptide <1..959
/gene="ORF1"
/product="p48"
mat_peptide 960..2057
/gene="ORF1"
/product="NTPase"
mat_peptide 2058..2588
/gene="ORF1"
/product="p22"
mat_peptide 2589..2987
/gene="ORF1"
/product="VPg"
mat_peptide 2988..3530
/gene="ORF1"
/product="Pro"
mat_peptide 3531..5060
/gene="ORF1"
/product="RdRp"
gene 5044..6666
/gene="ORF2"
CDS 5044..6666
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="AWT08327.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSSVNVCTFRGGVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML
TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG
STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRVV"
gene 6666..7472
/gene="ORF3"
CDS 6666..7472
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="AWT08328.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARITTYNAGHFSTPQPSRALPGRANLRDAVPARGPSNKSS
NSSIATSVYSNQTISTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRV"
ORIGIN
1 cttgcaacaa caacaacgac aaggaaaaat cttcaggtga aggcttattt acaaatatgt
61 cttccacctt aaagaaagcc ctcggggcta ggcccaaaca gcctgccccg agagacgaac
121 cacaaaagcc cccaagacca ccaactcccg agttggtcaa gaggataccc cctcctccac
181 ctaatggcga agaagaagaa gaaccagtca ttaggtatga ggttaagagt gggatctctg
241 gcctgcccga gctcacaaca gtcccccagc cggacgtggc caacacagca ttcagtgttc
301 caccactgag cttgagagaa aacagggagg ccaaggaacc gctaacaggg gcaatattag
361 agatgtggga cggagagata taccactatg gcatgtacgt ggagaaaggc ttagtgttgg
421 gtgtgcacaa accacctgca gccataagca tggcaagagt ggagctgacg ccgttgtcat
481 tgtactggcg tgtggtgtac actccccaat acctcatctc ccctgaaact ctcaggaggc
541 tcaacggaga ggcgttccct tacaccgcct tcgacaacaa ctgctatgcc ttttgctgct
601 gggtgttaga cctcaatgac tcatggctta gcaggaggat ggtgcaaaga acaacgggct
661 tcttcagacc ttaccaagat tggaacagaa aacccctgcc taccatggat gactccaaaa
721 taaagaaggt agcaaatata ttcctatgtt cattgtccac attgtttacc agacccataa
781 aagacctcat aggaaaaatt aaaccattaa acatattgaa catcctggca acgtgtgact
841 ggacgtttgc cggaatagtg gagtctctga tattacttgc tgaactcttc ggagttttct
901 ggacaccccc agatgtgtct gctatgatcg ctcccttact cggggattac gagttgcaag
961 ggccagaaga tctcgccgtt gaactcgtac ctgtggtaat gggaggggtt ggtttggtgt
1021 tgggattcac caaagagaaa attggcaaaa tgttgtcctc agcagcatca acactcaggg
1081 cttgcaaaga tcttggtgcc tatggcttag agatactcaa attggtcatg aagtggttct
1141 tcccaaagaa agaggaggcc aatgaactag ccatggtgag ggccatagag gatgccgtac
1201 tagatcttga ggcgatagaa aataaccaca tgacagccct gttgaaagac aaagacagct
1261 tagcaacata catgaaaaca ctggacatgg aggaggagaa agccagaagg ttgtccacaa
1321 aatctgcatc ccctgacata gttgggacaa tcaacgccct gctggctcga atagcagcgg
1381 ccaggtcatt agtccacagg gccaaggaag agctatctag caggataaga ccagtagttg
1441 ttatgatatc tggcaaacca ggaataggca aaactcatct ggccagggag gtggcaagaa
1501 aggtggcatc cactctcaca ggggatcaaa gagtcggact cataccaaga aacggtgtgg
1561 accactggga tgcatacaaa ggtgagagag tcgtgctgtg ggacgactat ggcatgagta
1621 accccattca tgatgctctt cgcatacagg aattggctga tacgtgcccc cttaccttaa
1681 attgtgacag aattgaaaat aagggaaaag tttttgacag tgaagtcata ataattacaa
1741 caaaccttgc caacccagcc ccacttgatt atgtcaactt tgaggcctgt tccaggagaa
1801 ttgatttcct ggtgtacgct gaggcaccag aagtagaaaa ggcaaaacgg gactttcctg
1861 gtcagccaga tatgtggaag gacgccttca agccggactt ttcacacatc aagttacagc
1921 ttgcacctca gggcggcttt gacaagaatg gcaacacccc acatgggaaa ggagtgatga
