Typing tool
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Typing tool
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Complete norovirus genomes
| MH279823 | GII.4 Sydney | |
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| GII.P16 |
ORF1: 1..5094
ORF2: 5075..6697
ORF3: 6697..7403
LOCUS MH279823 7403 bp RNA linear VRL 01-JUL-2018
DEFINITION Norovirus GII strain ST374 nonstructural polyprotein (ORF1) gene,
partial cds; VP1 (ORF2) gene, complete cds; and VP2 (ORF3) gene,
partial cds.
ACCESSION MH279823
VERSION MH279823.1
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 7403)
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JOURNAL Unpublished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 7403)
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..7403
/organism="Norovirus GII"
/mol_type="genomic RNA"
/strain="ST374"
/host="Homo sapiens"
/db_xref="taxon:122929"
/geo_loc_name="USA"
/collection_date="2017"
gene <1..5095
/gene="ORF1"
CDS <1..5094
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="AWX06069.1"
/translation="MASNDATVAVACNNNNDKEKSSGEGLFTNMSSTLKKALGARPKQ
PAPRDEPQKPPRPPTPELVKRIPPPPPNGEEEEEPVIRYEVKSGISGLPELTTVPQPD
VANTAFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAAIS
MARVELTPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLNDS
WLSRRMVQRTTGFFRPYQDWNRKPLPTMDDSKIKKVANIFLCSLSALFTRPIKDLIGK
IKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED
LAVELVPVVMGGVGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
KKEEANELAMVRAIEDAVLDLEAIENNHMTALLKDKDSLATYMKTLDMEEEKARKLST
KSASPDIVGTVNALLARIAAARSLVHRAKEELTSRIRPVVVMISGKPGIGKTHLAREV
ARKVASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELADTC
PLTLNCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK
AKRDFPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA
SGLLHERMDEFELQGPTITTYNFDRNRITTFRQLAAENKYGLVDTMKVGNQLKGVKTM
EELKQAIRNVTIKRCRIIYGGSTYDLESDGKGKVLVEKVKNTSVQTNNELVGALHHLK
HARIRYYVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEEAP
KSEDDEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKY
SIEEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLVTG
SEIRKRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSPSL
FITSTHVIPAGITEAFGVPVKQIQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEGTV
ATVLIKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDCG
CPYIYKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILGPG
GAPKLSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPRG
KPPRPSVLEAAKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFWNG
ETFTGKLADQASKANLMYEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDLST
MIRCARSFGGLMDEMKAHCISLPVRVGMNMNEDGPIVFEKHSRYKYHYDADYSRWDST
QQRAVLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCTSQ
WNSIAHWLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLKEY
GLKPTRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGPNH
EDPNETMIPHSQRPIQLMALLGEASLHGPSFYSRISKLVITELKEGGMDFYVPRQEPM
FRWMRFSDLSTWEGDRNLAPNFVNEDGVE"
mat_peptide <1..990
/gene="ORF1"
/product="p48"
mat_peptide 991..2088
/gene="ORF1"
/product="NTPase"
mat_peptide 2089..2619
/gene="ORF1"
/product="p22"
mat_peptide 2620..3018
/gene="ORF1"
/product="VPg"
mat_peptide 3019..3561
