Typing tool
|
|
|
|
|
|
Typing tool
|
Complete norovirus genomes
| MH260495 | GII.4 Sydney | |
|
|---|---|---|---|
| GII.P16 |
ORF1: 1..5100
ORF2: 5081..6703
ORF3: 6703..7493
LOCUS MH260495 7493 bp RNA linear VRL 16-JUN-2018
DEFINITION Norovirus GII isolate ST166 nonstructural polyprotein (ORF1) and
VP1 (ORF2) genes, complete cds; and VP2 (ORF3) gene, partial cds.
ACCESSION MH260495
VERSION MH260495.1
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 7493)
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JOURNAL Unpublished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 7493)
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..7493
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="ST166"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="USA"
/collection_date="2017"
/note="genotype: GII"
gene 1..5100
/gene="ORF1"
CDS 1..5100
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="AWT08339.1"
/translation="MKMASNDATVAVACNNNNDKEKSSGEGLFTNMSSTLKKALGARP
KQPAPRDEPQKPPRPPTPELVKRIPPPPPNGEEEEEPVIRYEVKSGISGLPELTTVPQ
PDVANTAFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAA
ISMARVELTPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLN
DSWLSRRMVQRTTGFFRPYQDWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLI
GKIKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGP
EDLAVELVPVVMGGVGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWF
FPKKEEANELAMVRAIEDAVLDLEAIENNHMTALLKDKDSLATYMKTLDMEEEKARRL
STKSASPDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAR
EVARKVASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELAD
TCPLTLNCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEV
EKAKRDFPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIA
RASGLLHERMDEFELQGPTITTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVK
TMEELKQAIRNVTIKRCRIIYGGSTYDLESDGKGKVLVEKVKNTSVQTNNELVGALHH
LKHARIRYYVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEE
APKSEDDEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
KYSIEEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLV
TGSEIRKRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSP
SLFITSTHVIPAGITEAFGVPVKQIQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEG
TVATVLIKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGD
CGCPYIYKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILG
PGGAPKLSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEP
RGKPPRPSVLEAAKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFW
NGETFTGKLADQASKANLMYEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDL
STMIRCARSFGGLMDEMKAHCISLPVRVGMNMNEDGPIVFEKHSRYKYHYDADYSRWD
STQQRAVLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCT
SQWNSIAHWLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLK
EYGLKPTRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGP
NHEDPNETMIPHSQRPIQLMALLGEASLHGPSFYSRISKLVITELKEGGMDFYVPRQE
PMFRWMRFSDLSTWEGDRNLAPNFVNEDGVE"
mat_peptide 1..996
/gene="ORF1"
/product="p48"
mat_peptide 997..2094
/gene="ORF1"
/product="NTPase"
mat_peptide 2095..2625
/gene="ORF1"
/product="p22"
mat_peptide 2626..3024
/gene="ORF1"
/product="VPg"
mat_peptide 3025..3567
/gene="ORF1"
/product="Pro"
mat_peptide 3568..5097
/gene="ORF1"
/product="RdRp"