1981 agaccctcac tactggttct ctgattgccc gtgcatcagg cctactgcat gagaggatgg
2041 atgaatttga actccaaggt cccacaatca ccaccttcaa tttcgaccgg aacagaatca
2101 cagcattcag acaattggct gcagaaaaca agtatggatt ggtggatacc atgaaagttg
2161 gcaatcaact aaaaggagtg aaaaccatgg aagaactcaa acaagcaatc aggaatgtga
2221 ccatcaagag gtgccgaatc atctatggtg gctccacgta tgaccttgaa tctgatggca
2281 agggcaaagt tttggtggaa aaggtcaaga acacctctgt acagaccaac aacgagttgg
2341 tcggggccct gcaccacctc aaacacgccc gaatcaggta ctatgtcaaa tgtgtgcaag
2401 aagcagtcta ttccatcata caaattgccg gcgctgcgtt tgtcaccacg cgcattgcac
2461 gccgcatgaa catacaagaa ctctggtcga agccacaatt agaccaaaat gaatcagaga
2521 ctaaggaaga ggcccccaag tcagaagatg acgagttcat catatcttct aaggacatca
2581 aggaggaagg aaagaagggc aaaaacaaaa ctggccgtgg caagaaacac actgcattct
2641 ccagcaaggg cttgagcgat gaagagtatg acgagtacaa gaggataaga gaagagagaa
2701 atgggaagta ctctatagag gagtatcttc aagatagaga caggtactat gaggagctcg
2761 ccattgccaa ggccacggag gaagacttct gtgaagagga ggagatcaaa atccgtcaga
2821 gaattttccg tcccaccagg aaacaaagaa aggaagagag ggccacatta gggctggtga
2881 caggttcaga aatcagaaaa agaaaccccg atgacttcaa acccaaaggg aagctgtggg
2941 ccgatgacaa cagaagtgtt gactacaatg agaaactgga ctttgaggcc cccccaagca
3001 tatggtctag gattgtgagc tttggttctg gctggggctt ctgggtatca ccaagcctgt
3061 tcataacatc aactcatgta atccccgcag gcataacaga agcatttgga gtccccgtca
3121 aacaaattca gatccacaaa tcaggtgaat tctgccgatt cagattccca aaaccaatta
3181 gaccagatgt gacagggatg atcttggaag aaggtgcgcc tgagggcacc gtggcaactg
3241 tgctcatcaa acgccccacc ggagagctca tgcctcttgc agccagaatg ggaacacacg
3301 caaccatgaa aattcaaggc cgcatggttg gcggacagat gggtatgttg ctcactggat
3361 caaatgctaa aggaatggat ttgggaacaa ctcctggtga ctgtggctgt ccttacatct
3421 ataaaagggg caatgactat atagtcattg gggtgcacac tgcagcagcc cgtggtggaa
3481 acaccgtcat ctgtgccaca cagggaagtg agggtgaggc aactcttgag ggtggagatg
3541 acaaaggaac atactgtggg gcacccattc taggccctgg gggtgcacca aaattgagca
3601 ccaaaaccaa attttggagg tcatcgaaca cgccccttcc accagggaca tatgagcctg
3661 cctacctcgg tggccgtgat ccgcgtgtta agggtgggcc ctccttgcag caggtgatga
3721 gagaccagtt gaagccattc actgaaccca ggggcaaacc tccaagacca agtgtattgg
3781 aagcagccaa acaaaccatt atcaatgttc tcgaacaaac cctggaccct ccgcaaaagt
3841 ggacatacgc acaggcgtgt gcctcacttg acaaaaccac ctccagcggg catccccatc
3901 acgtccgaaa gaatgaattc tggaatggtg agaccttcac tggtaaactg gcagaccaag
3961 catcaaaagc aaacctaatg tatgaggaag ggaaacacat gacaccagtg tatacagcag
4021 cactcaagga cgagctagtc aagactgaga aaatctatgg aaagatcaag aagagactgc
4081 tctggggctc tgacttgtcc actatgatcc ggtgcgctag gtcatttggt gggctcatgg
4141 acgagatgaa ggcacactgc atatcactcc cagtacgagt tggcatgaat atgaatgaag
4201 atggcccaat agtatttgag aaacattcca gatacaaata ccactatgat gcagactact
4261 ctcgttggga ttcaacacaa cagagggcag tgctagcagc agccttggaa atcatggtca
4321 gattctctgc agaaccacaa ttggcacaaa tagtcgctga ggatctactg gcccctagtg
4381 tagtagatgt aggagacttt aaaatcacaa taaatgaagg gctcccatct ggtgtgccat
4441 gcacttctca atggaactcc atcgcacact ggctgctaac tctctgtgcc ttgtctgaag
4501 tcaccaaact gtcccctgac attatacaag caaattccat gttctcattt tacggtgatg
4561 acgagattgt cagcaccgac ataaaattgg accctgaaca gttaactgcc aagctgaagg
4621 agtacggcct gaaaccaacc cgcccagaca agaccgaggg acccctgatc atcagtgaag
4681 atttaaacgg actcaccttc ctccgtagga cggtgactcg tgacccagct ggctggtttg