/gene="ORF1"
/product="Pro"
mat_peptide 3562..5091
/gene="ORF1"
/product="RdRp"
gene 5075..6697
/gene="ORF2"
CDS 5075..6697
/gene="ORF2"
/codon_start=1
/product="VP1"
/protein_id="AWX06067.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFIVQPQNGRCTTDGVLLGTT
QLSSVNVCTFRGGVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML
TQTTRTDGSTRGHRATVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG
STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRVV"
gene 6697..>7403
/gene="ORF3"
CDS 6697..>7403
/gene="ORF3"
/codon_start=1
/product="VP2"
/protein_id="AWX06068.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARITTYNAGHFSTPQPSRALPGRANLRDAVPARGPSNKSS
NSSIATSVYSNQTISTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVST"
ORIGIN
1 atggcgtcta acgacgctac cgttgccgtt gcttgcaaca acaacaacga caaggaaaaa
61 tcttcaggtg aaggcttatt cacaaatatg tcttccacct taaagaaagc cctcggggct
121 aggcccaaac agcctgcccc gagagacgaa ccacaaaagc ccccaagacc accaactccc
181 gagttggtca agaggatacc ccctcctcca cctaatggcg aagaagaaga agaaccagtc
241 attaggtatg aggttaagag tgggatctct ggcctgcccg agctcacaac agtcccccag
301 ccggacgtgg ccaacacagc attcagtgtt ccaccactga gcttgagaga aaacagggag
361 gccaaggaac cgctaacagg ggcaatatta gagatgtggg acggagagat ataccactat
421 ggcctgtacg tggagaaagg cttagtgttg ggtgtgcaca aaccacctgc agccataagc
481 atggcaagag tggagctgac gccgttgtca ttgtactggc gtgtggtgta cactccccaa
541 tacctcatct cccctgaaac tctcaggagg ctcaacggag aggcgttccc ttacaccgcc
601 ttcgacaaca actgctatgc cttttgctgc tgggtgttag acctcaatga ctcatggctt
661 agcaggagga tggtgcaaag aacaacgggc ttcttcagac cttaccaaga ttggaacaga
721 aaacccctgc ctaccatgga tgactccaaa ataaagaagg tagcaaatat attcctatgt
781 tcattgtccg cattgtttac cagacccata aaagacctca taggaaaaat taaaccatta
841 aacatattga acatcctggc aacgtgtgac tggacgtttg ccggaatagt ggagtctctg
901 atattacttg ctgaactctt cggagttttc tggacacccc cagatgtgtc tgctatgatc
961 gctcccttac tcggggacta cgagttgcaa gggccagaag acctcgccgt tgaactcgta
1021 cctgtggtaa tgggaggggt tggtttggtg ttgggattca ccaaagagaa aattggcaaa
1081 atgttgtcct cagcagcatc aacactcagg gcttgcaaag atcttggtgc ctatggctta
1141 gagatactca aattggtcat gaagtggttc ttcccaaaga aagaggaggc caatgaacta
1201 gccatggtga gggccataga ggatgccgta ctagatcttg aggcgataga aaataaccac
1261 atgacagccc tgttgaaaga caaagacagc ttagcaacat acatgaaaac actggacatg
1321 gaggaggaga aagccagaaa gttgtccaca aaatctgcat cccctgacat agttgggaca
1381 gtcaacgccc tgctggctcg aatagcagcg gccaggtcat tagtccacag ggccaaggaa
1441 gagcttacta gcaggataag accagtagtt gttatgatat ctggcaaacc aggaataggc
1501 aaaactcatc tggccaggga ggtggcaaga aaggtggcat ccactctcac aggggatcaa
1561 agagtcggac tcataccaag aaacggtgtg gaccactggg atgcatacaa aggtgagaga
1621 gtcgtgctgt gggacgacta tggcatgagt aaccccattc atgatgctct tcgcatacag
1681 gaattggctg atacgtgccc ccttacctta aattgtgaca gaattgaaaa taagggaaaa
1741 gtttttgaca gtgaagtcat aataattaca acaaaccttg ccaacccagc cccacttgat
1801 tatgtcaact ttgaggcctg ttccaggaga attgatttcc tggtgtacgc tgaggcacca
1861 gaagtagaaa aggcaaaacg ggactttcct ggtcagccag atatgtggaa ggacgccttc
1921 aagccggact tttcacacat caagttacag cttgcacctc agggcggctt tgacaagaat
1981 ggcaacaccc cacatgggaa aggagtgatg aagaccctca ctactggttc tctgattgcc
