Typing tool
|
|
|
|
|
|
Typing tool
|
Complete norovirus genomes
| MF140662 | GII.4 Farmington Hills | |
|
|---|---|---|---|
| GII.P4 Yerseke |
ORF1: 1..5088
ORF2: 5069..6691
ORF3: 6691..7497
LOCUS MF140662 7540 bp RNA linear VRL 24-OCT-2017
DEFINITION Norovirus GII strain
Norovirus/GII/Hu/NL/2010/GII.P4-GII.4/Rotterdam/E1300269_p15_d476
ORF1 gene, partial cds; and ORF2 and ORF3 genes, complete cds.
ACCESSION MF140662
VERSION MF140662.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7540)
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 7540)
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..7540
/organism="Norovirus GII"
/mol_type="genomic RNA"
/strain="Norovirus/GII/Hu/NL/2010/GII.P4-
GII.4/Rotterdam/E1300269_p15_d476"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="Netherlands"
/collection_date="23-Sep-2010"
/note="genotype: GII.P4-GII.4"
CDS <1..5088
/codon_start=1
/product="ORF1"
/protein_id="ATN23682.1"
/translation="SNDASAAAVANSNNDTAKSSSDGVFSNMAVTFKRALGARPKQPP
PREIPQKPPRPPTPELVKNIPPPPPNGEDEIVVSYSVKDGISGLPDLSTVRQPEESNT
AFSVPPLNQRENRDAVEPLPGTILEMWDGEIYHYGIYVERGLVLGVHKPPAAISLARI
ELTPLSLYWRPVYTPQYLISPDSLKKLHEETFPYTAFDNNCYAFCCWVLDLNDSWLSR
RMIQRTTGFFRPYQEWNRKPLPTMDDSKLKKVANIFLCALSSLFTRPIKDIIGKLRPL
NILNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDFQLQGPEDLAVE
LVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLIMKWFFPKKEE
ANELAMVRSIEDAVLDLEAIENNHLTILLKDKDSLATYMRTLDLEEEKARKLSTKSAS
PDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREVAKKI
AASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCPLTL
NCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRD
FPGQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLL
HERLDEFEMQGPALTTFNFDRNKVLAFRQLAAENKYGLIDTMKVGRQLKDVRTMPELK
QALKNISIKKCQIVYGGCTYTLESDGKGNVKVDKVQSASVQTNNELTGALHHLRCARI
RYYVKCVQEALYSIIQIAGAAFVTTRIVKRMNIQDLWSRPQVENTEETTSKDGCPKPR
DDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGRYSI
EEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPSRKQRKEERASLGLVTGSE
IRKRNPDDFKPKGKLWADDDRNVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSPSLFI
TSTHVIPQGTKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVVT
LLIKRPTGELMPLAVRMGTHATMRIQGRAVGGQMGMLLTGSNAKSMDLGTTPGDCGCP
YIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEAILEGGDNKGTYCGAPILGPGNA
PKLSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRGKP
PKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCWNGES
FTGKLADQASKANLMFEEGKNMTPVYTAALKDELVKTDKIYKKIKKRLLWGSDLATMI
RCARAFGGLMDELKAHCVSLPIRVGMNMNEDGPIIFERHSRYTYHYDADYSRWDSTQQ
RDVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCTSQWN
SIAHWLLTLCALSEVTNLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLREYGL
KPTRPDKTEGPLVISDDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHGD
PTETMIPHSQRPIQLMSLLGEAALHGPAFYSKVSKLVIAELKEGGMDFYVPRQEPMFR
WMRFSDLSTWEGDRNLAPSFVNEDGVE"
CDS 5069..6691
/codon_start=1
/product="ORF2"
/protein_id="ATN23683.1"
/translation="MKMASNDATPSDGPAANLVPAVNNEVMALDPVAGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGISPCQVTMFPHIITDVRQLEPVLIPLPD
VRNNFYHYNQSNEPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTQIGSTQTYTMNLASQNWNNYDPTEEIPAPLGTPDFVGRIQGML
TQTTKSDGSTRGHVATVSTGSAHFTPKLGRVQFSTDTSNDLEARQNTRFTPVGVIQDG
GTTHRNEPQQWVLPNYSGRDNHNVHLAPAVAPTFPGEQLLFFRSTIPGCSGYPNMELD
CLLPQEWVQYFYQESAPAQSDVALLRFVNPDTSRVLFECKLHKQGFVTVAHTGQHDLI
