Typing tool
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Typing tool
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Complete norovirus genomes
| MH260486 | GII.4 Sydney | |
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| GII.P16 |
ORF1: 1..5022
ORF2: 5003..6625
ORF3: 6625..7431
LOCUS MH260486 7454 bp RNA linear VRL 16-JUN-2018
DEFINITION Norovirus GII isolate ST347 nonstructural polyprotein (ORF1) gene,
partial cds; and VP1 (ORF2) and VP2 (ORF3) genes, complete cds.
ACCESSION MH260486
VERSION MH260486.1
DBLINK BioProject: PRJNA338014
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7454)
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JOURNAL Unpublished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 7454)
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..7454
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="ST347"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="USA"
/collection_date="2017"
/note="genotype: GII"
gene <1..5022
/gene="ORF1"
CDS <1..5022
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="AWT08314.1"
/translation="GLFTNMSSTLKKALGARSKQPAPRDEPQKPPRPPTPELVKRIPP
PPPNGEEEEEPVIRYEVKSGISGLPELTTVPQPDVANTAFSVPPLSLRENREAKEPLT
GAILEMWDGEIYHYGLYVEKGLVLGVHKPPAAISMARVELTPLSLYWRVVYTPQYLIS
PETLRRLNGEAFPYTAFDNNCYAFCCWVLDLNDSWLSRRMVQRTTGFFRPYQDWNRKP
LPTMDDSKIKKVANIFLCSLSALFTRPIKDLIGKIKPLNILNILATCDWTFAGIVESL
ILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVELVPVVMGGVGLVLGFTKEKI
GKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEANELAMVRAIEDAVLDLEAI
ENNHMTALLKDKDSLATYMKTLDMEEEKARKLSTKSASPDIVGTVNALLARIAAARSL
VHRAKEELSSRIRPVVVMISGKPGIGKTHLAREVARKVASTLTGDQRVGLIPRNGVDH
WDAYKGERVVLWDDYGMSNPIHDALRIQELADTCPLTLNCDRIENKGKVFDSEVIIIT
TNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRDFPGQPDMWKDAFKPDFSHIK
LQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLHERMDEFELQGPTITTYNFD
RNRITTFRQLAAENKYGLVDTMKVGNQLKGVKTMEELKQAIRNVTIKRCRIIYGGSTY
DLESDGKGKVLVEKVKNTSVQTNNELVGALHHLKHARIRYYVKCVQEAVYSIIQIAGA
AFVTTRIARRMNIQELWSKPQLDQNESETKEEAPKSEDDEFIISSKDIKEEGKKGKNK
TGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEEYLQDRDRYYEELAIAKATEE
DFCEEEEIKIRQRIFRPTRKQRKEERATLGLVTGSEIRKRNPDDFKPKGKLWADDNRS
VDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSPSLFITSTHVIPAGITEAFGVPVKQIQ
IHKSGEFCRFRFPKPIRPDVTGMILEEGAPEGTVATVLIKRPTGELMPLAARMGTHAT
MKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDCGCPYIYKRGNDYIVIGVHTAAARGG
NTVICATQGSEGEATLEGGDDKGTYCGAPILGPGGAPKLSTKTKFWRSSNTPLPPGTY
EPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPRGKPPRPSVLEAAKQTIINVLEQTLD
PPQKWTYAQACASLDKTTSSGHPHHVRKNEFWNGETFTGKLADQASKANLMYEEGKHM
TPVYTAALKDELVKTEKIYGKIKKRLLWGSDLSTMIRCARSFGGLMDEMKAHCISLPV
RVGMNMNEDGPIVFEKHSRYKYHYDADYSRWDSTQQRAVLAAALEIMVRFSAEPQLAQ
IVAEDLLAPSVVDVGDFKITINEGLPSGVPCTSQWNSIAHWLLTLCALSEVTKLSPDI
IQANSMFSFYGDDEIVSTDIKLDPEQLTAKLKEYGLKPTRPDKTEGPLIISEDLNGLT
FLRRTVTRDPAGWFGKLDQSSILRQMYWTRGPNHEDPNETMIPHSQRPIQLMALLGEA
SLHGPSFYSRISKLVITELKEGGMDFYVPRQEPMFRWMRFSDLSTWEGDRNLAPNFVN
EDGVE"
gene 5003..6625
/gene="ORF2"
CDS 5003..6625
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="AWT08312.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFIVQPQNGRCTTDGVLLGTT
QLSSVNVCTFRGGVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML
TQTTRTDGSTRGHRATVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG
STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRVV"
gene 6625..7431
/gene="ORF3"
CDS 6625..7431
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="AWT08313.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARITTYNAGHFSTPQPSRALPGRANLRDAVPARGPSNKSS
NSSIATSVYSNQTISTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRV"
ORIGIN
1 ggcttattca caaatatgtc ttccacctta aagaaagccc tcggggctag gtccaaacag
61 cctgccccga gagacgaacc acaaaagccc ccaagaccac caactcccga gttggtcaag
121 aggatacccc ctcctccacc taatggcgaa gaagaagaag aaccagtcat taggtatgag
181 gttaagagtg ggatctctgg cctgcccgag ctcacaacag tcccccagcc ggacgtggcc
241 aacacagcat tcagtgttcc accactgagc ttgagagaaa acagggaggc caaggaaccg
301 ctaacagggg caatattaga gatgtgggac ggagagatat accactatgg cctgtacgtg
361 gagaaaggct tagtgttggg tgtgcacaaa ccacctgcag ccataagcat ggcaagagtg
421 gagctgacgc cgttgtcatt gtactggcgt gtggtgtaca ctccccaata cctcatctcc
481 cctgaaactc tcaggaggct caacggagag gcgttccctt acaccgcctt cgacaacaac
541 tgctatgcct tttgctgctg ggtgttagac ctcaatgact catggcttag caggaggatg
601 gtgcaaagaa caacgggctt cttcagacct taccaagatt ggaacagaaa acccctgcct
661 accatggatg actccaaaat aaagaaggta gcaaatatat tcctatgttc attgtccgca
721 ttgtttacca gacccataaa agacctcata ggaaaaatta aaccattaaa catattgaac
781 atcctggcaa cgtgtgactg gacgtttgcc ggaatagtgg agtctctgat attacttgct
841 gaactcttcg gagttttctg gacaccccca gatgtgtctg ctatgatcgc tcccttactc
901 ggggactacg agttgcaagg gcctgaagac ctcgccgttg aactcgtacc tgtggtaatg
961 ggaggggttg gtttggtgtt gggattcacc aaagagaaaa ttggcaaaat gttgtcctca
1021 gcagcatcaa cactcagggc ttgcaaagat cttggtgcct atggcttaga gatactcaaa
1081 ttggtcatga agtggttctt cccaaagaaa gaggaggcca atgaactagc catggtgagg
1141 gccatagagg atgccgtact agatcttgag gcgatagaaa ataaccacat gacagccctg
1201 ttgaaagaca aagacagctt agcaacatac atgaaaacac tggacatgga ggaggagaaa
1261 gccagaaagt tgtccacaaa atctgcatcc cctgacatag ttgggacagt caacgccctg
1321 ctggctcgaa tagcagcggc caggtcatta gtccacaggg ccaaggaaga gctatctagc
1381 aggataagac cagtagttgt tatgatatct ggcaaaccag gaataggcaa aactcatctg
1441 gccagggagg tggcaagaaa ggtggcatcc actctcacag gggatcaaag agtcggactc
1501 ataccaagaa acggtgtgga ccactgggat gcatacaaag gtgagagagt cgtgctgtgg
1561 gacgactatg gcatgagtaa ccccattcat gatgctcttc gcatacagga attggctgat
1621 acgtgccccc ttaccttaaa ttgtgacaga attgaaaata agggaaaagt ttttgacagt
1681 gaagtcataa taattacaac aaaccttgcc aacccagccc cacttgatta tgtcaacttt
1741 gaggcctgtt ccaggagaat tgatttcctg gtgtacgctg aggcaccaga agtagaaaag
1801 gcaaaacggg actttcctgg tcagccagat atgtggaagg acgccttcaa gccggacttt
1861 tcacacatca agttacagct tgcacctcag ggcggctttg acaagaatgg caacacccca
1921 catgggaaag gagtgatgaa gaccctcact actggttctc tgattgcccg tgcatcaggc
1981 ctactgcatg agaggatgga tgaatttgaa ctccaaggtc ccacaatcac cacctacaat
2041 ttcgaccgga acagaatcac aacattcaga caattggccg cagaaaacaa gtatggattg
2101 gtggatacca tgaaagttgg caatcaacta aaaggagtga aaaccatgga agaactcaaa
2161 caagcaatca ggaatgtgac catcaagagg tgccgaatca tctatggtgg ctccacgtat
