Typing tool
|
|
|
|
|
|
Typing tool
|
Complete norovirus genomes
| MF140649 | GII.4 Apeldoorn | |
|
|---|---|---|---|
| GII.P4 New Orleans |
ORF1: 1..5083
ORF2: 5064..6686
ORF3: 6686..7492
LOCUS MF140649 7538 bp RNA linear VRL 24-OCT-2017
DEFINITION Norovirus GII strain
Norovirus/GII/Hu/NL/2010/GII.P4-GII.4/Rotterdam/E7800012_p13_d0
ORF1 gene, partial cds; and ORF2 and ORF3 genes, complete cds.
ACCESSION MF140649
VERSION MF140649.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norovirus norwalkense.
REFERENCE 1 (bases 1 to 7538)
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 7538)
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..7538
/organism="Norovirus GII"
/mol_type="genomic RNA"
/strain="Norovirus/GII/Hu/NL/2010/GII.P4-
GII.4/Rotterdam/E7800012_p13_d0"
/host="Homo sapiens"
/db_xref="taxon:122929"
/geo_loc_name="Netherlands"
/collection_date="22-Dec-2010"
/note="genotype: GII.P4-GII.4"
CDS <1..5083
/codon_start=2
/product="ORF1"
/protein_id="ATN23643.1"
/translation="DASAAAVANSNNDIAKSSSDGVLSSMAVTFKRALGARPKQPPPR
EKPQRPPRPPTPELVKNIPPPPPNGEDEVVVSYSVKDGVSGLPDLSTVRQPEESNTAF
SVPPLSQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAISLAKVEL
APLSLYWRPVYTPQYLIPPDTLKKLSGETFPYTAFDNNCYAFCCWVLDLNDSWLSRRM
IQRTTGFFRPYQDWNRKPLPTMDDSKIKKVANIFLCALSSLFTRPIKDIIGKIRPLNI
LNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVELV
PVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEAN
ELAIVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLSTKSASPD
IVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREVAKRIAA
SLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCPLTLNC
DRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRDFP
GQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLHE
RLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGKQLKDVRTMPELKQA
LKNVSIKKCQIVYSGCTYILESDGKGNVKVDRIQSAAVQTNNELAGALHHLRCARIRY
YVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQDLWSKPQVENTEETTSKDGCPKPKDD
EEFVISSNDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEE
YLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLVTGSEIR
KRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSPSLFITS
THVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVVTLL
IKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCGCPYI
YKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILGPGSAPT
LSTKTKFWRSSTASLPPGTYEPAYLGGKDPRVKGGPSLQQVMREQLKPFTEPRGKPPK
PSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHVRKNDCWNGESFT
GKLADQASKANLMFEEGKNMTPVYTAALKDELVKTDKIYGKIKKRLLWGSDLATMIRC
ARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFERHSRYTYHYDADYSRWDSTQQRA
VLAAALEIMVKFSPEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCTSQWNSI
AHWLLTLCALSEVTNLSPDTIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLREYGLKP
TRPDKTEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHGDPS
ETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQEPMFRWM
RFSDLSTWEGDRNLAPSFVNEDGVE"
CDS 5064..6686
/codon_start=1
/product="ORF2"
/protein_id="ATN23644.1"
/translation="MKMASSDANPSDGSTANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVIHIPGSRNYTMNLASQNWNSYDPTEEIPAPLGTPDFVGKIQGVL