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL"
CDS 6691..7497
/codon_start=1
/product="ORF3"
/protein_id="ATN23684.1"
/translation="MAGAFFAGLASDVLGSGLSSLINAGAGTINQKVDFDNNRKLQQA
SFQYSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKIKQTMLLEGGFSETDAARGAIN
APMTKVLDWNGTRYWAPDARITTYNAGHFSTTQPSGAPPGRTNLRATTPARGSSSTLS
NASTVTSVHSNQTASTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGVHNI
SFVTPPSSRSSSQGTVSTVPKEVLNSWTGAFNTRRQPLFAHIQKRGESRV"
ORIGIN
1 tctaacgacg cttccgctgc cgctgttgcc aacagcaaca acgacaccgc aaaatcttca
61 agtgacggag tgttttctaa catggctgtc acttttaaac gagccctcgg ggcgcggcct
121 aaacagcctc ccccgaggga aataccacaa aaacccccac gaccacctac tccagaactg
181 gtcaaaaata tcccccctcc cccgcccaat ggagaggatg aaatagtggt ttcttacagt
241 gtcaaagatg gtatttccgg tttgcctgat ctttccaccg tcaggcaacc ggaagaatct
301 aacacggcct tcagtgtccc tccactcaat cagagggaaa atagagacgc tgtggaacca
361 ttacctggaa cgattctgga aatgtgggat ggagaaatct accattatgg catatatgtg
421 gagcgaggtc ttgtactagg cgtgcacaaa ccaccagccg ccattagcct cgctaggatc
481 gagctaacac cactctcctt gtactggaga cctgtgtata cccctcaata cctcatctct
541 ccagactctc tcaagaaatt acatgaagag acgttcccct acacagcctt cgacaacaac
601 tgctatgcct tttgttgttg ggtcctggac ctaaacgact catggctgag taggaggatg
661 atccagagaa caactggctt cttcaggccc taccaagaat ggaacaggaa acctctcccc
721 actatggatg attccaaact 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 ttggcaagat gctgtcatct
1081 gctgcgtcca ccttgagagc ttgtaaagat cttggtgcat atgggctaga gatcctaaag
1141 ttgattatga agtggttctt cccgaagaaa gaggaagcaa atgaactggc tatggtaaga
1201 tccatcgagg atgcagtcct ggacctcgag gcaattgaaa acaatcactt aaccatcttg
1261 ctcaaagaca aagacagtct ggcaacctac atgagaaccc ttgatcttga ggaggagaaa
1321 gccaggaaac tctcaaccaa atctgcttca cctgacattg tgggcacaat caacgccctt
1381 ctggcaagga tcgctgctgc acgttctctg gtgcatcgag cgaaggagga actttccagc
1441 agaccaagac ctgtagtgtt gatgatatca ggcagaccag gaatagggaa gacccacctt
1501 gctagggaag tggccaagaa aatcgcagcc tcccttacag gagaccagcg cgtgggcctc
1561 atcccacgca atggtgtcga ccattgggat gcgtacaagg gtgagagggt cgtcctatgg
1621 gatgactatg gaatgagcaa tcccatccac gatgccctca ggttgcaaga actcgctgac
1681 acttgccctc tcaccctaaa ctgtgacagg attgagaaca 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 ggcatcaggt
2041 ctgctccatg 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 ggccctgtac tccatcatcc agattgctgg agctgcattt
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 ttcaggccgt caaggaaaca acgcaaggag
2881 gaaagggctt ctctcggttt ggtcacaggc tctgaaatta gaaaaagaaa tccagatgat
2941 ttcaaaccca aggggaaact atgggctgat gatgacagga atgtggacta caacgagaaa
3001 ctcagttttg aagccccacc aagcatctgg tcgaggatag tcaactttgg ttcaggttgg
3061 ggattctggg tctcccccag tttgttcata acatcaaccc atgtcatacc ccagggcaca
3121 aaggagttct ttggagtccc tatcaaacaa atccaggtac 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 agggtccaac gccaaaagca tggatctggg aaccacacca
3421 ggtgattgtg gctgtcctta catctacaag agaggaaatg actatgtggt cattggggtc
3481 cacacggctg ccgctcgtgg ggggaacact gttatatgtg ccacccaggg aagtgagggg
3541 gaggccatac ttgaaggtgg tgacaataaa gggacatact gtggtgcacc aatcctagga
3601 ccagggaatg ccccaaaact tagcaccaag accaagttct ggagatcgtc cacagcacca
3661 ctcccacctg gtacctacga gccagcctat cttggtggca aggaccctag agtcaagggt
3721 ggcccttcac tgcagcaagt catgagggat caattgaagc cgttcacaga gcctaggggc
3781 aagccaccaa agccaagtgt gctagaagct gccaagaaaa ccatcatcaa tgttcttgag
