Typing tool
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Typing tool
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Complete norovirus genomes
| MF140656 | GII.4 Farmington Hills | |
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| GII.P4 Yerseke |
ORF1: 1..5088
ORF2: 5069..6691
ORF3: 6691..7492
LOCUS MF140656 7492 bp RNA linear VRL 24-OCT-2017
DEFINITION Norovirus GII strain
Norovirus/GII/Hu/NL/2009/GII.P4-GII.4/Rotterdam/E1300263_p15_d41
ORF1 gene, partial cds; ORF2 gene, complete cds; and ORF3 gene,
partial cds.
ACCESSION MF140656
VERSION MF140656.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7492)
AUTHORS van Beek,J., de Graaf,M., Smits,S.L., Schapendonk,C.M.E.,
Verjans,G.M.G.M., Vennema,H., van der Eijk,A.A., Phan,M.V.T.,
Cotten,M.L. and Koopmans,M.P.G.
TITLE Whole genome next generation sequencing to study within-host
evolution of chronic norovirus infection among immunocompromised
patients
JOURNAL J. Infect. Dis. (2017) In press
PUBMED 29029115
REMARK Publication Status: Available-Online prior to print
REFERENCE 2 (bases 1 to 7492)
AUTHORS van Beek,J., de Graaf,M., Smits,S.L., Schapendonk,C.M.E.,
Verjans,G.M., Vennema,H., van der Eijk,A.A., Phan,M.V.T.,
Cotten,M.L. and Koopmans,M.P.G.
TITLE Direct Submission
JOURNAL Submitted (19-MAY-2017) Centre for infectious Disease Control
(Cib), National Institute for Public Health and the Environment
(RIVM), Antonie van Leeuwenhoeklaan 9, Bilthoven, Utrecht 3721 MA,
Netherlands
COMMENT ##Assembly-Data-START##
Assembly Method :: SPAdes v. 3.9.0
Sequencing Technology :: Illumina
##Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..7492
/organism="Norovirus GII"
/mol_type="genomic RNA"
/strain="Norovirus/GII/Hu/NL/2009/GII.P4-
GII.4/Rotterdam/E1300263_p15_d41"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="Netherlands"
/collection_date="15-Jul-2009"
/note="genotype: GII.P4-GII.4"
CDS <1..5088
/codon_start=1
/product="ORF1"
/protein_id="ATN23664.1"
/translation="SNDASAAAVANSNNDTAKSSSDGVLSSMAVTFKRALGARPKQPP
PREIPQRPPRPPTPELVKNIPPPPPNGEDEIVVSYSVKDGISGLPDLSTVRQPEESNT
AFSVPPLNQRENRDAVEPLPGTILEMWDGEIYHYGIYVERGLVLGVHKPPAAISLARI
ELTPLSLYWRPVYTPQYLISPDSLKKLHEETFPYTAFDNNCYAFCCWVLDLNDSWLSR
RMIQRTTGFFRPYQEWNRKPLPTMDDSKLKKVANIFLCALSSLFTRPIKDIIGKLRPL
NILNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDFQLQGPEDLAVE
LVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEE
ANELAIVRSIEDAVLDLEAIENNHLTILLKDKDSLATYMRTLDLEEEKARKLSTKSAS
PDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREVAKRI
AASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCPLTL
NCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRD
FPGQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLL
HERLDEFEMQGPALTTFNFDRNKVLAFRQLAAENKYGLIDTMKVGRQLKDVRTMPELK