TQTTRTNGSTRGHKATVYTGSADFSPKLGRVQFATDTDNDFETNQNTKFTPVGVIQDG
STTPRNEPQQWVLPSYSGRNIHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL"
CDS 6686..7492
/codon_start=1
/product="ORF3"
/protein_id="ATN23645.1"
/translation="MAGAFFAGLASDVLGSGLGSLISAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMRVKQAMLLEGGFSETDAARGAIN
APMTKTLDWSGTRYWAPDARTTTYNAGRFSTPQPSGAPPGRANLRATVPARGSSSTSS
NSSIATSVYSNQTTSTRLGSTAGSGTSVSSLPSTARTRSWIEDQNRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRKRGESRV"
ORIGIN
1 cgacgcttcc gctgccgctg ttgctaacag caacaacgac atcgcaaaat cttcaagtga
61 cggtgtgctt tctagcatgg ctgtcacttt taaacgagcc ctcggggcgc ggcctaaaca
121 gcctcccccg agggaaaaac cacaaagacc cccacgacca cctactccag aactggtcaa
181 aaatattccc cctcccccac ccaacggaga ggatgaagta gtggtttctt atagtgtcaa
241 agatggtgtt tccggcttgc ctgacctttc caccgtcagg caaccggaag aatctaacac
301 ggccttcagt gtccctccac tcagtcagag ggagaataga gatgctaagg agccacttac
361 tggaacaatt ctggaaatgt gggacgggga aatctaccat tatggcctgt atgtggagcg
421 aggtcttgta ctaggtgtgc acaaaccacc agctgccatc agcctcgcta aggttgagct
481 agcaccactc tccttgtact ggagacctgt gtacactcct cagtacctca tccctccaga
541 cactctcaag aaattatccg gagaaacgtt cccctacaca gcctttgaca acaactgtta
601 tgccttttgt tgctgggtcc tggaccttaa tgactcgtgg ctgagcagga gaatgatcca
661 gagaacaact ggtttcttca ggccctacca agactggaat aggaaacccc ttcccactat
721 ggatgactcc aaaataaaga aggtagctaa catattcctg tgtgctctgt cctcgctgtt
781 caccagaccc ataaaagata taatagggaa gataaggcct cttaacatcc tcaacatcct
841 agcctcatgt gattggactt ttgcaggcat agtggagtcc ctgatactct tggcagaact
901 ctttggagtt ttctggacac ccccagatgt gtctgcgatg attgccccct tacttggtga
961 ctacgagcta caaggacctg aggatcttgc agtggagctc gtccccgtgg tgatgggggg
1021 aattggtttg gtgctaggat tcaccaaaga gaagattggg aaaatgttgt catctgccgc
1081 gtccaccttg agagcttgta aagaccttgg tgcatatggg ctagagatcc tgaagttggt
1141 catgaagtgg ttcttcccga agaaggagga ggcaaatgag ctggctatag tgaggtccat
1201 cgaggatgca gtcctggatc tcgaggcaat tgaaaacaac catatgacca ccttgctcaa
1261 agacaaagac agtctggcaa cctatatgag aacacttgac cttgaggagg agaaagccag
1321 gaaactctca accaagtctg cctcacccga catcgtgggc acaatcaacg ccctcctggc
1381 gaggatcgct gccgcacgtt ctctggtgca tcgggcgaag gaggagcttt ccagcagacc
1441 aagacctgtg gtgttgatga tatcaggcag gccaggaata gggaagaccc acctcgctag
1501 ggaagtggct aagagaatcg cagcctccct tacaggagac cagcgtgtgg gcctcatccc
1561 acgcaatggc gtcgaccatt gggatgcgta caagggggag agggtcgtcc tgtgggacga
1621 ttatggaatg agcaacccta ttcacgacgc cctcaggctg caagaactcg ctgatacatg
1681 ccccctcact ctaaactgtg acaggattga aaataaagga aaggtctttg acagcgatgt
1741 catcattatc accactaatc tggccaaccc agcaccactg gactatgtca actttgaagc
1801 atgctcgagg cgcatcgact tcctcgtgta tgcagaagcc cctgaagtcg 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 ttgaattaca gggcccagct ctcaccacct tcaatttcga
2101 tcgcaataaa gtgcttgcct tcaggcagct tgctgctgaa aataaatatg gattgatgga
2161 cacaatgaga gttgggaaac agctcaagga tgtcagaacc atgccagaac tcaaacaagc
2221 actcaagaat gtctcaatca agaagtgcca aatagtgtat agtggttgca cctacatact
2281 tgagtctgat ggcaagggca atgtgaaagt tgacagaatc caaagcgccg ccgtgcagac
