Typing tool
|
|
|
|
|
|
Typing tool
|
Complete norovirus genomes
| MH260479 | GII.4 Sydney | |
|
|---|---|---|---|
| GII.P16 |
ORF1: 5..5104
ORF2: 5085..6707
ORF3: 6707..7494
LOCUS MH260479 7494 bp RNA linear VRL 16-JUN-2018
DEFINITION Norovirus GII isolate ST709 nonstructural polyprotein (ORF1) and
VP1 (ORF2) genes, complete cds; and VP2 (ORF3) gene, partial cds.
ACCESSION MH260479
VERSION MH260479.1
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 7494)
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JOURNAL Unpublished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 7494)
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..7494
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="ST709"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="USA"
/collection_date="2017"
/note="genotype: GII"
gene 5..5104
/gene="ORF1"
CDS 5..5104
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="AWT08291.1"
/translation="MKMASNDATVAVACNNNNDKEKSSGEGLFTNMSSTLKKALGAKP
KRPAPRDEPQKPPRPSTPELVKRIPPPPPNGEEEEEPVIRYEVKSGISGLPELTTVPQ
PDVANTAFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAA
ISMARVELTPLSLYWRVVYTPQYLIPPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLN
DSWLSRRMVQRTTGFFRPYQDWNRKPLPTMDDSKIKKVANIFLCSLSALFTRPIKDLI
GKIKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGP
EDLAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWF
FPKKEEVNELAMVRAIEDAVLDLEAIENNHMTALLKDKDSLATYMKTLDMEEEKARKL
STKSASPDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAR
EVARKVASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELAD
TCPLTLNCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEV
EKAKRDFPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIA
RASGLLHERMDEFELQGPTITTYNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVK
TMEELKQAIRNVTIKRCRIIYGGSTYDLESDGKGKVLVEKVKNTSVQTNNELDGALHH
LKHARIRYYVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNEPETKEE
APKSEDDEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
KYSIEEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLV
TGSEIRKRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSP
SLFITSTHVIPAGITEAFGVPVKQIQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEG
TVATVLIKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGD
CGCPYIYKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILG
PGGAPKLSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEP
RGKPPRPSVLEAAKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFW
NGETFTGKLADQASKANLMYEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDL
STMIRCARSFGGLMDEMKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWD
STQQRAVLAAALEIMVRFSAEPQLTQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCT
SQWNSIAHWLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLK
EYGLKPTRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGP
NHEDPNETMIPHSQRPIQLMALLGEASLHGPSFYSRISKLVITELREGGMDFYVPRQE
PMFRWMRFSDLSTWEGDRNLAPNFVNEDGVE"
mat_peptide 5..1000
/gene="ORF1"
/product="p48"
mat_peptide 1001..2098
/gene="ORF1"
/product="NTPase"
mat_peptide 2099..2629
/gene="ORF1"
/product="p22"
mat_peptide 2630..3028
/gene="ORF1"
/product="VPg"
mat_peptide 3029..3571
/gene="ORF1"
/product="Pro"
mat_peptide 3572..5101
/gene="ORF1"
/product="RdRp"
gene 5085..6707