QALKNISIKKCQIVYGGCTYTLESDGKGNVKVDKVQSASVQTNNELTGALHHLRCARI
RYYVKCVQEALYSIIQIAGAAFVTTRIVKRMNIQDLWSRPQVENTEETTSKDGCPKPR
DDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGRYSI
EEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPSRKQRKEERASLGLVTGSE
IRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSPSLFI
TSTHVIPQGTKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVVT
LLIKRPTGELMPLAVRMGTHATMRIQGRAVGGQMGMLLTGSNAKSMDLGTTPGDCGCP
YIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEAILEGGDNKGTYCGAPILGPGNA
PKLSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRGKP
PKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCWNGES
FTGKLADQASKANLMFEEGKNMTPVYTAALKDELVKTDKIYKKIKKRLLWGSDLATMI
RCARAFGGLMDELKAHCVSLPIRVGMNMNEDGPIIFERHSRYTYHYDADYSRWDSTQQ
RDVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCTSQWN
SIAHWLLTLCALSEVTNLSPDTIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLREYGL
KPTRPDKTEGPLVISDDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHGD
PAETMIPHSQRPIQLMSLLGEAALHGPAFYSKVSKLVIAELKEGGMDFYVPRQEPMFR
WMRFSDLSTWEGDRNLAPSFVNEDGVE"
CDS 5069..6691
/codon_start=1
/product="ORF2"
/protein_id="ATN23665.1"
/translation="MKMASNDATPSDGPAASLVPAVNNEVMALDPVAGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
VEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPCQVTMFPHLIIDVRQLEPVLIPLPD
VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTQIGSTQSYTMNLASQNWNNYDPTEEIPAPLGTPDFVGRIQGML
TQTTKSDGSTRGHVATVSTGSAYFTPKLGRVQFSTDTSNDLEARQNTRFTPVGVIQDG
STTHRNEPQQWVLPEYSGRDSHNVHLAPAVAPTFPGEQLLFFRSTIPGCSGYPNMELD
CLLPQEWVQHFYQESAPAQSDVALLRFVNPDTSRVLFECKLYKQGYVTVAHTGQHDLI
IPPNGYFRFDSWVNQFYTLAPMGNGAGRRRAL"
CDS 6691..>7492
/codon_start=1
/product="ORF3"
/protein_id="ATN23666.1"
/translation="MAGAFFAGLASDVLGSGLSSLINAGAGTINQKVDFDNNRKLQQA
SFQYSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKIKQTMLLEGGFSETDAARGAVN
APMTKVLDWSGTRYWAPDARITTYNAGHFSTPQPSGAPPGRTNLRATTPARGSSSTLS
NASTVTSVHSNQTASTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGVHNI
SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRKRGESR"
ORIGIN
1 tctaacgacg cttccgctgc cgctgttgct aacagcaaca acgacaccgc aaaatcttca
61 agtgacggag tgctttctag catggctgtc acttttaaac gagccctcgg ggcgcggcct
121 aagcagcctc ccccgaggga aataccacaa agacccccac gaccacctac tccagaactg
181 gtcaaaaata tcccccctcc cccgcccaat ggagaggatg aaatagtggt ttcttacagt
241 gtcaaagatg gtatttccgg tttgcctgat ctttccaccg tcaggcaacc ggaagaatct
301 aacacggcct tcagtgtccc tccactcaat cagagggaga atagagatgc tgtggagcca
361 ttacctggaa caattctgga aatgtgggat ggagaaatct accattatgg catatatgtg
421 gagcgaggtc ttgtactagg cgtgcataaa ccaccagccg ccattagcct cgctaggatc
481 gagctaacac cactctcctt gtactggaga cctgtgtata cccctcaata cctcatctct