gene 5081..6703
/gene="ORF2"
CDS 5081..6703
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="AWT08340.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSSVNVCTFRGGVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML
TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG
STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRVV"
gene 6703..>7493
/gene="ORF3"
CDS 6703..>7493
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="AWT08341.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARITTYNAGHFSTPQPSRALPGRANLRDAVPARGPSNKSS
NSSIATSVYSNQTISTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRG"
ORIGIN
1 atgaagatgg cgtctaacga cgctaccgtt gccgttgctt gcaacaacaa caacgacaag
61 gaaaaatctt caggtgaagg cttattcaca aatatgtctt ccaccttaaa gaaagccctc
121 ggggctaggc ccaaacagcc tgccccgaga gacgaaccac aaaagccccc aagaccacca
181 actcccgagt tggtcaagag gataccccct cctccaccta atggcgaaga agaagaagaa
241 ccagtcatta ggtatgaggt taagagtggg atctctggcc tgcccgagct cacaacagtc
301 ccccagccgg acgtggccaa cacagcattc agtgttccac cactgagctt gagagaaaac
361 agggaggcca aggaaccgct aacaggggca atattagaga tgtgggacgg agagatatac
421 cactatggcc tgtacgtgga gaaaggctta gtgttgggtg tgcacaaacc acctgcagcc
481 ataagcatgg caagagtgga gctgacgccg ttgtcattgt actggcgtgt ggtgtacact
541 ccccaatacc tcatctcccc tgaaactctc aggaggctca acggagaggc gttcccttac
601 accgccttcg acaacaactg ctatgccttt tgctgctggg tgttagacct caatgactca
661 tggcttagca ggaggatggt gcaaagaaca acgggcttct tcagacctta ccaagattgg
721 aacagaaaac ccctgcctac catggatgac tccaaaataa agaaggtagc aaatatattc
781 ctatgttcat tgtccacatt gtttaccaga cccataaaag acctcatagg aaaaattaaa
841 ccattaaaca tattgaacat cctggcaacg tgtgactgga cgtttgccgg aatagtggag
901 tctctgatat tacttgctga actcttcgga gttttctgga cacccccaga tgtgtctgct
961 atgatcgctc ccttactcgg ggactacgag ttgcaagggc cagaagacct cgccgttgaa
1021 ctcgtacctg tggtaatggg aggggttggt ttggtgttgg gattcaccaa agagaaaatt
1081 ggcaaaatgt tgtcctcagc agcatcaaca ctcagggctt gcaaagatct tggtgcctat
1141 ggcttagaga tactcaaatt ggtcatgaag tggttcttcc caaagaaaga ggaggccaat
1201 gaactagcca tggtgagggc catagaggat gccgtactag atcttgaggc gatagaaaat
1261 aaccacatga cagccctgtt gaaagacaaa gacagcttag caacatacat gaaaacactg
1321 gacatggagg aggagaaagc cagaaggttg tccacaaaat ctgcatcccc tgacatagtt
1381 gggacaatca acgccctgct ggctcgaata gcagcggcca ggtcattagt ccacagggcc
1441 aaggaagagc tatctagcag gataagacca gtagttgtta tgatatctgg caaaccagga
1501 ataggcaaaa ctcatctggc cagggaggtg gcaagaaagg tggcatccac tctcacaggg
1561 gatcaaagag tcggactcat accaagaaac ggtgtggacc actgggatgc atacaaaggt
1621 gagagagtcg tgctgtggga cgactatggc atgagtaacc ccattcatga tgctcttcgc
1681 atacaggaat tggctgatac gtgccccctt accttaaatt gtgacagaat tgaaaataag
1741 ggaaaagttt ttgacagtga agtcataata attacaacaa accttgccaa cccagcccca
1801 cttgattatg tcaactttga ggcctgttcc aggagaattg atttcctggt gtacgctgag
1861 gcaccagaag tagaaaaggc aaaacgggac tttcctggtc agccagatat gtggaaggac
1921 gccttcaagc cggacttttc acacatcaag ttacagcttg cacctcaggg cggctttgac
1981 aagaatggca acaccccaca tgggaaagga gtgatgaaga ccctcactac tggttctctg
2041 attgcccgtg catcaggcct actgcatgag aggatggatg aatttgaact ccaaggtccc
2101 acaatcacca ccttcaattt cgaccggaac agaatcacag cattcagaca attggctgca
