Typing tool
|
|
|
|
|
|
Typing tool
|
Complete norovirus genomes
| MF140644 | GII.4 Sydney | |
|
|---|---|---|---|
| GII.P4 New Orleans |
ORF1: 1..5088
ORF2: 5069..6691
ORF3: 6691..7497
LOCUS MF140644 7520 bp RNA linear VRL 24-OCT-2017
DEFINITION Norovirus GII strain
Norovirus/GII/Hu/NL/2014/GII.P4-GII.4/Rotterdam/E7800018_p11_d413
ORF1 gene, partial cds; and ORF2 and ORF3 genes, complete cds.
ACCESSION MF140644
VERSION MF140644.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7520)
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 7520)
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..7520
/organism="Norovirus GII"
/mol_type="genomic RNA"
/strain="Norovirus/GII/Hu/NL/2014/GII.P4-
GII.4/Rotterdam/E7800018_p11_d413"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="Netherlands"
/collection_date="10-Mar-2014"
/note="genotype: GII.P4-GII.4"
CDS <1..5088
/codon_start=1
/product="ORF1"
/protein_id="ATN23628.1"
/translation="SHDASAAAVANSNNDTAKSSSDGVLSSMAVTFKRALGARPKQPP
PREKPQRPPRPPTPELVKNIPPPPPNGEDEIVVSYSVKDGVSGLPDLSTVRQPEESNT
AFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVDRGLVLGVHKPPAAISLAKV
ELAPLSLYWRPVYTPQYLISPDTLKRLSGETFPYTAFDNNCYAFCCWVLDLNDSWLSR
RMIQRTTGFFRPYQDWNRKPLPTMDDSKIKKVANIFLCALSSLFTRPIKDIIGKIRPL
NILNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVE
LVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEE
ANELAMVRSIEDAVLDLEAIENNHLTTLLKDKDSLATYMRTLDLEEEKARKLSTKSAS
PDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREVAKRI
AASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCPLTL
NCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPDVEKAKRD
FPGQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLL
HERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGKQLKDVKTMPELK
QALKNVSIKKCQIVYSGCTYMLESDGKGNVKVDRIQSAAVQTNNELAGALHHLRCARI
RYYVKCVQEALYSILQIAGAAFVTTRIAKRMNIQDLWSKPQVENTEETTSKDGCPKPK
DDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSI
EEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERVSLGLVTGSE
IRKRNPEDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSPSLFI
TSTHVIPQGAKEFFGVPIKQIQVYKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVVS
LLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKGMDLGTTPGDCGCP
YIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILGPGSA
PTLSTKTKFWRSSTASLPPGTYEPAYLGGKDPRVKGGPSLQQVMREQLKPFTEPRGKP
PKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCWNGET
FTGKLADQASKANLMFEEGKNMTPVYTAALKDELVKTDKIYGKIKKRLLWGSDLATMI
RCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFERHSRYTYHYDADYSRWDSTQQ
RAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCTSQWN
SIAHWLLTLCALSEVTNLSPDTIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLREYGL
KPTRPDKTEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHGD
PSETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQEPMFR
WMRFSDLSTWEGDRNLAPSFVNEDGVE"
CDS 5069..6691
/codon_start=1
/product="ORF2"
/protein_id="ATN23629.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKVIFAAVPPNFPTEGLSPSQVTMFPHIVVDVRQLEPVLIPLPD
VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFIVQPQNGRCTTDGVLLGTT
QLSPVNICTFKGSVTHITGSHHYTMNLASQNWNNYDPTEEIPAPLGAPDFVGKIQGVL
TQTTRSNGSTRGHKATVYTGSADFTPKLGRIQFETDTNNDFEANQNTKFTPVGVIQDG
NTTHRNEPQQWKLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGAGRRRVV"
CDS 6691..7497
/codon_start=1
/product="ORF3"
/protein_id="ATN23630.1"
/translation="MAGAFFAGLASDVLGSGLSSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
APMTRALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALSGRANLRDAAPARGSSSKSS
NSSTATSVYSNQTTSTRLGSTAGSGTSVSSIPSTARTRSWVEDQSRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTHRQPLFAYIRSRGESRV"
ORIGIN
1 tctcacgacg cttccgctgc cgctgttgct aacagcaaca acgacaccgc aaaatcttca
61 agtgacggag tgctttctag catggctgtc acttttaaac gagccctcgg ggcgcggcct
121 aaacagcctc ccccgaggga aaaaccacaa agacccccac gaccacccac cccagaactg
181 gttaaaaaca ttccccctcc cccacccaac ggagaggatg aaatagtggt ttcttatagt
241 gtcaaagatg gtgtttccgg tttgcctgac ctttccaccg tcaggcaacc ggaagaatcc
301 aacacggcct tcagtgtccc tccactcaat cagagggaga atagagatgc taaggaacca
361 ctcactggaa caattctgga aatgtgggac ggggaaatct accattatgg cctgtatgtg
421 gatcgaggtc ttgtactagg cgtgcacaaa ccaccagctg ccatcagcct cgctaaggtt
481 gagctagcac cactctcctt gtactggaga cctgtgtaca ctcctcagta cctcatctcc
541 ccagacactc tcaagagatt gtccggagaa acgttcccct acacagcctt tgacaacaac
601 tgctatgcct tttgttgctg ggtcctggac ctaaatgact cgtggctgag caggagaatg
661 atccagagaa cgactggttt cttcaggccc taccaagact ggaataggaa accccttccc
721 actatggatg actccaaaat aaaaaaggta gctaacatat ttctgtgtgc tctgtcctcg
781 ctattcacca gacccataaa agatataata gggaagataa ggcctcttaa catcctcaac
841 atcttagcct catgtgattg gacctttgcg ggcatagtgg agtccctgat actcttggca
901 gaactctttg gagttttctg gacaccccca gatgtgtctg cgatgattgc ccccttactt
961 ggtgactacg agctacaagg acctgaggac cttgcagtgg aactcgtccc cgtggtgatg
1021 gggggaattg gtttggtgct aggattcacc aaagagaaga ttgggaagat gttgtcatct
1081 gctgcgtcca ccttaagagc ttgcaaagac cttggtgcat atgggctaga gatcctaaag
1141 ttagtcatga agtggttctt cccgaaaaag gaggaggcaa atgagctggc tatggtgagg
1201 tccatcgagg atgcagttct ggatctcgag gcaattgaaa acaatcattt gaccaccttg
1261 cttaaagata aagacagtct ggcaacctac atgagaacac ttgaccttga agaggagaaa
1321 gccaggaaac tctcaaccaa gtctgcctca cccgacatcg tgggcacaat caacgccctc
1381 ctggcgagaa tcgctgccgc acgttctctg gtgcatcgag cgaaggagga gctttccagc
1441 agaccaagac ctgtggtgtt gatgatatca ggcaggccag gaatagggaa gacccacctc
1501 gctagggaag tggctaagag aatcgcagcc tcccttacag gagaccagcg tgttggcctc
1561 atcccacgca atggcgtcga ccactgggat gcgtacaagg gggagagggt cgtcctatgg
1621 gacgattatg gaatgagcaa ccctattcac gatgccctca gactgcaaga actcgctgac
1681 acttgccccc tcactctgaa ctgtgacagg attgaaaata aaggaaaggt ctttgacagc
1741 gatgtcatca ttatcaccac caatctggcc aacccagcac cactggacta tgtcaacttt
1801 gaagcatgct cgaggcgcat tgacttcctc gtgtatgcag aagctcctga tgtcgaaaag
1861 gcgaagcgtg acttcccagg ccaacctgac atgtggaaga acgctttcag ttctgacttc
1921 tcacacataa aactagcact ggccccacag ggtggtttcg acaagaacgg gaacacccca