541 ccagactctc tcaagaaatt acatgaagag acgttcccct acacagcctt cgacaacaac
601 tgctatgcct tttgttgttg ggtcctggac ctaaacgact cgtggctgag taggaggatg
661 atccagagaa caactggctt cttcaggccc taccaagaat ggaacaggaa acctctcccc
721 actatggatg attccaagct aaagaaggtg gctaacatat tcctgtgtgc tctgtcttcg
781 ctattcacca ggcccataaa agatataata gggaagctaa ggcctcttaa catccttaac
841 atcttggcct catgtgattg gacttttgca ggcatagtgg agtctttgat actcttggca
901 gaactctttg gagttttctg gacaccccca gatgtgtctg cgatgattgc ccccttgctc
961 ggtgatttcc agttgcaagg accggaggac cttgcggtgg aactcgtccc tgtagtgatg
1021 gggggaattg gtttggtgtt agggttcacc aaagagaaga ttggtaagat gttgtcatct
1081 gctgcgtcca ccttgagagc ttgtaaagat cttggtgcat atgggctaga gatcctaaag
1141 ttggttatga agtggttctt cccgaagaaa gaggaagcaa atgaactggc tatagtaaga
1201 tccatcgagg atgcagtcct ggatctcgag gcaattgaaa acaatcactt aaccatcttg
1261 ctcaaagaca aagacagtct ggcaacctac atgagaaccc ttgatcttga ggaggagaaa
1321 gccaggaaac tctcaaccaa gtctgcttca cctgacattg tgggcacaat caacgccctt
1381 ctggcaagga tcgctgctgc acgttctctg gtgcatcgag cgaaggagga actttccagc
1441 agaccaagac ctgtagtatt gatgatatca ggcagaccag gaatagggaa gacccacctt
1501 gctagggaag tggccaagag aatcgcagcc tcccttacag gagaccagcg cgtgggcctc
1561 atcccacgca atggtgtcga ccattgggat gcgtacaagg gtgagagggt cgtcctatgg
1621 gatgactatg gaatgagcaa tcccatccac gatgccctca ggttgcaaga actcgctgac
1681 acttgccctc tcaccctaaa ctgtgacagg attgagaata aaggaaaggt ttttgacagc
1741 gatgtcatca tcatcaccac taatctggcc aacccagcac cactggacta cgtcaacttt
1801 gaagcatgct cgaggcgcat cgacttcctc gtgtatgcag aagctcctga agtcgagaag
1861 gcgaagcgtg acttcccagg ccagcccgac atgtggaaga acgccttcag ctctgatttc
1921 tcacacataa aactagcatt ggctccacag ggtggcttcg acaagaacgg gaacacccca
1981 cacgggaagg gcgtcatgaa gactctcacc actggctccc ttattgctcg ggcatcaggg
2041 ctactccatg agaggttaga tgagtttgaa atgcagggtc cagctctcac caccttcaac
2101 tttgatcgca acaaagtgct tgcctttaga caacttgctg ctgaaaacaa atatgggttg
2161 atagacacaa tgaaagttgg gaggcagctc aaggatgtca gaacaatgcc agaacttaag
2221 caagcactca agaatatctc aatcaagaag tgccagatag tgtatggtgg ttgcacctac
2281 acacttgagt ctgatggcaa gggtaatgtg aaagttgata aagttcaaag cgcctccgtg
2341 cagaccaaca atgagctgac tggcgccctg caccacctac ggtgcgccag aatcagatac
2401 tacgtcaagt gtgtccagga ggccctgtat tccatcatcc agattgctgg ggctgcattt
2461 gtcaccacgc gcatcgtcaa gcgcatgaac atacaagacc tatggtccag accacaagtg
2521 gagaacacag aggagactac cagcaaggac gggtgtccaa aacccagaga tgatgaggag
2581 ttcgtcattt catccgacga catcaaaact gagggtaaga aaggaaagaa caagactggt
2641 cgcggcaaga aacacacagc cttctcaagc aaaggtctca gtgatgaaga gtacgatgag
2701 tacaaaagga ttagagagga aaggaatggc aggtactcca tagaagaata ccttcaggac
2761 agggacaaat actacgagga ggtggccatt gccagggcaa ccgaggagga cttctgtgag
2821 gaggaagagg ccaagatccg gcaaaggatc ttcaggccat caaggaaaca acgcaaggag
