Typing tool
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Typing tool
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Complete norovirus genomes
| MW284783 | GII.4 Sydney | |
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| GII.P4 New Orleans |
ORF1: 1..5083
ORF2: 5064..6686
ORF3: 6686..7489
LOCUS MW284783 7489 bp RNA linear VRL 28-NOV-2020
DEFINITION Norovirus GII isolate P1D3 nonstructural polyprotein (ORF1) gene,
partial cds; VP1 (ORF2) gene, complete cds; and VP2 (ORF3) gene,
partial cds.
ACCESSION MW284783
VERSION MW284783.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7489)
AUTHORS Kelly,D., Jere,K.C., Darby,A.C., Allen,D.J. and Iturriza-Gomara,M.
TITLE Magnetic bead enrichment and complete genome characterisation of
human norovirus populations: A longitudinal comparison of acute and
chronic infection
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 7489)
AUTHORS Kelly,D., Jere,K.C., Darby,A.C., Allen,D.J. and Iturriza-Gomara,M.
TITLE Direct Submission
JOURNAL Submitted (21-NOV-2020) Institute of Infection, Veterinary and
Ecological Sciences., University of Liverpool, 8 West Derby Street,
Liverpool, Merseyside L69 7BE, United Kingdom
COMMENT ##Assembly-Data-START##
Assembly Method :: SPAdes v. 3.5.0
Sequencing Technology :: Illumina
##Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..7489
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="P1D3"
/isolation_source="stool sample"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="United Kingdom: Liverpool"
/collection_date="Dec-2013"
/note="genotype: GII.P4/GII.4"
gene <1..5083
/gene="ORF1"
CDS <1..5083
/gene="ORF1"
/codon_start=2
/product="nonstructural polyprotein"
/protein_id="QPG52059.1"
/translation="DASAAAVANSNNDTAKSSSDGVLSSMAVTFKRALGARPKQPPPR
EKPQRPPRPPTPELVKNIPPPPPNGEDEIVVSYSVKDGVSGLPDLSTVRQPEESNTAF
SVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAISLAKVEL
APLSLYWRPVYTPQYLISPDTLKKLSGETFPYTAFDNNCYAFCCWVLDLNDSWLSRRM
IQRTTGFFRPYQDWNRKPLPTMDDSKIKKVANIFLCALSSLFTRPIKDIIGKIRPLNI
LNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVELV
PVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEAN
ELAIVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLSTKSASPD
IVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREVAKRIAA
SLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCPLTLNC
DRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPDVEKAKRDFP
GQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLHE
RLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGKQLKDVKTMPELKQA
LKNVSIKKCQIVYSGCTYMLESDGKGNVKVDRIQSAAVQTNNELAGALHHLRCARIRY
YVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQDLWSKPQVENTEETTSKDGCPKPKDD
EEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEE
YLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERVSLGLVTGSEIR
KRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSPSLFITS
THVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVVTLL
IKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCGCPYI
YKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILGPGSAPT
LSTKTKFWRSSTASLPPGTYEPAYLGGKDPRVKGGPSLQQVMREQLKPFTEPRGKPPK
PSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCWNGESFT
GKLADQASKANLMFEEGKNMTPVYTAALKDELVKTDKIYGKIKKRLLWGSDLATMIRC
ARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFERHSRYTYHYDADYSRWDSTQQRA
VLAAALEIMVKFSPEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCTSQWNSI
AHWLLTLCALSEVTNLSPDTIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLREYGLRP
TRPDKTEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHGDPS
ETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQEPMFRWM
RFSDLSTWEGDRNLAPSFVNEDGVE"
mat_peptide <1..973
/gene="ORF1"
/product="p48"
mat_peptide 974..2071
/gene="ORF1"
/product="NTPase"
mat_peptide 2072..2608
/gene="ORF1"
/product="p22"
mat_peptide 2609..3007
/gene="ORF1"
/product="VPg"
mat_peptide 3008..3550
/gene="ORF1"
/product="Pro"
mat_peptide 3551..5080
/gene="ORF1"
/product="RdRp"
gene 5064..6686
/gene="ORF2"
CDS 5064..6686
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="QPG52060.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKVIFAAVPPNFPTEGLSPSQVTMFPHIVVDVRQLEPVLIPLPD
VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGAPDFVGKIQGML
TQTTRADGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG
STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGAGRRRVV"
gene 6686..>7489
/gene="ORF3"
CDS 6686..>7489
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="QPG52061.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARTTTHNAGRFSTPQPSGALPGRANLRDAVPARGSSSKSS
NSSIVTSVYSNQTTSTRLGSTAGSGTSVSSLPSTARTRSWVEDQSRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAYIRNRGESRV"
ORIGIN
1 cgacgcttcc gctgccgctg ttgctaacag caacaacgac accgcaaaat cttcaagtga
61 cggagtgctt tctagcatgg ctgtcacttt taaacgagcc ctcggggcgc ggcctaaaca
121 gcctcccccg agggaaaaac cacaaagacc cccacgacca cctactccag aactggttaa
181 aaatattccc cctcccccac ccaacggaga ggatgaaata gtggtttctt atagtgtcaa
241 agatggtgtt tccggcttgc ctgacctttc caccgtcagg caaccggaag aatccaacac
301 ggccttcagt gtccctccac tcaatcagag ggagaataga gatgctaagg aaccactcac
361 tggaacaatt ctggaaatgt gggacgggga aatctaccat tatggcctgt atgtggagcg
421 aggtcttgta ctaggcgtgc acaaaccgcc agctgccatc agcctcgcta aggttgagct
481 agcaccactc tccttgtact ggagacctgt gtacactcct cagtacctca tctctccaga
541 cactctcaag aaattgtccg gagaaacgtt cccctacaca gcctttgaca acaactgcta
601 tgccttttgt tgctgggtcc tggacctaaa tgactcgtgg ctgagcagga gaatgatcca
661 gagaacaact ggtttcttca ggccctacca agactggaat aggaaacccc ttcccaccat
721 ggatgactcc aaaataaaga aggtagctaa catattcctg tgtgctctgt cctcgctatt
781 caccagaccc ataaaagata taatagggaa gataaggccc cttaacatcc tcaacatctt
841 agcctcatgt gattggacct ttgcgggcat agtggagtcc ctgatactct tggcagaact
901 ctttggagtt ttctggacac ccccagatgt gtctgcgatg attgccccct tacttggtga
961 ctacgagcta caaggacctg aggaccttgc agtggaactc gtccccgtgg tgatgggggg
1021 aattggtttg gtgctaggat tcaccaaaga gaagattggg aaaatgttgt catctgctgc
1081 gtccaccttg agagcttgca aagaccttgg tgcatatggg ctagagatcc taaagttagt
1141 catgaagtgg ttcttcccga agaaggagga ggcaaatgag ctggctatag tgaggtccat
1201 cgaggatgca gtcctggatc tcgaggcaat tgaaaacaat catatgacca ccttgcttaa
1261 agataaagac agtctggcaa cctacatgag aacacttgac cttgaagagg agaaagccag
1321 gaaactctca accaagtctg cctcacccga catcgtgggc acaatcaacg ccctcctggc
1381 gagaatcgct gccgcacgtt ctctggtgca tcgagcgaag gaggagcttt ccagcagacc
1441 aagacctgtg gtgttgatga tatcaggcag gccaggaata gggaagaccc acctcgctag
1501 ggaagtggct aagagaatcg cagcctccct cacaggagac caacgtgttg gcctcatccc
1561 acgcaatggc gtcgatcatt gggatgcgta caagggggag agggtcgtcc tatgggacga
1621 ttatggaatg agcaacccta ttcacgatgc cctcaggctg caagaactcg ctgacacttg
1681 ccccctcact ctgaactgtg acaggattga aaataaagga aaggtctttg acagcgatgt
1741 catcattatc accactaatc tggccaatcc agcaccactg gactatgtca actttgaagc
