Typing tool
|
|
|
|
|
|
Typing tool
|
Complete norovirus genomes
| OP727609 | GII.4 Sydney | |
|
|---|---|---|---|
| GII.P31 |
ORF1: 1..5080
ORF2: 5061..6683
ORF3: 6683..7489
LOCUS OP727609 7498 bp RNA linear VRL 01-NOV-2022
DEFINITION Norovirus GII isolate OCS2 nonstructural polyprotein (ORF1) gene,
partial cds; and VP1 (ORF2) and VP2 (ORF3) genes, complete cds.
ACCESSION OP727609
VERSION OP727609.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7498)
AUTHORS Kelly,D., Allen,D.J. and Iturriza-Gomara,M.
TITLE Direct Submission
JOURNAL Submitted (27-OCT-2022) Clinical Infection, Microbiology and
Immunity, Institute of Infection and Global Health, 8 West Derby
Street, Liverpool, Please select. L697BE, United Kingdom
COMMENT ##Assembly-Data-START##
Assembly Method :: SPAdes v. 3.15.4
Sequencing Technology :: Illumina
##Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..7498
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="OCS2"
/isolation_source="stool sample"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="United Kingdom"
/collection_date="Jan-2017"
/note="genotype: GII.P31/GII.4"
gene <1..5080
/gene="ORF1"
CDS <1..5080
/gene="ORF1"
/codon_start=2
/product="nonstructural polyprotein"
/protein_id="UYR40577.1"
/translation="ASAAAVANSNNDIAKSSSDGVFSNMAVTFKRALGARPKQPPPKE
TPPRPPRPPTPELVKKIPPPPPNGEDELVVSYSAKDGVSGLPELTTVRQPEETNTAFS
VPPLNQRESRDAKEPLTGTIIEMWDGEIYHYGLYVERGLILGVHKPPAAISLAKVELA
PLSLFWRPVYTPQYLISPDTLRRLHGESFPYTAFDNNCYAFCCWVLDLNDSWLSRRMI
QRTTGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCTLSSLFTRPIKDIIGKLKPLNIL
NILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVELVP
IVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEANE
LAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLSTKSASPDI
VGTINSLLARIAAARSLVHRAKEELSSRPRPVVVMISGRPGIGKTHLARELAKKIAAS
LTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCPLTLNCD
RIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRDFPG
QPDMWKNAFSPDFSHIKLSLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLHER
LDEYELQGPALTTFNFDRNKILAFRQLAAENKYGLMDTMRVGKQLKDVKTMSDLKQAL
KNIAIKKCQIVYNGGTYTLEADGKGSVKVDKVQSATVQTNNELAGALHHLRCARIRYY
VKCVQEALYSIIQIAGAAFVTTRIAKRMNIQNLWSKPQVEDTEEMANKDGCLKPKDDE
EFVVSSDDIKTEGKKGKNKSGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEEY
LQDRDRYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLVTGSEIRK
RNPEDFKPKGKLWADDDRSVDYNEKLNFEAPPSIWSRIVNFGSGWGFWVSPSLFITST
HVIPQGAKEFFGVPIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVATLLI
KRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCGCPYIY
KRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDSKGTYCGAPILGPGSAPKL
STKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRGKPPRP
NVLEAAKKTIINVLEQTIDPPQKWSFAQACASLDKTTSSGHPHHMRKNDCWNGESFTG
KLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKVYGKVKKRLLWGSDLATMIRCA
RAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFEKHSRYRYHYDADYSRWDSTQQRDV
LAAALEIMVKFSPEPHLAQIVAEDLLSPSVMDVGDFQISISEGLPSGVPCTSQWNSIA
HWLLTLCALSEVTDLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLKEYGLKPT
RPDKTEGPLVISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHEDPFE
TMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQEPMFRWMR
FSDLSTWEGDRNLAPSFVNEDGVE"
mat_peptide <1..970
/gene="ORF1"
/product="p48"
mat_peptide 971..2068
/gene="ORF1"
/product="NTPase"