/gene="ORF2"
CDS 5085..6707
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="AWT08292.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
HNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEMQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPTPLEKLFTGPSSAFIVQPQNGRCTTDGVLLGTT
QLSSVNICTFRGDVTHTTGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML
TQTTRTDGSTRGHRATVRTGSADFAPKLGRVQFETDTDHDFDTNQNTKFTPVGVIQDG
STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRVV"
gene 6707..>7494
/gene="ORF3"
CDS 6707..>7494
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="AWT08293.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARTTTYNAGHFSTPQPSRALPGRANLRDAVPARGPSNKSS
NPSIATSVHSNQTLSTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKR"
ORIGIN
1 gtgaatgaag atggcgtcta acgacgctac cgttgccgtt gcttgcaaca acaacaacga
61 caaggaaaaa tcttcaggtg aaggcttatt cacaaatatg tcctccacct taaagaaagc
121 cctcggggct aagcccaaac ggcctgcccc gagagacgaa ccacaaaagc ccccaagacc
181 atcaactccc gagttggtca agaggatacc ccctcctcca cctaatggcg aagaagaaga
241 agaaccagtc attaggtatg aggttaagag tgggatctct ggcctgcccg agctcacaac
301 agtcccccag ccggacgtgg ccaacacagc attcagtgtt ccgccactga gcttgagaga
361 aaacagggag gccaaggaac cgctaacagg ggcaatatta gagatgtggg acggagagat
421 ataccactat ggcctgtacg tggagaaagg cttagtgttg ggtgtgcaca aaccacctgc
481 agccataagc atggcaagag tggagctgac gccgttgtca ttgtactggc gtgtggtgta
541 cactccccaa tacctcatcc cccctgaaac tctcaggagg ctcaacggag aggcgttccc
601 ttacaccgcc ttcgacaaca actgctatgc cttttgttgc tgggtgttag acctcaatga
661 ttcatggctt agcaggagga tggtgcaaag aacaacgggc ttcttcagac cttaccaaga
721 ttggaacaga aaacccctgc ctactatgga tgactccaaa ataaagaagg tagcaaatat
781 attcctatgt tcattgtccg cattatttac cagacccata aaagacctca taggaaaaat
841 taaaccatta aacatattga acatcctggc aacgtgtgac tggacgtttg ccggaatagt
901 ggagtccctg atattacttg ctgaactctt cggagttttc tggacacccc cagatgtgtc
961 tgctatgatc gctcccttac tcggggacta cgagttgcaa gggccagaag acctcgccgt
1021 tgaactcgta cctgtggtaa tgggagggat tggtttggtg ttgggattca ccaaagagaa
1081 aattggcaaa atgttgtcct cagcagcatc aacactcagg gcttgcaaag atcttggtgc
1141 ctatggctta gagatactca aattggtcat gaagtggttc ttcccaaaga aagaggaggt
1201 caatgaacta gccatggtga gggccataga ggatgccgta ctagatcttg aggcgataga
1261 aaataaccac atgacagccc tgttgaaaga caaagacagc ttggcaacat acatgaaaac
1321 actggacatg gaggaggaga aagccagaaa gttgtccaca aaatctgcat cccctgacat
1381 agttgggaca atcaacgccc tgctggctcg aatagcagcg gccaggtcat tagtccacag
1441 ggccaaggaa gagctatcta gcaggataag accagtagtt gttatgatat ctggcaaacc
1501 aggaataggc aaaactcatc tggccaggga ggtggcaaga aaggtggcat ccactctcac
1561 aggggatcaa agagtcggac tcataccaag aaacggtgtg gaccactggg atgcatacaa
1621 aggtgagaga gtcgtgctgt gggacgacta tggcatgagt aaccccattc atgatgctct
1681 tcgcttacag gaattggctg acacgtgccc ccttacctta aattgtgaca gaattgaaaa
1741 taagggaaaa gtttttgaca gtgaagtcat aataattaca acaaaccttg ccaacccagc
1801 cccacttgat tatgtcaact ttgaggcctg ttccaggaga attgatttcc tggtgtacgc
1861 tgaggcacca gaagtagaaa aggcaaaacg ggactttcct ggtcagccag atatgtggaa
1921 ggacgccttc aagccggact tttcacacat caagttacag cttgcacctc agggcggctt
1981 tgacaagaat ggcaacaccc cacatgggaa aggagtgatg aagaccctca ctactggttc
2041 tctgattgcc cgtgcatcag gcctactgca tgagaggatg gatgaatttg aactccaagg