1801 atgctcgaga cgcattgact tcctcgtgta tgcagaagcc cctgatgtcg aaaaggcgaa
1861 gcgtgacttc ccaggccagc ctgacatgtg gaagaacgct ttcagttctg atttctcaca
1921 cataaaacta gcactggccc cacagggtgg tttcgacaag aacgggaaca ccccacacgg
1981 aaagggcgtc atgaagactc tcaccactgg ctcccttatt gcccgggcat cagggctact
2041 ccatgagagg ttagatgaat ttgaactgca gggcccagct ctcaccacct tcaatttcga
2101 tcgcaacaaa gtgcttgcct ttagacagct tgctgctgaa aataaatatg gattgatgga
2161 cacaatgagg gttgggaaac agctcaagga tgtcaaaacc atgccagaac tcaaacaagc
2221 gctcaagaat gtctcaatca agaagtgtca aatagtgtat agtggttgca cctacatgct
2281 tgagtctgat ggcaagggca atgtgaaagt tgacaggatc caaagcgccg ccgtgcagac
2341 caacaatgag ctggctggtg ccctgcacca cttgaggtgc gccagaatca gatactatgt
2401 caagtgtgtc caggaagccc tgtattccat catccagatt gctggggctg catttgtcac
2461 cacgcgcatt gccaagcgca tgaacataca agacctatgg tccaagccac aagtggaaaa
2521 cacagaggag actaccagca aggacgggtg cccaaaacct aaggatgatg aggagtttgt
2581 catttcatcc gacgacatca aaactgaggg caagaaaggg aagaacaaga ctggccgtgg
2641 caagaagcac acagcatttt caagcaaagg cctcagtgat gaagagtacg atgaatacaa
2701 gaggattaga gaagaaagga atggcaagta ctctatagaa gagtaccttc aggacaggga
2761 caaatactat gaggaggtgg ccattgccag agcgactgag gaagacttct gtgaagagga
2821 ggaagccaag atccggcaaa ggatctttag gccaacaagg aaacaacgca aggaggaaag
2881 agtctctctc ggtttggtca caggctctga aattaggaaa agaaacccag atgacttcaa
2941 acccaagggg aaattgtggg ctgacgatga caggagtgtg gactacaatg agaaactcag
3001 ttttgaggcc ccaccaagta tttggtcgag aatagtcaac tttggttcag gctggggatt
3061 ctgggtctcc cccagcttgt tcataacatc aacccatgtt ataccccagg gcgcaaagga
3121 gttctttgga gtccccatca aacaaataca ggtacacaag tcaggcgagt tctgtcgctt
3181 gagattccct aaaccaatca ggactgatgt gacgggcatg atcttagaag aaggcgcacc
3241 tgagggcacc gtggtcacac tactcatcaa aaggtccact ggggaactta tgcccctagc
3301 agctaggatg gggacccatg cgaccatgaa gatccaaggg cgcactgttg ggggccagat
3361 gggcatgctt ctgacaggat ccaacgccaa gagtatggac ctgggtacta caccaggtga
3421 ttgtggctgc ccctatatct acaagagagg taatgactat gtggtcattg gagtccacac
3481 ggctgccgca cgtgggggga acactgtcat atgtgccacc caggggagtg aaggagaggc
3541 tacacttgag ggtggtgaca acaaggggac atactgtggt gcaccaatcc taggcccagg
3601 gagtgcccca acacttagca ccaagaccaa attctggaga tcgtccacag catcactccc
3661 acctggcacc tatgaaccag cctatcttgg tggcaaggac cctagagtca agggtggccc
3721 ttcactgcag caagtcatga gggaacagtt gaagccattc acagagccca ggggcaagcc
3781 accaaaacca agtgtgttag aagctgccaa gaagaccatc attaatgtcc ttgagcaaac
3841 aattgatcca cctgagaagt ggtcgttcgc acaagcttgc gcgtcccttg acaagaccac
3901 ttccagtggt catccgcacc acatgcggaa aaacgactgc tggaacgggg agtccttcac
3961 aggcaagctg gcagaccagg cttccaaggc caacctgatg tttgaagaag ggaagaacat
4021 gaccccagtc tacacagctg cgctcaagga tgagttagtt aaaactgaca aaatttatgg
4081 taagatcaag aagaggcttc tttggggctc ggacttggcg accatgatcc ggtgtgctcg
4141 agcattcgga ggcctaatgg atgaactcaa agcgcactgt gtcacgcttc ccattagagt
4201 tggcatgaat atgaatgagg atggccccat catcttcgag aggcattcca ggtacacgta
4261 ccactatgat gctgattact ctcgatggga ttcaacacaa cagagagccg tgttggcagc
4321 agctttagaa atcatggtta aattctcccc agaaccacat ttggctcagg tagtcgcgga
4381 agaccttctt tctcctagcg tggtggacgt gggcgacttc acaatatcaa tcaacgaggg
4441 tcttccctct ggggtgccct gcacctccca atggaactcc atcgcccact ggcttctcac
4501 tctctgtgcg ctctccgaag tcacaaacct gtctcctgat accatacagg ctaattctct
4561 cttctctttt tatggtgatg atgaaattgt tagcacagac ataaaattgg acccagagaa