4741 gaaaactgga ccaaagttca atcttgaggc aaatgtactg gactagagga ccaaatcatg
4801 aagaccccaa tgaaacaatg ataccccact ctcaaagacc catacagctc atggcactgc
4861 ttggtgaagc ctctcttcac ggaccctctt tctatagtag aatcagtaaa ttggtcataa
4921 ctgaactcaa agaaggtggg atggactttt acgtgccaag gcaggaaccc atgttcaggt
4981 ggatgaggtt ttctgacttg agcacgtggg agggcgatcg caatctggct cccaattttg
5041 tgaatgaaga tggcgtcgag tgacgccaac ccatctgatg ggtccgcagc caacctcgta
5101 ccagaggtca acaatgaggt tatggctttg gagcccgttg ttggtgccgc tattgcggca
5161 cctgtagcgg gccaacaaaa tgtaattgac ccctggatta gaaataattt tgtacaagcc
5221 cctggtgggg agtttacagt atcccctaga aacgctccag gtgaaatact atggagcgcg
5281 cccctaggcc ctgacctaaa tccctaccta tcccatttgg ccagaatgta caatggttat
5341 gcaggtggtt ttgaagtgca ggtaattctc gcggggaacg cgttcaccgc cgggaagatt
5401 atatttgcag cagtcccacc aaattttcca actgaaggct taagtcctag ccaggttact
5461 atgttccccc atataatagt agatgttaga caattagaac ctgtgctgat tcccttaccc
5521 gatgttagga ataacttcta tcattacaat cagtcaaatg attccactat taagttgata
5581 gcaatgttgt atacaccact tagggctaat aatgctgggg atgatgtttt cacagtttcg
5641 tgtcgagtcc tcacgagacc atcccccgat tttgatttca tatttttggt gccacccacg
5701 gttgagtcaa gaactaagcc attctctgtc ccagttttaa ctgttgagga gatgaccaat
5761 tcaagattcc ccatcccttt ggaaaagttg ttcacaggcc ccagcagtgc ctttgttgtt
5821 caaccacaaa acggcaggtg cacaactgat ggcgtgctcc taggcaccac ccaactttct
5881 tctgtcaacg tctgcacctt cagagggggt gtcacccaca tcacaggtag tcgcaactac
5941 acaatgaatt tggcttctca aaattggaac aactatgacc caacagaaga aatcccagcc
6001 cctctaggaa ctccagattt tgtggggaag attcaaggca tgctcaccca aaccacaagg
6061 acagatggct caacacgcgg ccacaaagct acagtgtaca ctgggagcgc cgactttgct
6121 ccaaaactgg gtagagttca atttgaaact gacacagacc atgattttga agctaatcaa
6181 aacacaaagt tcaccccagt cggtgtcatc caagatggta gcaccaccca ccgaaacgaa
6241 ccccaacagt gggtgctccc aagttactca ggcagaaata ctcacaatgt acatttggcc
6301 cccgctgtag cccccacttt tccgggtgag caacttctct tcttcagatc caccatgccc
6361 ggatgcagcg ggtaccccaa catggatttg gactgtctgc tcccccagga atgggtgcag
6421 tatttctacc aagaggcagc cccagcacaa tctgatgtgg ctctgctaag atttgtgaat
6481 ccagacacag gtagggtttt gtttgagtgc aagcttcaca aatcaggcta tgttacagtg
6541 gctcacactg gccaacatga tttggttatc ccccccaatg gttactttag gtttgattcc
6601 tgggtcaacc agttctacac gcttgccccc atgggaaatg gaacggggcg tagacgtgta
6661 gtataatggc tggagctttc tttgctggat tggcatctga tgtccttggc tctggacttg
6721 gttcccttat caatgctggg gctggggcca tcaaccaaaa agtcgagttt gaaaataaca
6781 gaaaattgca acaagcatcc ttccaattta gcagcaatct gcaacaggct tcttttcaac
6841 atgataaaga gatgctccaa gcacaaattg aggccaccaa aaagctacaa caggaaatga
6901 tgaaagttaa gcaggcaatg ctcctagagg gtgggttctc tgagacagat gcagcccgcg
6961 gggcaattaa cgcccccatg acaaaagctt tggactggag cgggacaagg tactgggctc
7021 cagatgctag gattacaaca tacaatgcag gccacttttc cacccctcaa ccatcgaggg
7081 cactgccagg aagagctaat cttagggatg ctgtccctgc acggggaccc tccaataaat
7141 cttctaactc ttctattgcc acctctgtgt attcaaatca aactatttca acgagacttg
7201 gttctacagc tggttctgga accagtgtct ctagcctccc gtcaactgca aggactagga
7261 gctgggttga ggatcaaaat aggaatttgt cacctttcat gaggggggcc cacaacatat
7321 cgtttgtcac cccaccatct agcagatcct ctagccaagg cacagtctca accgtgccta
7381 aagagatttt ggactcctgg actggcgctt tcaacacgcg caggcagcct ctcttcgctc
7441 acattcgtaa gcgaggggag tcacgggtgt aatgtgaaaa gacaaaactg attat
//