2101 tcccacaatc accacctaca atttcgaccg gaacagaatc acagcattca gacaattggc
2161 cgcagaaaac aagtatggat tggtggacac catgaaagtt ggcaatcaac taaaaggagt
2221 gaaaaccatg gaagaactca aacaggcaat caggaatgtg accatcaaga ggtgccgaat
2281 catctatggt ggctccacgt atgaccttga atctgatggc aagggcaaag ttttggtgga
2341 aaaggtcaag aacacctctg tacagaccaa caacgagttg gacggggccc tgcaccacct
2401 caaacacgcc cgaatcaggt actatgtcaa atgtgtgcaa gaagcagtct attccatcat
2461 acaaattgcc ggcgctgcgt ttgtcaccac gcgcattgca cgccgcatga acatacaaga
2521 actctggtcg aagccacaat tagaccaaaa cgaaccagag actaaggaag aggcccccaa
2581 gtcagaagat gacgagttca tcatatcttc taaggacatc aaggaggaag gaaagaaggg
2641 caaaaacaaa actggccgtg gcaagaaaca cactgcattc tccagcaagg gcttgagcga
2701 tgaagagtat gacgagtaca agaggataag agaagagaga aatgggaagt actctataga
2761 ggagtatctt caagacagag acaggtacta tgaggagctc gccattgcca aggccacgga
2821 ggaagacttc tgtgaagagg aggagatcaa aatccgtcag agaattttcc gtcccaccag
2881 gaaacaaaga aaggaagaga gggccacatt agggctggtg acaggttcag aaatcagaaa
2941 aagaaacccc gatgacttca aacccaaagg gaagctgtgg gccgatgaca acagaagtgt
3001 tgactacaat gagaaactgg actttgaggc ccccccaagc atatggtcta ggattgtgag
3061 ctttggttct ggctggggct tctgggtatc accaagcctg ttcataacat caactcatgt
3121 aatccccgca ggcataacag aagcatttgg agtccccgtc aaacaaattc agatccacaa
3181 atcaggtgaa ttctgccgat tcagattccc aaaaccaatt agaccagatg tgacagggat
3241 gatcttggaa gaaggtgcac ctgaaggcac cgtggcaact gtgctcatca aacgccccac
3301 cggagagctc atgcctcttg cagccagaat gggaacacac gcaaccatga aaattcaagg
3361 ccgcatggtt ggcgggcaga tgggtatgtt gctcactgga tcaaatgcta aaggaatgga
3421 tttgggaaca actcctggtg actgtggctg tccttacatc tataaaaggg gcaatgacta
3481 tatagtcatt ggggtgcaca ctgcagcagc ccgtggtgga aacaccgtca tctgtgccac
3541 acagggaagt gagggtgagg caactcttga gggtggagat gacaaaggaa catactgtgg
3601 ggcacccatt ctaggccctg ggggtgcacc aaaattgagc accaaaacca aattttggag
3661 gtcatcgaac acgccccttc caccagggac atatgagcct gcctacctcg gtggccgtga
3721 tccgcgcgtt aagggtgggc cctccttgca gcaggtgatg agagaccagt tgaagccatt
3781 cactgaaccc aggggcaaac ctccaagacc aagtgtattg gaagcagcca aacaaaccat
3841 tatcaatgtt ctcgaacaaa ccctggaccc tccgcaaaag tggacatacg cacaggcgtg
3901 tgcctcactt gacaagacca cctccagcgg gcatccccat cacgtccgaa agaatgaatt
3961 ctggaatggt gagaccttca ctggtaaact ggcagaccaa gcatcaaaag caaacctaat
4021 gtatgaggaa ggaaaacaca tgacaccagt gtatacagca gcactcaagg acgagctagt
4081 caagactgag aaaatctatg gaaagatcaa gaagagactg ctctggggct ctgacttgtc
4141 cactatgatc cggtgcgcta ggtcatttgg tgggctcatg gacgagatga aggcacactg
4201 catatcactc ccagtacgag ttggcatgaa tatgaatgaa gatggcccaa taatatttga
4261 gaaacattcc agatacaaat accactatga tgcagactac tctcgttggg attcaacaca
4321 acagagggca gtgctagcag cagccttgga aatcatggtc agattctctg cagaaccaca
4381 attgacacaa atagtcgctg aggatctact ggcccctagt gtagtagatg taggagactt
4441 taaaatcaca ataaatgaag ggctcccatc tggtgtgcca tgcacttctc aatggaactc
4501 catcgcacac tggctgctaa ctctctgtgc cttgtctgaa gtcaccaaac tgtcccctga
4561 cattatacaa gcaaattcca tgttctcatt ttacggtgat gacgagattg tcagcaccga
4621 cataaaattg gaccctgagc agttgactgc caagctgaag gagtacggcc tgaaaccaac
4681 ccgtccagac aagaccgagg gacccctgat catcagtgaa gatttaaacg gactcacctt
4741 cctccgtagg acggtgactc gtgacccagc tggctggttt ggaaaactgg accaaagttc