2341 caacaatgag ctggctggtg ccctgcacca tttgaggtgc gccagaatca gatactatgt
2401 caagtgtgtc caggaggccc tgtactccat catacaaatt gctggggctg cattcgtcac
2461 cacgcgcatt gccaagcgca tgaacataca agacctatgg tccaagccac aagtggaaaa
2521 cacagaggag accaccagca aggacgggtg cccaaaacct aaggatgatg aggagtttgt
2581 catttcatcc aacgacatca aaactgaggg taagaagggg aagaacaaga ctggccgcgg
2641 caagaagcac acagcatttt caagcaaagg tctcagtgat gaagagtacg atgagtacaa
2701 gaggattaga gaagaaagga atggcaagta ctccatagaa gagtaccttc aagacaggga
2761 caaatactat gaggaggtgg ccattgccag ggcgactgag gaagacttct gtgaagagga
2821 ggaggccaag atccggcaaa ggatctttag gccaacaagg aaacaacgca aggaggaaag
2881 agcttctctc ggtctggtca caggctctga aattaggaaa agaaacccag atgacttcaa
2941 gcccaagggg aagttgtggg ctgacgatga caggagtgtg gactacaatg agaaactcag
3001 ttttgaggcc ccaccaagca tctggtcgag aatagtcaac tttggttcag gctggggatt
3061 ctgggtctcc cccagcctgt tcataacatc aacccatgtc ataccccaag gcgcaaagga
3121 gttctttgga gtccccatca aacaaataca ggtgcacaag tcaggcgagt tctgtcgctt
3181 gagattccca aaaccaatca ggactgatgt gacgggcatg atcttagaag aaggcgcacc
3241 tgagggcacc gtggtcacac tactcatcaa aaggtccact ggggaactca tgcccctagc
3301 agctaggatg gggacccatg cgaccatgaa gatccaaggg cgcactgttg gaggccagat
3361 gggcatgctt ctgacaggat ccaacgccaa gagcatggac ctgggtacta caccaggtga
3421 ttgtggctgc ccctatatct acaagagagg taatgactat gtggtcattg gagtccacac
3481 ggctgccgca cgtgggggaa acactgtcat atgtgccacc caggggagtg aaggagaggc
3541 cacacttgaa ggtggtgaca acaaggggac atactgtggt gcaccaatcc taggcccagg
3601 gagtgcccca acacttagca ccaagaccaa attctggaga tcgtccacag catcactccc
3661 acctggcacc tatgagccag cctatcttgg tggcaaggac cctagagtca agggtggccc
3721 ttcactgcag caagtcatga gggaacagtt gaagccattc acagagccaa ggggtaagcc
3781 accaaaacca agtgtattag aagctgccaa gaagaccatc atcaatgtcc ttgagcaaac
3841 aattgatcca cctgagaaat ggtcgttcgc acaagcttgc gcgtcccttg acaagaccac
3901 ttccagtggt catccgcacc atgtgcggaa aaacgactgc tggaacggag agtccttcac
3961 aggcaagctg gcagaccagg cttctaaggc caacctgatg tttgaagaag ggaagaacat
4021 gaccccagtc tacacagctg cactcaagga tgagttagtc aaaactgaca aaatttatgg
4081 taagatcaag aagaggcttc tctggggctc ggacttggcg accatgatcc ggtgtgctcg
4141 agcattcgga ggcctaatgg atgaactcaa agcacactgt gtcacacttc ccattagagt
4201 tggcatgaat atgaatgagg atggccccat catcttcgag aggcattcca gatacacata
4261 tcactatgat gctgattact ctcgatggga ctcaacacaa cagagagccg tgctggcagc
4321 agctttagaa atcatggtta aattctcccc agaaccacat ttggctcagg tagtcgcgga
4381 agaccttctt tctcctagcg tggtggacgt gggcgacttc acaatatcaa tcaacgaggg
4441 tcttccctct ggggtgccct gcacctccca atggaactcc atcgcccact ggcttctcac
4501 tctctgtgcg ctctctgaag tcacgaacct atcccctgat accatacagg ctaactccct
4561 cttctctttt tatggtgatg atgaaattgt tagcacagac ataaaattgg acccagaaaa
4621 attgacagcg aagctcagag aatatgggtt aaaaccaacc cgccctgaca aaactgaagg
4681 gccccttgtc atctctgaag acctgaatgg cctaactttc ctgcggagaa ctgtgacccg
4741 cgacccggct ggttggtttg gaaaactgga acagagttca atactcaggc aaatgtactg
4801 gactaggggt cccaaccatg gagacccatc tgaaacaatg attccacact cccaaaggcc
4861 catacaattg atgtccctac tgggggaggc cgctctccac ggcccagcat tttacagcaa