2161 gaaaacaagt atggattggt ggataccatg aaagttggca atcaactaaa aggagtgaaa
2221 accatggaag aactcaaaca agcaatcagg aatgtgacca tcaagaggtg ccgaatcatc
2281 tatggtggct ccacgtatga ccttgaatct gatggcaagg gcaaagtttt ggtggaaaag
2341 gtcaagaaca cctctgtaca gaccaacaac gagttggtcg gggccctgca ccacctcaaa
2401 cacgcccgaa tcaggtacta tgtcaaatgt gtgcaagaag cagtctattc catcatacaa
2461 attgccggcg ctgcgtttgt caccacgcgc attgcacgcc gcatgaacat acaagaactc
2521 tggtcgaagc cacaattaga ccaaaatgaa tcagagacta aggaagaggc ccccaagtca
2581 gaagatgacg agttcatcat atcttctaag gacatcaagg aggaaggaaa gaagggcaaa
2641 aacaaaactg gccgtggcaa gaaacacact gcattctcca gcaagggctt gagcgatgaa
2701 gagtatgacg agtacaagag gataagagaa gagagaaatg ggaagtactc tatagaggag
2761 tatcttcaag acagagacag gtactatgag gagctcgcca ttgccaaggc cacggaggaa
2821 gacttctgtg aagaggagga gatcaaaatc cgtcagagaa ttttccgtcc caccaggaaa
2881 caaagaaagg aagagagggc cacattaggg ctggtgacag gttcagaaat cagaaaaaga
2941 aaccccgatg acttcaaacc caaagggaag ctgtgggccg atgacaacag aagtgttgac
3001 tacaatgaga aactggactt tgaggccccc ccaagcatat ggtctaggat tgtgagcttt
3061 ggttctggct ggggcttctg ggtatcacca agcctgttca taacatcaac tcatgtaatc
3121 cccgcaggca taacagaagc atttggagtc cccgtcaaac aaattcagat ccacaaatca
3181 ggtgaattct gccgattcag attcccaaaa ccaattagac cagatgtgac agggatgatc
3241 ttggaagaag gtgcgcctga aggcaccgtg gcaactgtgc tcatcaaacg ccccaccgga
3301 gagctcatgc ctcttgcagc cagaatggga acacacgcaa ccatgaaaat tcaaggccgc
3361 atggttggcg gacagatggg tatgttgctc actggatcaa atgctaaagg aatggatttg
3421 ggaacaactc ctggtgactg tggctgtcct tacatctata aaaggggcaa tgactatata
3481 gtcattgggg tgcacactgc agcagcccgt ggtggaaaca ccgtcatctg tgccacacag
3541 ggaagtgagg gtgaggcaac tcttgagggt ggagatgaca aaggaacata ctgtggggca
3601 cccattctag gccctggggg tgcaccaaaa ttgagcacca aaaccaaatt ttggaggtca
3661 tcgaacacgc cccttccacc agggacatat gagcctgcct acctcggtgg ccgtgatccg
3721 cgtgttaagg gtgggccctc cttgcagcag gtgatgagag accagttgaa gccattcact
3781 gaacccaggg gcaaacctcc aagaccaagt gtattggaag cagccaaaca aaccattatc
3841 aatgttctcg aacaaaccct ggaccctccg caaaagtgga catacgcaca ggcgtgtgcc
3901 tcacttgaca aaaccacctc cagcgggcat ccccatcacg tccgaaagaa tgaattctgg
3961 aatggtgaga ccttcactgg taaactggca gaccaagcat caaaagcaaa cctaatgtat
4021 gaggaaggga aacacatgac accagtgtat acagcagcac tcaaggacga gctagtcaag
4081 actgagaaaa tctatggaaa gatcaagaag agactgctct ggggctctga cttgtccact
4141 atgatccggt gcgctaggtc atttggtggg ctcatggacg agatgaaggc acactgcata
4201 tcactcccag tacgagttgg catgaatatg aatgaagatg gcccaatagt atttgagaaa
4261 cattccagat acaaatacca ctatgatgca gactactctc gttgggattc aacacaacag
4321 agggcagtgc tagcagcagc cttggaaatc atggtcagat tctctgcaga accacaattg
4381 gcacaaatag tcgctgagga tctactggcc cctagtgtag tagatgtagg agactttaaa
4441 atcacaataa atgaagggct cccatctggt gtgccatgca cttctcaatg gaactccatc
4501 gcacactggc tgctaactct ctgtgccttg tctgaagtca ccaaactgtc ccctgacatt
4561 atacaagcaa attccatgtt ctcattttac ggtgatgacg agattgtcag caccgacata
4621 aaattggacc ctgaacagtt aactgccaag ctgaaggagt acggcctgaa accaacccgc
4681 ccagacaaga ccgagggacc cctgatcatc agtgaagatt taaacggact caccttcctc
4741 cgtaggacgg tgactcgtga cccagctggc tggtttggaa aactggacca aagttcaatc