2041 cgtgcatcag gcctactgca tgagaggatg gatgaatttg aactccaagg tcccacaatc
2101 accacctaca atttcgaccg gaacagaatc acaacattca gacaattggc cgcagaaaac
2161 aagtatggat tggtggatac catgaaagtt ggcaatcaac taaaaggagt gaaaaccatg
2221 gaagaactca aacaagcaat caggaatgtg accatcaaga ggtgccgaat catctatggt
2281 ggctccacgt atgaccttga atctgatggc aagggcaaag ttttggtgga aaaggtcaag
2341 aacacctctg tacagaccaa caacgagttg gtcggggccc tgcaccacct caaacacgcc
2401 cgaatcaggt actatgtcaa atgtgtgcaa gaagcagtct attccatcat acaaattgcc
2461 ggcgctgcgt ttgtcaccac gcgcattgca cgccgcatga acatacaaga actctggtcg
2521 aagccacaat tagaccaaaa tgaatcagag actaaggaag aggcccccaa gtcagaagat
2581 gacgagttca tcatatcttc taaggacatc aaggaggaag gaaagaaggg caaaaacaaa
2641 actggccgtg gcaagaaaca cactgcattc tccagcaagg gcttgagcga tgaagagtat
2701 gacgagtaca agaggataag agaagagaga aatgggaagt actctataga ggagtatctt
2761 caagacagag acaggtacta tgaggagctc gccattgcca aggccacgga ggaagacttc
2821 tgtgaagagg aggagatcaa aatccgtcag agaattttcc gtcccaccag gaaacaaaga
2881 aaggaagaga gggccacatt agggctggtg acaggttcag aaatcagaaa aagaaacccc
2941 gatgacttca aacccaaagg gaagctgtgg gccgatgaca acagaagtgt tgactacaat
3001 gagaaactgg actttgaggc ccccccaagc atatggtcta ggattgtgag ctttggttct
3061 ggctggggct tctgggtatc accaagcctg ttcataacat caactcatgt aatccccgca
3121 ggcataacag aagcatttgg agtccccgtc aaacaaattc agatccacaa atcaggtgaa
3181 ttctgccgat tcagattccc aaaaccaatt agaccagatg tgacagggat gatcttggaa
3241 gaaggtgcgc ctgaaggcac cgtggcaact gtgctcatca aacgccccac cggagagctc
3301 atgcctcttg cagccagaat gggaacacac gcaaccatga aaattcaagg ccgcatggtt
3361 ggcggacaga tgggtatgtt gctcactgga tcaaatgcta aaggaatgga tttgggaaca
3421 actcctggtg actgtggctg tccttacatc tataaaaggg gcaatgacta tatagtcatt
3481 ggggtgcaca ctgcagcagc ccgtggtgga aacaccgtca tctgtgccac acagggaagt
3541 gagggtgagg caactcttga gggtggagat gacaaaggaa catactgtgg ggcacccatt
3601 ctaggccctg ggggtgcacc aaaattgagc accaaaacca aattttggag gtcatcgaac
3661 acgccccttc caccagggac atatgagcct gcctacctcg gtggccgtga tccgcgcgtt
3721 aagggtgggc cctccttgca gcaggtgatg agagaccagt tgaagccatt cactgaaccc
3781 aggggcaaac ctccaagacc aagtgtattg gaagcagcca aacaaaccat tatcaatgtt
3841 ctcgaacaaa ccctggaccc tccgcaaaag tggacatacg cacaggcgtg tgcctcactt
3901 gacaagacca cctccagcgg gcatccccat cacgtccgaa agaatgaatt ctggaatggt
3961 gagaccttca ctggtaaact ggcagaccaa gcatcaaaag caaacctaat gtatgaggaa
4021 gggaaacaca tgacaccagt gtatacagca gcactcaagg acgagctagt caagactgag
4081 aaaatctatg gaaagatcaa gaagagactg ctctggggct ctgacttgtc cactatgatc
4141 cggtgcgcta ggtcatttgg tgggctcatg gacgagatga aggcacactg catatcactc
4201 ccagtacgag ttggcatgaa tatgaatgaa gatggcccaa tagtatttga gaaacattcc
4261 agatacaaat accactatga tgcagactac tctcgttggg attcaacaca acagagggca
4321 gtgctagcag cagccttgga aatcatggtc agattctctg cagaaccaca attggcacaa
4381 atagtcgctg aggatctact ggcccctagt gtagtagatg taggagactt taaaatcaca
4441 ataaatgaag ggctcccatc tggtgtgcca tgcacttctc aatggaactc catcgcacac
4501 tggctgctaa ctctctgtgc cttgtctgaa gtcaccaaac tgtcccctga cattatacaa
4561 gcaaattcca tgttctcatt ttacggtgat gacgagattg tcagcaccga cataaaattg
4621 gaccctgaac agttaactgc caagctgaag gagtacggcc tgaaaccaac ccgcccagac
4681 aagaccgagg gacccctgat catcagtgaa gatttaaacg gactcacctt cctccgtagg