mat_peptide 2069..2605
/gene="ORF1"
/product="p22"
mat_peptide 2606..3004
/gene="ORF1"
/product="VPg"
mat_peptide 3005..3547
/gene="ORF1"
/product="Pro"
mat_peptide 3548..5077
/gene="ORF1"
/product="RdRp"
gene 5061..6683
/gene="ORF2"
CDS 5061..6683
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="UYR40578.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKVIFAAVPPNFPTEGLSPSQVTMFPHIVVDVRQLEPVLIPLPD
VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHITGSHNYTMNLASQNWSNYDPTEEIPAPLGTPDFVGKIQGVL
TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTNHDFEANQNTKFTPVGVIQDG
GTTHQNEPQQWVLPSYSGRNTPNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL"
gene 6683..7489
/gene="ORF3"
CDS 6683..7489
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="UYR40579.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKRLQQEMMKVKQAMLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRDAVPARGSSSKSS
NSSTAISVYSNQTISTRLGSTAGSGTSVSSFPSTARTRSWVEDQSRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRA"
ORIGIN
1 cgcttccgct gccgctgttg ccaacagcaa caacgacatc gcaaaatctt caagtgacgg
61 tgtgttttcc aacatggctg tcacttttaa acgggccctc ggggcgcggc ctaaacagcc
121 gcccccgaag gaaacaccac ccagaccccc gcgaccaccc acaccagaat tggtcaaaaa
181 gatccctcct cccccaccca atggggagga tgaactagtg gtctcttaca gcgccaaaga
241 tggcgtttcc ggactgcctg agctcaccac tgtcagacaa ccggaagaga ccaacacggc
301 gttcagtgtc cccccactca accaaaggga gagcagggac gccaaggagc cactaactgg
361 aacaattatt gaaatgtggg atggagaaat ctaccattac ggcctgtacg tggaacgagg
421 tcttatactt ggtgtgcaca agccaccagc agccattagc cttgccaagg tcgagctggc
481 accgctctct ttgttttgga gacctgtata caccccccag tacctcatct ctccagacac
541 tcttaggaga ttacatggag agtcattccc ctacactgca tttgacaaca actgctacgc
601 cttttgttgt tgggtattag acctaaacga ctcatggcta agcaggagaa tgattcagag
661 aacaacaggc ttcttcaggc cgtaccagga ttggaacagg aaacccctcc ccactatgga
721 tgattccaaa ttaaagaagg tagccaacat attcttgtgc actttgtctt cactattcac
781 cagacccatt aaggatataa tagggaagtt gaaacctctt aacatcctta atattctggc
841 tacatgtgat tggaccttcg caggcatagt ggaatcctta atactcttgg cagaactctt
901 tggagttttc tggacacccc cagatgtgtc tgcgatgatc gcccccttac taggtgatta
961 tgaactgcaa ggacctgagg accttgcagt ggaactggtc ccaatagtga tgggagggat
1021 aggtttggtg ctaggattta ccaaagagaa aatcggaaag atgctgtcat ccgctgcatc
1081 cactttaaga gcttgtaaag accttggtgc atacggactg gaaatcttaa aattggtcat
1141 gaagtggttc ttcccaaaga aagaggaagc aaatgaactg gctatggtga gatccatcga
1201 ggatgcagta ctagacctcg aggcaattga aaacaaccac atgaccaccc tgctcaaaga
1261 taaagacagc ttggcaacct acatgagaac ccttgacctt gaggaggaga aagccagaaa
1321 actctcaacc aaatctgctt cacccgatat tgtgggcaca atcaactctc ttctggcaag
1381 aatcgctgct gcacgctccc tagtgcatcg ggcgaaagaa gagctctcca gcaggccgag
1441 acctgtcgtt gtaatgatat cgggaagacc agggataggg aaaactcacc ttgccaggga
1501 gctggccaag aagatcgcgg cctccctcac aggggaccag cgtgtgggtc ttatcccacg
1561 caatggtgtc gaccactggg acgcatacaa gggcgaaaga gttgtcctat gggacgacta
1621 tggaatgagc aaccccatcc atgatgccct caggttgcag gagcttgctg acacttgccc
1681 cctcacgcta aattgtgaca gaattgagaa caaaggaaaa gtctttgaca gtgatgccat
1741 aattatcacc accaacctgg ccaacccagc accactggat tatgtcaatt ttgaagcgtg
1801 ctcgagacgc attgatttcc tcgtgtatgc agaagcccct gaggtggaga aggcaaagcg
1861 cgacttccca ggtcaacctg acatgtggaa gaacgctttc agtcctgact tctcacacat