4921 aatcagcaaa ttggtcattg cagagctaaa agaaggtggc atggattttt acgtgcccag
4981 acaagagcca atgttcagat ggatgagatt ctcagatctg agcacgtggg agggcgatcg
5041 caatctggct cccagttttg tgaatgaaga tggcgtcgag tgacgctaac ccatctgatg
5101 ggtccacagc caacctcgtc ccagaggtca acaatgaggt tatggctttg gagcccgtag
5161 ttggtgccgc tattgcggca cctgtagcgg gccaacaaaa tgtaattgac ccctggatta
5221 gaaacaattt tgtgcaagcc cctggtggag agttcacagt atcccctaga aacgctccag
5281 gtgaaatact atggagcgcg cccttaggtc ctgatttgaa tccctacctt tcccatttgg
5341 ccagaatgta caatggttat gcaggtggtt ttgaagtgca ggtaatcctc gcggggaacg
5401 cgttcaccgc cgggaaaatc atatttgcag cagtcccacc aaatttccca actgaaggtt
5461 tgagccccag ccaggtcact atgttccccc acataatagt agatgttagg caattggaac
5521 ctgtgttgat ccccttaccc gatgttagga ataatttcta ccactataat caatcaaatg
5581 accccaccat caaattgata gcaatgttgt acacaccact tagggctaat aatgccgggg
5641 atgatgtctt cacagtttct tgtcgagttc tcacgagacc atcccccgat tttgatttca
5701 tatttttggt gccacccaca gttgaatcaa gaactaaacc attctctgtc ccagttttaa
5761 ctgttgagga gatgaccaat tcaaggttcc ccattccttt ggaaaagttg tttacgggcc
5821 ccagtagtgc ctttgttgtt caaccacaaa acggcaggtg cacgactgat ggcgtgctcc
5881 taggtactac ccaactgtcc cctgtcaaca tctgcacctt cagaggggat gtcatccata
5941 ttccaggcag tcgtaactac acaatgaatt tggcctccca aaattggaat agttacgatc
6001 caacagaaga aatcccagcc cctctaggaa ctccagattt cgtggggaag attcaaggtg
6061 tgctcaccca aaccacaaga acaaatggct cgactcgcgg ccacaaagcc acagtgtata
6121 ctgggagcgc cgacttttct ccaaaactgg gtagagttca atttgccact gacacagaca
6181 atgattttga aactaaccaa aacacaaagt ttaccccagt cggtgttatc caggatggta
6241 gtactacccc ccgaaatgaa ccccagcaat gggtgctccc aagttactca ggcagaaaca
6301 ttcataatgt gcacctggcc cccgctgtgg cccccacttt cccgggcgag cagctcctct
6361 tcttcagatc tactatgccc ggatgcagcg ggtaccccaa catggatttg gactgcctgc
6421 tcccccagga atgggtgcag tatttctacc aggaggcagc cccagcacaa tctgacgtgg
6481 ctctgttaag atttgtgaat ccagacacag gtagggtttt gtttgagtgt aagctccata
6541 aatcaggcta tgttacagtg gctcacactg gccaacatga tttggtcatc ccccccaatg
6601 gttattttag atttgattcc tgggtcaacc agttctacac acttgccccc atgggaaatg
6661 ggacggggcg tagacgtgca ttataatggc tggagctttc tttgctggat tggcatctga
6721 cgtccttggc tctggacttg gttccctaat cagtgctggg gctggggcca tcaatcaaaa
6781 agttgaattt gaaaacaaca gaaaattgca acaagcttcc ttccaattta gtagcaatct
6841 acaacaggct tcctttcaac atgacaagga gatgctccaa gcacaaattg aggccaccaa
6901 aaagttgcaa caggaaatga tgagagttaa acaagcaatg ctcctagagg gtggattctc
6961 tgagacagat gcagcccgtg gggcaatcaa cgcccccatg acaaaaactt tggactggag
7021 cgggacaagg tactgggctc ccgatgctag gactacaaca tataatgcag gtcgcttttc
7081 cacccctcaa ccctcggggg caccaccagg aagagctaat cttagggcta ctgtccccgc
7141 ccggggttcc tccagcacgt cttctaattc ttctattgct acttctgtgt attcaaatca
7201 aaccacctca acgagacttg gttctacagc tggttctggt accagtgtct cgagcctccc
7261 gtcaactgca aggactagga gctggattga ggatcaaaat aggaatttgt cacctttcat
7321 gaggggggcc cacaacatct cgtttgtcac cccaccatct agcagatcct ctagccaagg
7381 cacagtctca accgtgccca aagaagtttt ggactcctgg actggcgctt tcaacacgcg
7441 caggcagcct ctcttcgccc acattcgcaa gcgaggggag tcacgggtgt aatgtgaaaa
7501 gacaaaattg attatctttc ttttctttag tgtctttt
//