1981 cacggaaagg gcgtcatgaa gactctcacc actggctccc ttattgcccg ggcatcaggg
2041 ctgctccatg agaggttaga tgaatttgaa ctgcagggtc cagctctcac caccttcaat
2101 ttcgatcgca ataaagtgct tgcctttagg cagcttgctg ctgaaaataa atatggattg
2161 atggacacaa tgagggttgg gaaacagctc aaggatgtca aaaccatgcc agaactcaaa
2221 caagcactca agaatgtctc aatcaagaag tgtcaaatag tgtatagtgg ttgcacctac
2281 atgcttgagt ctgatggcaa gggcaatgtg aaagttgaca ggatccagag cgccgccgtg
2341 cagaccaaca atgagctggc tggcgccctg caccatttga ggtgcgccag aatcagatac
2401 tatgtcaagt gtgtccagga agccctgtat tccatcctcc aaattgctgg ggctgcattt
2461 gtcaccacgc gcattgccaa gcgcatgaac atacaagacc tatggtccaa gccacaagtg
2521 gaaaacacag aggagactac cagcaaggac ggatgcccaa aacctaagga tgatgaggag
2581 tttgtcattt catccgacga catcaaaact gagggcaaga aagggaagaa caagactggc
2641 cgtggcaaga agcacacggc attttcaagc aaaggcctca gtgatgaaga gtacgatgaa
2701 tacaagagga ttagagaaga aaggaatggc aagtactcta tagaagagta ccttcaggac
2761 agggacaaat attatgagga ggtggccatt gccagagcga ctgaggaaga cttctgtgaa
2821 gaggaggaag ccaagatccg gcaaaggatc tttaggccga caaggaaaca acgcaaggag
2881 gaaagagtct ctctcggctt ggtcacaggt tctgaaatta ggaaaagaaa cccagaagac
2941 ttcaaaccca aggggaaatt atgggctgac gatgacagga gtgtggacta caatgagaaa
3001 ctcagttttg aggccccacc aagcatttgg tcgagaatag tcaactttgg ttcaggctgg
3061 ggattctggg tctcccccag cttgttcata acatcaaccc atgttatacc ccagggcgca
3121 aaggagttct ttggagtccc catcaaacaa atacaggtat acaagtcagg cgagttctgt
3181 cgcttgagat tccctaaacc aatcaggact gatgtgacgg gcatgatctt agaagaaggc
3241 gcacctgagg gcaccgtggt ctcactactc atcaaaaggt ccactgggga acttatgccc
3301 ctagcagcta ggatggggac ccatgcgacc atgaagatcc aagggcgcac tgttgggggc
3361 cagatgggca tgcttctgac aggatccaac gccaagggta tggacctggg tactacacca
3421 ggtgattgtg gctgccccta tatctacaag agaggtaatg actatgtggt cattggagtc
3481 cacacggctg ccgcacgtgg ggggaacact gtcatatgtg ccacccaggg gagtgaagga
3541 gaggctacac ttgagggtgg tgacaacaag gggacatact gtggtgcacc aatcctaggc
3601 ccagggagtg ccccaacact tagcaccaag actaaattct ggagatcgtc cacagcatca
3661 ctcccacctg gcacctatga accagcctat cttggtggta aggaccctag agtcaagggt
3721 ggcccttcac tgcagcaagt catgagggaa cagttgaagc cattcacaga gcccaggggc
3781 aagccaccaa aaccaagtgt gttagaagct gccaagaaga ccatcatcaa tgtccttgag
3841 caaacaattg atccacctga gaaatggtcg ttcgcacaag cttgcgcgtc ccttgacaag
3901 accacttcca gtggtcatcc gcaccacatg cggaaaaacg actgctggaa cggggagacc
3961 ttcacaggca agctggcaga ccaggcttcc aaggccaacc tgatgtttga agaagggaag
4021 aacatgaccc cagtctacac agctgcgctc aaggatgagt tagttaaaac tgacaaaatt
4081 tatggcaaga tcaagaagag gcttctttgg ggctcggact tggcgaccat gatccggtgt
4141 gctcgagcat tcggaggctt aatggatgaa ctcaaagcgc actgtgtcac acttcccatt
4201 agagttggca tgaatatgaa tgaggatggc cccatcatct tcgagaggca ttccaggtac
4261 acgtaccact atgatgctga ttactctcga tgggattcaa cacaacagag agccgtgttg
4321 gcagcagctc tagaaatcat ggttaaattc tccccagaac cacatttggc tcaggtagtc
4381 gcggaagacc ttctttctcc tagcgtggtg gacgtgggcg acttcacaat atcaatcaac
4441 gagggtctcc cctctggggt gccctgcacc tcccaatgga actccatcgc ccactggctt