4741 acggtgactc gtgacccagc tggctggttt ggaaaactgg accaaagttc aatcttgagg
4801 caaatgtact ggactagagg accaaatcat gaagacccca atgaaacaat gataccccac
4861 tctcaaagac ccatacagct catggcactg cttggtgaag cctctcttca cggaccctct
4921 ttctatagta gaatcagtaa attggtcata actgaactca aagaaggtgg gatggacttt
4981 tacgtgccaa ggcaggaacc catgttcagg tggatgaggt tttctgactt gagcacgtgg
5041 gagggcgatc gcaatctggc tcccaatttt gtgaatgaag atggcgtcga gtgacgccaa
5101 cccatctgat gggtccgcag ccaacctcgt accagaggtc aacaatgagg ttatggcttt
5161 ggagcccgtt gttggtgccg ctattgcggc acctgtagcg ggccaacaaa atgtaattga
5221 cccctggatt agaaataatt ttgtacaagc ccctggtggg gagtttacag tatcccctag
5281 aaacgctcca ggtgaaatac tatggagcgc gcccctaggc cctgacctaa atccctacct
5341 atcccatttg gccagaatgt acaatggtta tgcaggtggt tttgaagtgc aggtaattct
5401 cgcggggaac gcgttcaccg ccgggaagat tatatttgca gcagtcccac caaattttcc
5461 aactgaaggc ttaagtccta gccaggttac tatgttcccc catataatag tagatgttag
5521 acaattagaa cctgtgctga ttcccttacc cgatgttagg aataacttct atcattacaa
5581 tcagtcaaat gattccacta ttaagttgat agcaatgttg tatacaccac ttagggctaa
5641 taatgctggg gatgatgttt tcacagtttc gtgtcgagtc ctcacgagac catcccccga
5701 ttttgatttc atatttttgg tgccacccac ggttgagtca agaactaagc cattctctgt
5761 cccagtttta actgttgagg agatgaccaa ttcaagattc cccatccctt tggaaaagtt
5821 gttcacaggc cccagcagtg cctttattgt tcaaccacaa aacggcaggt gcacaactga
5881 tggcgtgctc ctaggcacca cccaactttc ttctgtcaac gtctgcacct tcagaggggg
5941 tgtcacccac atcacaggta gtcgcaacta cacaatgaat ttggcttctc aaaattggaa
6001 caactatgac ccaacagaag aaatcccagc ccctctagga actccagatt ttgtggggaa
6061 gattcaaggc atgctcaccc aaaccacaag gacagatggc tcaacacgcg gccacagagc
6121 tacagtgtac actgggagcg ccgactttgc tccaaaactg ggtagagttc aatttgaaac
6181 tgacacagac catgattttg aagctaatca aaacacaaag ttcaccccag tcggtgtcat
6241 ccaagatggt agcaccaccc accgaaacga accccaacag tgggtgctcc caagttactc
6301 aggcagaaat actcacaatg tacatttggc ccccgctgta gcccccactt ttccgggtga
6361 gcaacttctc ttcttcagat ccaccatgcc cggatgcagc gggtacccca acatggattt
6421 ggactgtctg ctcccccagg aatgggtgca gtatttctac caagaggcag ccccagcaca
6481 atctgatgtg gctctgctaa gatttgtgaa tccagacaca ggtagggttt tgtttgagtg
6541 caagcttcac aaatcaggct atgttacagt ggctcacact ggccaacatg atttggttat
6601 cccccccaat ggttacttta ggtttgattc ctgggtcaac cagttctaca cgcttgcccc
6661 catgggaaat ggaacggggc gtagacgtgt agtataatgg ctggagcttt ctttgctgga
6721 ttggcatctg atgtccttgg ctctggactt ggttccctta tcaatgctgg ggctggggcc
6781 atcaaccaaa aagttgagtt tgaaaataac agaaaattgc aacaagcatc cttccaattt
6841 agcagcaatc tgcaacaggc ttcttttcaa catgataaag agatgctcca agcacaaatt
6901 gaggccacca aaaagctaca acaggaaatg atgaaagtta agcaggcaat gctcctagag
6961 ggtgggttct ctgagacaga tgcagcccgc ggggcaatta acgcccccat gacaaaagct
7021 ttggactgga gcgggacaag gtactgggct ccagatgcta ggattacaac atacaatgca
7081 ggccactttt ccacccctca accatcgagg gcactgccag gaagagctaa tcttagggat
7141 gctgtccctg cacggggacc ctccaataaa tcttctaact cttctattgc cacctctgtg
7201 tactcaaatc aaactatttc aacgagactt ggttctacag ctggttctgg aaccagtgtc
7261 tcgagcctcc cgtcaactgc aaggactagg agctgggttg aggatcaaaa taggaatttg
7321 tcacctttca tgaggggggc ccacaacata tcgtttgtca ccccaccatc tagcagatcc
7381 tctagccaag gcacagtctc aac
//