2881 gaaagggctt ctctcggttt ggtcacaggc tctgaaatta gaaaaagaaa tccagatgat
2941 ttcaaaccca aggggaaact atgggctgat gatgacagaa gtgtggacta caacgagaaa
3001 ctcagttttg aagccccacc aagcatctgg tcgaggatag tcaactttgg ttcaggttgg
3061 ggattctggg tctcccccag tttgttcata acatcaaccc atgtcatacc ccagggcaca
3121 aaggagttct ttggagtccc tatcaaacaa attcaggtac acaaatcagg cgagttctgt
3181 cgcttgagat tcccaaagcc aatcaggact gatgtgacag gcatgatctt agaagaaggt
3241 gcacccgagg gcaccgtggt tacactgctc atcaaaaggc ccactggaga actcatgccc
3301 ctggcagtta ggatggggac ccatgcaacc atgagaattc aagggcgcgc tgttggaggc
3361 caaatgggca tgcttctgac aggatccaac gccaaaagca tggatctggg taccacacca
3421 ggtgattgtg gctgtcctta catctacaag agaggaaatg actatgtggt cattggggtc
3481 cacacggctg ccgctcgtgg ggggaacact gttatatgtg ccacccaggg aagtgaggga
3541 gaggccatac ttgaaggtgg tgacaataaa gggacatact gtggtgcacc aatcctagga
3601 ccagggaatg ccccaaaact tagcaccaag accaagttct ggagatcgtc cacagcacca
3661 ctcccacctg gtacctacga gccagcctat cttggtggca aggaccccag agtcaagggt
3721 ggcccttcac tgcagcaagt catgagggat caattgaagc cgttcacaga gcctaggggc
3781 aagccaccaa agccaagtgt gctagaagct gccaagaaaa ccatcatcaa tgttcttgag
3841 caaacaattg atccgcctga gaaatggtca ttcgcacaag cttgcgcgtc ccttgacaag
3901 accacttcca gtggccaccc gcaccacatg cggaaaaacg actgctggaa cggggaatcc
3961 ttcacaggca agctggcaga ccaggcttcc aaggccaacc taatgtttga agaaggaaag
4021 aacatgaccc cagtctacac agctgcgctt aaggatgaat tagttaaaac tgacaaaatc
4081 tataaaaaga tcaagaagag actcctctgg ggctcggatt tggcgaccat gatccggtgt
4141 gctcgagcat tcggaggcct aatggatgaa ctcaaagcgc actgtgtctc acttcccatt
4201 agagttggta tgaatatgaa tgaggatggc cccatcatct tcgagaggca ttccaggtac
4261 acataccact atgatgctga ttactcacga tgggattcaa cacaacaaag agacgtattg
4321 gcagcagctc tagaaatcat ggttaaattc tccccagaac cacatttggc tcaggtagtc
4381 gcagaagacc ttctctctcc tagcgtggtg gacgtgggtg acttcacaat atcaatcaac
4441 gagggtcttc cctctggggt gccctgcacc tcccaatgga attccatcgc ccactggctt
4501 ctcactctct gtgcgctctc tgaagttaca aatttgtctc ctgacaccat acaggctaat
4561 tccctcttct ctttttatgg tgatgatgaa attgttagca cagacataaa attggaccca
4621 gaaaagttga cagcaaaact cagggaatat gggttaaagc caacccgccc tgataaaact
4681 gaaggacccc ttgtcatctc tgacgacttg aatggcctga ctttcctgcg gagaactgtg
4741 acccgcgacc cagctggttg gtttggaaaa ctggagcaga gttcaatact caggcaaatg
4801 tactggacta ggggtcccaa ccacggggat ccagctgaaa caatgattcc acactctcaa
4861 agacccatac aattgatgtc cctactgggg gaggctgcac ttcacggccc agcattctac
4921 agcaaagtca gcaagttggt catcgcagag ctaaaagagg gtggcatgga tttttacgtg
4981 cccagacaag agccaatgtt cagatggatg aggttctcag atctgagcac gtgggagggc
5041 gatcgcaatc tggctcccag ttttgtgaat gaagatggcg tcgaatgacg ccaccccatc
5101 tgatgggccc gcagccagcc tcgtcccagc ggtcaacaat gaggttatgg ctttggatcc