4801 ttgaggcaaa tgtactggac tagaggacca aatcatgaag accccaatga aacaatgata
4861 ccccactctc aaagacccat acagctcatg gcactgcttg gtgaagcctc tcttcacgga
4921 ccctctttct atagtagaat cagtaaattg gtcataactg aactcaaaga aggtgggatg
4981 gacttttacg tgccaaggca ggaacccatg ttcaggtgga tgaggttttc tgacttgagc
5041 acgtgggagg gcgatcgcaa tctggctccc aattttgtga atgaagatgg cgtcgagtga
5101 cgccaaccca tctgatgggt ccgcagccaa cctcgtacca gaggtcaaca atgaggttat
5161 ggctttggag cccgttgttg gtgccgctat tgcggcacct gtagcgggcc aacaaaatgt
5221 aattgacccc tggattagaa ataattttgt acaagcccct ggtggggagt ttacagtatc
5281 ccctagaaac gctccaggtg aaatactatg gagcgcgccc ctaggccctg acctaaatcc
5341 ctacctatcc catttggcca gaatgtacaa tggttatgca ggtggttttg aagtgcaggt
5401 aattctcgcg gggaacgcgt tcaccgccgg gaagattata tttgcagcag tcccaccaaa
5461 ttttccaact gaaggcttaa gtcctagcca ggttactatg ttcccccata taatagtaga
5521 tgttagacaa ttagaacctg tgctgattcc cttacccgat gttaggaata acttctatca
5581 ttacaatcag tcaaatgatt ccactattaa gttgatagca atgttgtata caccacttag
5641 ggctaataat gctggggatg atgttttcac agtttcgtgt cgagtcctca cgagaccatc
5701 ccccgatttt gatttcatat ttttggtgcc acccacggtt gagtcaagaa ctaagccatt
5761 ctctgtccca gttttaactg ttgaggagat gaccaattca agattcccca tccctttgga
5821 aaagttgttc acaggcccca gcagtgcctt tgttgttcaa ccacaaaacg gcaggtgcac
5881 aactgatggc gtgctcctag gcaccaccca actttcttct gtcaacgtct gcaccttcag
5941 agggggtgtc acccacatca caggtagtcg caactacaca atgaatttgg cttctcaaaa
6001 ttggaacaac tatgacccaa cagaagaaat cccagcccct ctaggaactc cagattttgt
6061 ggggaagatt caaggcatgc tcacccaaac cacaaggaca gatggctcaa cacgcggcca
6121 caaagctaca gtgtacactg ggagcgccga ctttgctcca aaactgggta gagttcaatt
6181 tgaaactgac acagaccatg attttgaagc taatcaaaac acaaagttca ccccagtcgg
6241 tgtcatccaa gatggtagca ccacccaccg aaacgaaccc caacagtggg tgctcccaag
6301 ttactcaggc agaaatactc acaatgtaca tttggccccc gctgtagccc ccacttttcc
6361 gggtgagcaa cttctcttct tcagatccac catgcccgga tgcagcgggt accccaacat
6421 ggatttggac tgtctgctcc cccaggaatg ggtgcagtat ttctaccaag aggcagcccc
6481 agcacaatct gatgtggctc tgctaagatt tgtgaatcca gacacaggta gggttttgtt
6541 tgagtgcaag cttcacaaat caggctatgt tacagtggct cacactggcc aacatgattt
6601 ggttatcccc cccaatggtt actttaggtt tgattcctgg gtcaaccagt tctacacgct
6661 tgcccccatg ggaaatggaa cggggcgtag acgtgtagta taatggctgg agctttcttt
6721 gctggattgg catctgatgt ccttggctct ggacttggtt cccttatcaa tgctggggct
6781 ggggccatca accaaaaagt tgagtttgaa aataacagaa aattgcaaca agcatccttc
6841 caatttagca gcaatctgca acaggcttct tttcaacatg ataaagagat gctccaagca
6901 caaattgagg ccaccaaaaa gctacaacag gaaatgatga aagttaagca ggcaatgctc
6961 ctagagggtg ggttctctga gacagatgca gcccgcgggg caattaacgc ccccatgaca
7021 aaagctttgg actggagcgg gacaaggtac tgggctccag atgctaggat tacaacatac
7081 aatgcaggcc acttttccac ccctcaacca tcgagggcac tgccaggaag agctaatctt
7141 agggatgctg tccctgcacg gggaccctcc aataaatctt ctaactcttc tattgccacc
7201 tctgtgtact caaatcaaac tatttcaacg agacttggtt ctacagctgg ttctggaacc
7261 agtgtctcga gcctcccgtc aactgcaagg actaggagct gggttgagga tcaaaatagg
7321 aatttgtcac ctttcatgag gggggcccac aacatatcgt ttgtcacccc accatctagc
7381 agatcctcta gccaaggcac agtctcaacc gtgcctaaag agattttgga ctcctggact
7441 ggcgctttca acacgcgcag gcagcctctc ttcgctcaca ttcgtaagcg agg
//