4801 aatcttgagg caaatgtact ggactagagg accaaatcat gaagacccca atgaaacaat
4861 gataccccac tctcaaagac ccatacagct catggcactg cttggtgaag cctctcttca
4921 cggaccctct ttctatagta gaatcagtaa attggtcata actgaactca gagaaggtgg
4981 gatggacttt tacgtgccaa ggcaggaacc catgttcagg tggatgaggt tttctgactt
5041 gagcacgtgg gagggcgatc gcaatctggc tcccaatttt gtgaatgaag atggcgtcga
5101 gtgacgccaa cccatctgat gggtccgcag ccaacctcgt accagaggtc aacaatgagg
5161 ttatggcttt ggagcccgtt gttggtgccg ctattgcggc acctgtagcg ggccaacaca
5221 atgtaattga cccctggatt agaaataatt ttgtacaagc ccctggtggg gagtttacag
5281 tatcccctag aaacgctcca ggtgaaatac tatggagcgc gcccctaggc cctgacctaa
5341 atccctacct atcccatttg gccagaatgt acaatggtta tgcaggtggt tttgaaatgc
5401 aggtaattct cgcggggaac gcgttcaccg ccgggaagat tatatttgca gcagtcccac
5461 caaattttcc aactgaaggc ttaagtccta gccaggttac tatgttcccc catataatag
5521 tagatgttag acaattagaa cctgtgttga ttcccttacc cgatgttagg aataacttct
5581 atcattacaa tcagtcaaat gattccacta ttaagttgat agcaatgttg tacacaccac
5641 ttagggctaa taatgctggg gatgatgttt tcacagtttc gtgtcgagtt ctcacgagac
5701 catcccccga ttttgatttc atatttttgg tgccacccac ggttgagtca agaactaagc
5761 cattctctgt cccagtttta actgttgagg agatgaccaa ttcaagattc cccacccctt
5821 tggaaaagtt gttcacaggc cccagcagtg cctttattgt ccaaccacaa aacggcaggt
5881 gcacaactga tggcgtgctc ctaggcacca cccaactttc ttctgtcaac atctgcacct
5941 tcagagggga tgtcacccac accacaggta gtcgcaacta cacaatgaat ttggcttctc
6001 aaaattggaa caactatgac ccaacagaag aaatcccagc ccctctagga actccagatt
6061 ttgtggggaa gattcaaggc atgctcaccc aaaccacaag gacagatggc tcaacacgcg
6121 gccacagagc tacagtgcgc actgggagcg ccgactttgc tccaaaactg ggtagagttc
6181 aatttgaaac tgacacagac catgattttg atactaatca aaacacaaag ttcaccccag
6241 tcggtgtcat ccaagatggt agcaccaccc accgaaacga accccaacag tgggtgctcc
6301 caagttactc aggcagaaat actcacaatg tacatttggc ccccgctgta gcccccactt
6361 ttccgggtga gcaacttctc ttcttcagat ccaccatgcc cggatgcagc gggtacccca
6421 acatggattt ggactgtctg ctcccccagg aatgggtgca gcatttctac caagaggcag
6481 ccccagcaca atctgatgtg gctctgctaa gatttgtgaa tccagacaca ggtagggttt
6541 tgtttgagtg caagctccat aaatcaggct atgttacagt ggctcacact ggccaacatg
6601 atttggttat cccccccaat ggttacttta ggtttgactc ctgggtcaac cagttctaca
6661 cgcttgcccc catgggaaat ggaacggggc gtagacgtgt ggtataatgg ctggagcttt
6721 ctttgctgga ttggcatctg atgtccttgg ctctgggctt ggttccctta tcaatgctgg
6781 ggctggggcc atcaaccaaa aagttgagtt tgaaaataac agaaaattgc aacaagcatc
6841 cttccaattt agcagcaatc tgcaacaggc ttcttttcaa catgataaag agatgctcca
6901 agcacaaatt gaggccacca aaaagctaca acaggaaatg atgaaagtta agcaggcaat
6961 gctcctagag ggtgggttct ctgagacaga tgcagcccgc ggggcaatta acgcccccat
7021 gacaaaagct ttggactgga gcgggacaag gtactgggct ccagatgcta ggactacaac
7081 atacaatgca ggccactttt ccacccctca accatcgagg gcactgccag gaagagctaa
7141 tcttagggat gctgtccctg cacggggacc ctccaataaa tcttctaacc cttctattgc
7201 cacctctgtg cactcaaatc aaaccctttc aacgagactt ggttctacag ctggttctgg
7261 aaccagtgtc tcgagtctcc cgtcaactgc aaggactagg agctgggttg aggatcaaaa
7321 taggaatttg tcacctttca tgaggggggc ccacaacata tcgtttgtca ccccaccatc
7381 tagcagatcc tctagccaag gcacagtctc aaccgtgcct aaagagattt tggactcctg
7441 gactggcgct ttcaacacgc gcaggcagcc tctcttcgct cacattcgta agcg
//