2221 gaccttgaat ctgatggcaa gggcaaagtt ttggtggaaa aggtcaagaa cacctctgta
2281 cagaccaaca acgagttggt cggggccctg caccacctca aacacgcccg aatcaggtac
2341 tatgtcaaat gtgtgcaaga agcagtctat tccatcatac aaattgccgg cgctgcgttt
2401 gtcaccacgc gcattgcacg ccgcatgaac atacaagaac tctggtcgaa gccacaatta
2461 gaccaaaatg aatcagagac taaggaagag gcccccaagt cagaagatga cgagttcatc
2521 atatcttcta aggacatcaa ggaggaagga aagaagggca aaaacaaaac tggccgtggc
2581 aagaaacaca ctgcattctc cagcaagggc ttgagcgatg aagagtatga cgagtacaag
2641 aggataagag aagagagaaa tgggaagtac tctatagagg agtatcttca agacagagac
2701 aggtactatg aggagctcgc cattgccaag gccacggagg aagacttctg tgaagaggag
2761 gagatcaaaa tccgtcagag aattttccgt cccaccagga aacaaagaaa ggaagagagg
2821 gccacattag ggctggtgac aggttcagaa atcagaaaaa gaaaccccga tgacttcaaa
2881 cccaaaggga agctgtgggc cgatgacaac agaagtgttg actacaatga gaaactggac
2941 tttgaggccc ccccaagcat atggtctagg attgtgagct ttggttctgg ctggggcttc
3001 tgggtatcac caagcctgtt cataacatca actcatgtaa tccccgcagg cataacagaa
3061 gcatttggag tccccgtcaa acaaattcag atccacaaat caggtgaatt ctgccgattc
3121 agattcccaa aaccaattag accagatgtg acagggatga tcttggaaga aggtgcgcct
3181 gaaggcaccg tggcaactgt gctcatcaaa cgccccaccg gagagctcat gcctcttgca
3241 gccagaatgg gaacacacgc aaccatgaaa attcaaggcc gcatggttgg cggacagatg
3301 ggtatgttgc tcactggatc aaatgctaaa ggaatggatt tgggaacaac tcctggtgac
3361 tgtggctgtc cttacatcta taaaaggggc aatgactata tagtcattgg ggtgcacact
3421 gcagcagccc gtggtggaaa caccgtcatc tgtgccacac agggaagtga gggtgaggca
3481 actcttgagg gtggagatga caaaggaaca tactgtgggg cacccattct aggccctggg
3541 ggtgcaccaa aattgagcac caaaaccaaa ttttggaggt catcgaacac gccccttcca
3601 ccagggacat atgagcctgc ctacctcggt ggccgtgatc cgcgcgttaa gggtgggccc
3661 tccttgcagc aggtgatgag agaccagttg aagccattca ctgaacccag gggcaaacct
3721 ccaagaccaa gtgtattgga agcagccaaa caaaccatta tcaatgttct cgaacaaacc
3781 ctggaccctc cgcaaaagtg gacatacgca caggcgtgtg cctcacttga caagaccacc
3841 tccagcgggc atccccatca cgtccgaaag aatgaattct ggaatggtga gaccttcact
3901 ggtaaactgg cagaccaagc atcaaaagca aacctaatgt atgaggaagg gaaacacatg
3961 acaccagtgt atacagcagc actcaaggac gagctagtca agactgagaa aatctatgga
4021 aagatcaaga agagactgct ctggggctct gacttgtcca ctatgatccg gtgcgctagg
4081 tcatttggtg ggctcatgga cgagatgaag gcacactgca tatcactccc agtacgagtt
4141 ggcatgaata tgaatgaaga tggcccaata gtatttgaga aacattccag atacaaatac
4201 cactatgatg cagactactc tcgttgggat tcaacacaac agagggcagt gctagcagca
4261 gccttggaaa tcatggtcag attctctgca gaaccacaat tggcacaaat agtcgctgag
4321 gatctactgg cccctagtgt agtagatgta ggagacttta aaatcacaat aaatgaaggg
4381 ctcccatctg gtgtgccatg cacttctcaa tggaactcca tcgcacactg gctgctaact
4441 ctctgtgcct tgtctgaagt caccaaactg tcccctgaca ttatacaagc aaattccatg
4501 ttctcatttt acggtgatga cgagattgtc agcaccgaca taaaattgga ccctgaacag
4561 ttaactgcca agctgaagga gtacggcctg aaaccaaccc gcccagacaa gaccgaggga
4621 cccctgatca tcagtgaaga tttaaacgga ctcaccttcc tccgtaggac ggtgactcgt
4681 gacccagctg gctggtttgg aaaactggac caaagttcaa tcttgaggca aatgtactgg
4741 actagaggac caaatcatga agaccccaat gaaacaatga taccccactc tcaaagaccc
4801 atacagctca tggcactgct tggtgaagcc tctcttcacg gaccctcttt ctatagtaga