3841 caaacaattg acccgcctga gaaatggtca ttcgcacaag cttgcgcgtc ccttgataag
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 tggcaaccat gatccgatgt
4141 gctcgagcat tcggaggcct aatggatgaa ctcaaagcgc actgtgtctc acttcccatt
4201 agagttggta tgaatatgaa tgaggatggc cccatcatct tcgagaggca ttccaggtac
4261 acataccact atgatgctga ttactcacga tgggattcaa cacaacagag 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 ctgacatcat acaggctaat
4561 tccctcttct ctttttatgg tgatgatgaa attgttagca cagacataaa attggaccca
4621 gaaaagttga cagcaaaact cagggaatat gggttaaagc caacccgccc tgacaaaact
4681 gaaggacccc ttgtcatctc tgacgacttg aatggcctga ctttcctgcg gagaactgtg
4741 acccgcgacc cagctggttg gtttggaaaa ctggagcaga gttcaatact caggcaaatg
4801 tactggacta ggggtcctaa ccacggggat ccaactgaaa caatgattcc acactctcaa
4861 agacccatac aattgatgtc cctactgggg gaggctgcac ttcacggccc agcattctac
4921 agcaaagtca gcaagttggt cattgcagag ctaaaagagg gtggcatgga tttttacgtg
4981 cccagacaag agccgatgtt cagatggatg aggttctcag atctgagcac gtgggagggc
5041 gatcgcaatc tggctcccag ttttgtgaat gaagatggcg tcgaatgacg ccaccccatc
5101 tgatgggccc gcagccaacc tcgtcccagc ggtcaacaat gaggttatgg ctttggaccc
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 tggttttgag gtgcaggtaa tcctcgcggg
5401 gaacgcgttc accgccggga aaatcatatt tgcagcagtt ccaccaaatt tcccaaccga
5461 agggataagc ccctgccaag tcactatgtt cccccatata ataacagatg ttagacaact
5521 ggaacctgtg ttaatcccct tgcctgatgt taggaataac ttctatcatt ataatcaatc
5581 aaatgaaccc accatcaaat tgatagcaat gttgtacaca ccacttaggg ctaataatgc
5641 tggggacgat gtcttcacag tctcttgtcg agtcctcacg 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 actactcaac tgtctcctgt caacatctgc accttcagag gggatgtcac
5941 tcaaattgga agtactcaaa cttacacaat gaacctggcc tcccaaaatt ggaataatta
6001 tgatccaaca gaagaaatcc cagcccccct gggaacccca gattttgtag gaaggatcca
6061 aggcatgctc acccaaacca caaagagtga tggctcgacc cgtggtcacg tagccacagt
6121 gagcactgga agtgctcact ttactccaaa gttgggcaga gttcaattct ccactgacac
6181 aagcaatgac cttgaagctc gccaaaacac gagattcacc ccagtcggcg tcatccagga
6241 tggtggtacc acccaccgaa atgaacccca acaatgggtg ctcccaaatt attcaggtag
6301 agataatcac aatgtacacc tagcacctgc tgtggccccc acttttccgg gcgagcaact
6361 tcttttcttt aggtccacta tacccggatg cagcgggtac cccaacatgg aattggattg
6421 cctactcccc caggagtggg tgcagtactt ctaccaagaa tcagccccag cacaatctga
6481 tgtggcactg ctgagatttg tgaatccaga cacaagtagg gttttgtttg agtgcaagct
6541 tcataagcaa ggctttgtaa cagtggctca tactggccaa catgatttga ttatccctcc
6601 caatggctat tttagatttg attcctgggt taaccaattc tacacacttg cccccatggg
6661 aaatggaacg gggcgaagac gtgcattata atggctggag ctttctttgc tggattagca
6721 tctgatgtcc ttggctctgg acttagctct ctaatcaatg ctggggctgg gaccattaat
6781 caaaaagttg attttgacaa taatagaaaa ttgcaacaag cttccttcca atatagtagc
6841 aatctacaac aggcttcctt tcaacatgat aaagagatgc tccaagcaca aattgaggcc
6901 accaaaaagt tgcaacagga aatgatgaaa attaaacaga caatgctcct agagggtggg
6961 ttctctgaga cagatgcagc ccgtggggca atcaacgccc ccatgacaaa ggttttggac
7021 tggaacggaa caaggtactg ggctcccgat gctaggatta caacatacaa tgcaggccac
7081 ttttccacca ctcaaccctc gggagcacca ccagggagaa ccaatctcag ggctaccacc
7141 cccgctcgag gctcctccag tacactctca aatgcttcta ctgtcacttc 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 gttttgaact cctggactgg cgctttcaac
7441 acgcgcaggc agcctctctt cgcccacatt caaaagcgag gggagtcacg ggtgtaatgt
7501 gaaaagacaa aattgattat ccttcttttc tttagtgcct
//