4621 attgacagca aagctcagag aatatgggtt aagaccaacc cgccctgaca aaactgaagg
4681 accccttgtc atctctgaag acctgaatgg cctaactttc ctgcggagaa ctgtgacccg
4741 cgacccagct ggttggtttg gaaaactgga gcagagttca atactcaggc aaatgtactg
4801 gactaggggt cccaaccatg gagacccatc tgaaacaatg attccacact cccaaaggcc
4861 catacaattg atgtccctac tgggggaggc cgctctccac ggcccagcat tttacagtaa
4921 aatcagcaaa ttggtcattg cagagctaaa agaaggtggt atggattttt acgtgcccag
4981 acaagagcca atgttcagat ggatgagatt ctcagatctg agcacgtggg agggcgatcg
5041 caatctggct cccagttttg tgaatgaaga tggcgtcgag tgacgccaac ccatctgatg
5101 ggtccgcagc caacctcgtc ccagaggtca acaatgaggt tatggctctg gagcccgttg
5161 ttggtgccgc cattgcggca cctgtagcgg gccaacaaaa tgtaattgac ccctggatta
5221 gaaacaattt tgtacaagcc cctggtggag agtttacagt gtcccctaga aacgctccag
5281 gtgaaatact atggagcgcg cccttaggtc ctgatctaaa tccctaccta tcccatttgg
5341 ccagaatgta taatggttat gcaggtggtt ttgaagtgca ggtaattctc gcggggaacg
5401 cgttcaccgc cgggaaggtc atatttgcag cagtcccacc aaattttcca actgaaggct
5461 tgagccccag ccaggtcact atgttccccc atatagtagt agatgttagg caactagaac
5521 ctgtgttgat tcccttaccc gatgttagga ataatttcta tcattacaat caatcaaatg
5581 accccaccat taagttgata gcaatgttgt atacaccact tagggctaat aatgctgggg
5641 acgatgtctt cacagtctct tgccgagttc tcacgagacc atcccccgat tttgatttca
5701 tatttctagt gccacccaca gttgagtcta gaactaaacc attctctgtc ccagttttaa
5761 ctgttgagga gatgaccaat tcaagattcc ccattccatt ggaaaagttg ttcacgggtc
5821 ccagcagtgc ctttgttgtt caaccacaaa acggtaggtg cacgactgat ggcgtgctcc
5881 taggcaccac ccaattgtct cctgtcaaca tctgcacctt cagaggggat gtcacccaca
5941 tcacaggtag tcgtaactac acaatgaatt tggcttctca aaattggaac aattatgacc
6001 caacagaaga aatcccagcc cctctaggag ctccagattt tgtggggaag attcaaggca
6061 tgctcaccca aaccacaagg gcagatggct caacacgcgg ccacaaagct acagtgtaca
6121 ctgggagcgc cgactttgct ccaaaactgg gcagagttca atttgaaact gacacagacc
6181 atgattttga agctaaccaa aacacaaagt tcaccccagt cggtgtcatc caagatggta
6241 gcaccaccca ccgaaatgaa ccccaacagt gggtgctccc aagttactca ggcagaaata
6301 ctcataatgt tcatctggcc cccgctgtag cccccacttt tccgggtgag caacttctct
6361 tcttcagatc caccatgccc ggatgtagcg ggtaccccaa catggatttg gactgtctgc
6421 tcccccagga atgggtgcag tacttctacc aagaggcagc cccagcacaa tctgatgtgg
6481 ctctgctaag atttgtgaat ccagacacag gcagggtttt gtttgagtgt aagcttcata
6541 aatcaggcta tgttacagtg gctcacactg gccaacatga tttggttatc ccccccaatg
6601 gttattttag gtttgattcc tgggtcaacc agttctacac gcttgccccc atgggaaatg
6661 gagcggggcg tagacgtgta gtataatggc tggagctttc tttgctggat tagcatctga
6721 tgtccttggc tctggacttg gttcccttat caatgctggg gctggggcca tcaaccaaaa
6781 agttgagttt gaaaataaca gaaaattgca acaagcatcc ttccaattta gcagcaatct
6841 acaacaggct tcctttcaac atgacaaaga aatgctccaa gcacaaattg aggccaccaa
6901 aaagctacaa caggaaatga tgaaagttaa gcaggcaatg ctcctagagg gtgggttctc
6961 tgagacagat gcagcccgcg gggcaatcaa cgcccccatg acaaaagctt tggactggag
7021 cgggacaagg tattgggctc ccgatgctag gactacaaca cacaatgcag gccgcttttc
7081 cacccctcaa ccatcggggg cactgccagg aagagctaat cttagggatg ctgtccctgc
7141 tcggggctcc tccagtaaat cttctaactc ttctattgtt acttctgtgt attcaaatca
7201 aaccacttca acgagacttg gttctacagc tggttctggt accagtgtct cgagcctccc
7261 gtcaactgca aggactagga gctgggttga ggatcaaagt aggaatttgt ctcctttcat
7321 gaggggggcc cacaacatat cgtttgtcac cccaccatct agcagatcct ctagccaagg
7381 cacagtctca accgtgccta aagaagtttt ggactcctgg actggcgctt tcaacacgcg
7441 caggcagcct ctcttcgctt acattcgtaa tcgaggggag tcacgggtg
//