1921 aaaactgtca ttggctccac agggtggttt tgacaagaac ggcaacaccc cgcatggaaa
1981 aggggtcatg aagaccctca ccactggctc cctcatcgcc cgagcatcag ggttactcca
2041 tgagaggcta gatgaatatg aactgcaagg cccagccctc accactttca actttgaccg
2101 caacaagata cttgctttta gacagcttgc tgctgaaaac aagtatgggc tgatggacac
2161 aatgagagtt ggaaaacagc tcaaggatgt caagaccatg tcagacctca aacaagcact
2221 caagaacatc gcgatcaaga agtgccagat agtgtacaat ggtggcacct acacacttga
2281 ggctgatggc aagggtagtg tgaaagttga caaagtgcaa agtgccactg tgcagaccaa
2341 caatgaacta gccggtgccc tacaccacct aaggtgcgct agaatcagat actatgttaa
2401 gtgcgtccag gaggcactgt attccatcat ccaaatcgct ggggctgcat tcgtcaccac
2461 gcgcatcgct aagcgcatga atatacagaa tctctggtcc aagccacagg tggaagacac
2521 agaagagatg gccaacaaag atggttgcct aaaacccaaa gatgatgaag agtttgtcgt
2581 ctcatccgac gacatcaaaa ctgagggcaa gaaagggaag aacaagtccg gccgtggcaa
2641 gaagcacaca gccttttcaa gtaaaggact cagtgatgag gagtacgatg agtacaagag
2701 aatcagagaa gaaaggaacg gcaagtactc catagaagag taccttcagg acagagacag
2761 gtactacgag gaggtggcca ttgccagggc aaccgaagag gacttctgtg aagaagaaga
2821 ggccaaaatc cggcagagaa ttttcagacc aacaaggaaa caacgcaaag aagagagggc
2881 ctctctcggc ttggtcacag gctctgaaat caggaagaga aacccagaag acttcaaacc
2941 caagggaaag ctgtgggctg atgatgacag aagtgttgac tacaatgaga aactcaactt
3001 tgaggcccca ccaagcatct ggtcgcggat agtcaacttt ggttcaggct ggggcttctg
3061 ggtctccccc agtctgttta taacatcaac ccatgtcata ccccaaggtg caaaagagtt
3121 cttcggagtc cctatcaagc aaatccagat acacaagtca ggtgaattct gccggttgag
3181 attcccaaag ccaatcagaa ccgatgtgac gggtatgatt ctagaagaag gtgcgcccga
3241 ggggaccgtg gccacactgc tcatcaagag accaactgga gagctcatgc ctctggcagc
3301 cagaatgggg acccatgcaa ccatgaaaat tcaggggcgc acagttggag ggcaaatggg
3361 tatgctcctg acaggatcca acgccaagag tatggaccta ggcacaacac caggcgactg
3421 cggctgcccc tacatctaca agagggggaa tgactacgtg gtcataggag tccatacggc
3481 cgctgcccgt ggaggaaaca ctgtcatatg tgccacccag ggaagtgagg gagaggccac
3541 acttgaagga ggtgacagta aagggacata ctgtggcgca ccaatcttgg gcccagggag
3601 cgctccgaag ctcagcacca agactaagtt ttggagatca tccacaacac cactcccacc
3661 tggcacctac gaaccagcct acctcggtgg caaagaccct agagtcaaag gtggcccttc
3721 attgcaacaa gttatgaggg accagctgaa gccattcaca gaacccagag gcaaaccacc
3781 aagaccaaat gtgttggaag ctgccaagaa aaccatcatc aatgtccttg agcaaacaat
3841 tgatccaccc caaaaatggt catttgcgca agcttgcgca tcccttgaca aaaccacctc
3901 cagcggccac ccgcaccaca tgcggaaaaa cgactgttgg aatggggagt ccttcacagg
3961 aaaattggct gatcaagcct ccaaggccaa cctaatgttt gaagagggaa agaacatgac
4021 tccagtctac acaggtgcac ttaaagatga gttagtaaag accgataaag tttatggtaa
4081 ggtcaagaag aggcttctgt ggggttcaga tctggcgacc atgatacggt gcgcccgagc
4141 ttttggaggc cttatggatg aactcaaggc acactgtgtc acactccctg tcagagttgg
4201 tatgaacatg aatgaggatg gccccatcat cttcgagaag cactccagat atagatatca
4261 ctatgatgct gactattccc ggtgggactc aacacaacaa agggatgtgc tagcagcagc
4321 actagaaatc atggttaagt tctctccaga accacacctg gcccagatag ttgcagaaga
4381 cctcctctcc cctagcgtga tggatgtagg tgactttcaa atatcaataa gtgagggtct
4441 cccctctggg gtgccttgta cctcccagtg gaattccatc gcccactggc tcctcactct
4501 gtgtgcactc tctgaagtca cggacctgtc ccctgacatc attcaggcca actccctttt
4561 ctccttctat ggtgatgatg agattgtaag cacagacata aagttggacc cagagaagct
4621 gacagcaaaa ctcaaggagt acgggctgaa accaacccgc cccgacaaaa ctgaagggcc
4681 ccttgttatc tctgaagacc tggatggtct gacattcctc cggagaactg tgacccgtga