4861 atcagtaaat tggtcataac tgaactcaaa gaaggtggga tggactttta cgtgccaagg
4921 caggaaccca tgttcaggtg gatgaggttt tctgacttga gcacgtggga gggcgatcgc
4981 aatctggctc ccaattttgt gaatgaagat ggcgtcgagt gacgccaacc catctgatgg
5041 gtccgcagcc aacctcgtac cagaggtcaa caatgaggtt atggctttgg agcccgttgt
5101 tggtgccgct attgcggcac ctgtagcggg ccaacaaaat gtaattgacc cctggattag
5161 aaataatttt gtacaagccc ctggtgggga gtttacagta tcccctagaa acgctccagg
5221 tgaaatacta tggagcgcgc ccctaggccc tgacctaaat ccctacctat cccatttggc
5281 cagaatgtac aatggttatg caggtggttt tgaagtgcag gtaattctcg cggggaacgc
5341 gttcaccgcc gggaagatta tatttgcagc agtcccacca aattttccaa ctgaaggctt
5401 aagtcctagc caggttacta tgttccccca tataatagta gatgttagac aattagaacc
5461 tgtgctgatt cccttacccg atgttaggaa taacttctat cattacaatc agtcaaatga
5521 ttccactatt aagttgatag caatgttgta tacaccactt agggctaata atgctgggga
5581 tgatgttttc acagtttcgt gtcgagtcct cacgagacca tcccccgatt ttgatttcat
5641 atttttggtg ccacccacgg ttgagtcaag aactaagcca ttctctgtcc cagttttaac
5701 tgttgaggag atgaccaatt caagattccc catccctttg gaaaagttgt tcacaggccc
5761 cagcagtgcc tttattgtcc aaccacaaaa cggcaggtgc acaactgatg gcgtgctcct
5821 aggcaccacc caactttctt ctgtcaacgt ctgcaccttc agagggggtg tcacccacat
5881 cacaggtagt cgcaactaca caatgaattt ggcttctcaa aattggaaca actatgaccc
5941 aacagaagaa atcccagccc ctctaggaac tccagatttt gtggggaaga ttcaaggcat
6001 gctcacccaa accacaagga cagatggctc aacacgcggc cacagagcta cagtgtacac
6061 tgggagcgcc gactttgctc caaaactggg tagagttcaa tttgaaactg acacagacca
6121 tgattttgaa gctaatcaaa acacaaagtt caccccagtc ggtgtcatcc aagatggtag
6181 caccacccac cgaaacgaac cccaacagtg ggtgctccca agttactcag gcagaaatac
6241 tcacaatgta catttggccc ccgctgtagc ccccactttt ccgggtgagc aacttctctt
6301 cttcagatcc accatgcccg gatgcagcgg gtaccccaac atggatttgg actgtctgct
6361 cccccaggaa tgggtgcagt atttctacca agaggcagcc ccagcacaat ctgatgtggc
6421 tctgctaaga tttgtgaatc cagacacagg tagggttttg tttgagtgca agcttcacaa
6481 atcaggctat gttacagtgg ctcacactgg ccaacatgat ttggttatcc cccccaatgg
6541 ttactttagg tttgattcct gggtcaacca gttctacacg cttgccccca tgggaaatgg
6601 aacggggcgt agacgtgtag tataatggct ggagctttct ttgctggatt ggcatctgat
6661 gtccttggct ctggacttgg ttcccttatc aatgctgggg ctggggccat caaccaaaaa
6721 gttgagtttg aaaataacag aaaattgcaa caagcatcct tccaatttag cagcaatctg
6781 caacaggctt cttttcaaca tgataaagag atgctccaag cacaaattga ggccaccaaa
6841 aagctacaac aggaaatgat gaaagttaag caggcaatgc tcctagaggg tgggttctct
6901 gagacagatg cagcccgcgg ggcaattaac gcccccatga caaaagcttt ggactggagc
6961 gggacaaggt actgggctcc agatgctagg attacaacat acaatgcagg ccacttttcc
7021 acccctcaac catcgagggc actgccagga agagctaatc ttagggatgc tgtccctgca
7081 cggggaccct ccaataaatc ttctaactct tctattgcca cctctgtgta ctcaaatcaa
7141 actatttcaa cgagacttgg ttctacagct ggttctggaa ccagtgtctc gagcctcccg
7201 tcaactgcaa ggactaggag ctgggttgag gatcaaaata ggaatttgtc acctttcatg
7261 aggggggccc acaacatatc gtttgtcacc ccaccatcta gcagatcctc tagccaaggc
7321 acagtctcaa ccgtgcctaa agagattttg gactcctgga ctggcgcttt caacacgcgc
7381 aggcagcctc tcttcgctca cattcgtaag cgaggggagt cacgggtgta atgtgaaaag
7441 acaaaactga ttat
//