5161 cgttgctggt gccgctattg cagcacctgt agcgggccaa caaaatgtaa ttgacccctg
5221 gattagaaat aattttgtac aagcccctgg tggagaattc acagtatccc ctagaaacgc
5281 tccaggtgaa atactatgga gcgcgccctt gggccctgat ttgaatcctt acctttccca
5341 tttggccaga atgtataatg gttatgcagg tggtgttgaa gtgcaggtaa ttctcgcggg
5401 gaacgcgttc accgccggga aaatcatatt tgcagcagtc ccaccaaatt tcccaaccga
5461 aggactgagc ccctgccaag tcactatgtt cccccatttg ataatagatg ttagacaact
5521 ggaacctgtg ttgatcccct tgcctgatgt taggaacaat ttctaccatt acaatcaatc
5581 aaatgacccc accatcaaat tgatagcaat gctgtacaca ccacttaggg ctaataatgc
5641 tggggacgat gtcttcacag tctcttgtcg agttctcacg agaccatccc ccgattttga
5701 tttcatattt ctggtgccac ccacagttga gtcaagaacc aaaccattct ctgtcccagt
5761 cttaactgtt gaggagatga ccaactcaag attccccatt cctttagaaa agttgttcac
5821 gggtcccagc agtgcctttg ttgttcaacc acaaaatggc agatgcacga ctgatggcgt
5881 gctcttaggt actacccaac tgtctcctgt caacatctgc accttcagag gggatgtcac
5941 tcaaattgga agtactcaaa gttacacaat gaacctggcc tcccaaaatt ggaataatta
6001 tgatccaaca gaagaaatcc cagcccccct gggaacccca gattttgtag gaaggatcca
6061 aggcatgctc acccaaacca caaagagtga tggctcgacc cgtggtcacg tagccacagt
6121 gagcactgga agtgcttatt ttactccaaa gttgggcaga gttcaattct ccactgacac
6181 aagcaatgac cttgaagctc gccaaaacac gagattcacc ccagtcggcg tcatccagga
6241 tggtagtacc acccaccgaa atgaacccca acaatgggtg ctcccagagt attcaggtag
6301 agatagtcac aatgtacacc tagcacctgc tgtggccccc acttttccgg gcgagcaact
6361 tcttttcttt aggtccacta tacccggatg cagcgggtac cccaacatgg aattggattg
6421 cctactcccc caggagtggg tgcagcactt ctaccaagaa tcagccccag cacaatctga
6481 tgtggcactg ctgagatttg tgaatccaga cacaagtagg gttttgtttg agtgcaagct
6541 ttacaagcaa ggctatgtaa cagtggctca tactggccaa catgatttga ttatccctcc
6601 caatggctat tttagatttg actcctgggt taaccaattc tacacacttg cccccatggg
6661 aaatggagcg gggcgaagac gtgcattata atggctggag ctttctttgc tggattagca
6721 tctgatgtcc ttggctctgg acttagctct ctaatcaatg ctggggctgg gaccattaat
6781 caaaaagttg attttgataa taatagaaaa ttgcaacaag cttccttcca atatagtagc
6841 aatctacaac aggcttcctt tcaacatgat aaagagatgc tccaagcaca aattgaggcc
6901 accaaaaagt tacaacagga aatgatgaaa attaaacaga caatgctcct agagggtgga
6961 ttctctgaga cagatgcagc ccgtggggca gtcaacgccc ccatgacaaa ggttttggac
7021 tggagcggaa caaggtactg ggctcccgat gctaggatta caacatacaa tgcaggccac
7081 ttttccaccc ctcaaccctc gggagcacca ccagggagaa ccaatctcag ggctactacc
7141 cccgctcggg gctcctccag tacactttca aatgcttcta ctgttacttc tgtgcactca
7201 aatcaaactg cttcaacgag acttggttct acagctggtt ctggcaccag tgtctcgagc
7261 ctcccgtcaa ctgcaaggac taggagctgg gttgaggatc aaaacaggaa cttgtcacct
7321 ttcatgaggg gggtccacaa catatcattt gtcaccccac catctagcag atcctctagc
7381 caaggcacag tctcaaccgt gcctaaagaa gttttggact cctggactgg cgctttcaac
7441 acgcgcaggc agcctctctt cgcccacatt cgtaagcgag gggagtcacg gg
//