4741 tccagctggc tggtttggaa aattggaaca aagttcaatt cttaggcaaa tgtactggac
4801 caggggtccc aaccatgaag atccatttga aacaatgata ccacactccc aaagacccat
4861 acaattgatg tccttgctgg gcgaggctgc actccacggc ccggcattct acagcaaaat
4921 tagcaaatta gtcattgcag agttgaagga aggtggcatg gatttttacg tacccagaca
4981 agagccaatg ttcagatgga tgagattctc agatctgagc acgtgggagg gcgatcgcaa
5041 tctggctccc agttttgtga atgaagatgg cgtcgagtga cgccaaccca tctgatgggt
5101 ccgcagccaa cctcgtccca gaggtcaaca atgaggttat ggctctggag cccgttgttg
5161 gtgccgccat tgcggcacct gtagcgggcc aacaaaatgt aattgacccc tggattagaa
5221 ataattttgt acaagcccct ggtggagagt tcacagtatc ccctagaaac gctccaggtg
5281 aaatactatg gagcgcgccc ttgggccctg atctaaatcc ctacctatcc catttggcca
5341 gaatgtacaa tggttatgca ggtggttttg aagtgcaggt aattctcgcg gggaacgcgt
5401 tcaccgccgg gaaggtcata tttgcagcag tcccaccaaa ttttccaact gaaggcttga
5461 gccccagtca ggtcactatg ttcccccata tagtagtaga tgttaggcaa ctagaacctg
5521 tgttgattcc cttacccgat gttaggaata atttctatca ttacaatcaa tcaaatgacc
5581 ccaccattaa gttgatagca atgttgtata caccacttag ggccaataat gctggggatg
5641 atgtcttcac agtttcttgc cgagttctca cgagaccatc ccccgatttt gacttcatat
5701 ttctagtgcc acccacagtt gagtcaagaa ctaaaccatt ctctgtccca gttttaactg
5761 ttgaggagat gaccaattca agattcccca ttcctttgga aaagttgttc acgggtccca
5821 gcagtgcctt tgttgtccaa ccacaaaacg gcaggtgcac gactgatggc gtgctcctag
5881 gcaccaccca actgtctcct gtcaacatct gcaccttcag aggagatgtc acccatatca
5941 caggtagtca taactacaca atgaatttgg cttctcaaaa ttggagcaat tacgacccaa
6001 cagaagaaat cccagcccct ctaggaactc cagactttgt ggggaagatt caaggcgtgc
6061 ttacccaaac cacaaggaca gatggatcaa cacgcggcca caaagccaca gtgtacactg
6121 ggagcgccga ctttgctcca aaactgggta gagttcaatt tgaaactgac acaaaccatg
6181 attttgaagc taaccaaaac acaaagttca ccccagttgg tgtcatccaa gatggtggca
6241 ccactcacca aaatgaaccc caacagtggg tgctcccaag ttactcaggc agaaatactc
6301 ctaatgtgca tctggccccc gctgtagccc ccacttttcc gggtgagcaa cttctcttct
6361 tcagatccac tatgcccgga tgcagcgggt accccaacat ggatttggac tgtctgctcc
6421 cccaggaatg ggtacagtac ttctaccaag aggcagcccc agcacaatct gatgtggctc
6481 tgctaagatt tgtgaatcca gacacaggta gggttttgtt tgaatgtaag cttcataaat
6541 caggctatgt tacagtggct cacactggcc aacatgattt ggttatcccc cccaatggtt
6601 attttaggtt tgattcctgg gtcaaccagt tttacacgct tgcccccatg ggaaatggaa
6661 cggggcgtag acgtgcacta taatggctgg agctttcttt gctggattgg catctgatgt
6721 ccttggctct ggacttggtt cccttatcaa tgctggggct ggggccatca accaaaaagt
6781 tgagtttgaa aataacagaa aattgcaaca agcatccttc caatttagca gcaatctaca
6841 acaggcttcc tttcaacatg acaaagagat gctccaagca caaattgagg ccaccaaaag
6901 gttacaacag gaaatgatga aagttaagca ggcaatgctc ctagagggtg ggttctctga
6961 gacagatgca gcccgtgggg caatcaacgc ccccatgaca aaagctttgg actggagcgg
7021 gacaaggtac tgggctcctg atgctaggac tacaacatac aatgcaggcc gcttttccac
7081 ccctcaacca tcgggggcgc tgccaggaag agctaatctt agggatgctg tccctgctcg
7141 gggttcctct agtaagtctt ctaattcttc tactgctatt tctgtgtact caaatcaaac
7201 tatttcaacg agacttggtt ctacagctgg ttctggtacc agtgtctcga gcttcccgtc
7261 aactgcaagg actaggagct gggttgagga tcaaagtagg aatttgtcac ctttcatgag
7321 gggggcccac aacatatcgt ttgtcacccc accatctagc agatcctcta gccaaggcac
7381 agtctcaacc gtgcctaaag agattttgga ctcctggact ggcgctttca acacgcgcag
7441 gcagccactc ttcgctcaca ttcgtaagcg aggggagtca cgggcgtaat gtgaaaag
//