4501 ctcactctct gtgcgctctc cgaagtcaca aatctgtccc ctgataccat acaggccaat
4561 tctctcttct ctttttatgg tgatgatgaa attgttagca cagacataaa attggaccca
4621 gagaaattga cagcaaagct cagagaatat gggttaaaac caacccgccc tgacaaaact
4681 gaaggacccc ttgtcatctc tgaagacctg aatggcctaa ctttcctgcg gagaactgtg
4741 acccgcgacc cagctggttg gtttggaaaa ctggagcaga gttcaatact caggcaaatg
4801 tactggacta ggggtcccaa ccatggagac ccatctgaaa caatgattcc acactcccaa
4861 agacccatac aattgatgtc cctactgggg gaggccgccc tccacggccc agcattttac
4921 agtaaaatca gcaaattggt cattgcagag ctaaaagaag gtggtatgga tttttacgtg
4981 cccagacaag agccaatgtt cagatggatg agattctcag atctgagcac gtgggagggc
5041 gatcgcaatc tggctcccag ttttgtgaat gaagatggcg tcgagtgacg ccaacccatc
5101 tgatgggtcc gcagccaacc tcgtcccaga ggtcaacaat gaggttatgg ctctggagcc
5161 cgttgttggt gccgccattg cggcacctgt agcgggccaa caaaatgtaa ttgacccctg
5221 gattagaaac aattttgtac aagcccctgg tggagagttt acagtgtccc ctagaaacgc
5281 tccaggtgaa atactatgga gcgcgccctt aggccctgac ctaaatccct acctatccca
5341 tttggccaga atgtataatg gttatgcagg tggttttgaa gtgcaggtaa ttctcgcggg
5401 gaacgcgttc accgccggga aggtcatatt tgcagcagtc ccaccaaatt ttccaactga
5461 aggcttgagc cccagccagg tcactatgtt cccccatata gtagtagatg ttaggcaact
5521 agaacctgtg ttgattcccc tacccgatgt taggaataat ttctatcatt acaatcaatc
5581 aaatgacccc accattaagt tgatagcaat gctgtataca ccacttaggg ctaataatgc
5641 tggggacgat gtcttcacag tttcttgccg agttctcacg agaccatccc ccgattttga
5701 ttttatattt ctagtgccac ccacagttga gtctagaact aaaccattct ctgtcccagt
5761 tttaactgtt gaggagatga ccaattcaag attccccatt cctttggaaa agttgttcac
5821 gggtcccagc agtgccttta ttgttcaacc acaaaacggt aggtgcacga ctgatggcgt
5881 gctcctaggc accacccaat tgtctcctgt caacatctgc accttcaaag ggagtgtcac
5941 ccacatcaca ggtagtcatc actacacaat gaatttggct tctcaaaatt ggaacaatta
6001 tgacccaaca gaagaaatcc cagctcctct aggagctcca gattttgtgg ggaagattca
6061 aggcgtgctc acccaaacca caaggtcgaa tggctcaaca cgcggccaca aagccacagt
6121 gtacactggg agtgcagact ttactccaaa actgggcaga attcaatttg aaactgacac
6181 aaacaatgat tttgaagcta accaaaacac aaagttcacc ccagtcggtg tcatccaaga
6241 tggtaacacc acccaccgaa atgaacccca acagtggaag ctcccaagtt actcaggcag
6301 aaatactcat aatgttcatc tggcccccgc tgtagccccc acttttccgg gtgaacaact
6361 tctcttcttt agatccacca tgcccggatg tagcgggtac cccaatatgg atttggactg
6421 tctgctcccc caggaatggg tgcagtactt ctaccaagag gcagccccag cacaatctga
6481 tgtggctctg ctaagatttg tgaatccaga cacaggtagg gttttgtttg agtgtaagct
6541 ccataaatca ggctatgtta cagtggctca cactggccaa catgatttgg ttatcccccc
6601 caatggttat tttaggtttg attcctgggt caaccagttc tacacgcttg cccccatggg
6661 aaatggagcg gggcgtagac gtgtagtata atggctggag ctttctttgc tggattagca
6721 tctgatgtcc ttggctctgg acttagttcc cttatcaatg ctggggctgg ggccatcaac
6781 caaaaagttg agtttgaaaa taacagaaaa ttgcaacaag catccttcca atttagcagc
6841 aatctacaac aggcttcctt tcaacatgat aaagaaatgc tccaagcaca aattgaggcc
6901 accaaaaagc tacaacagga aatgatgaaa gttaagcagg caatgctcct agagggtggg
6961 ttctctgaga cagatgcagc ccgcggggca atcaacgccc ctatgacaag agctttggac
7021 tggagcggga caaggtactg ggctcccgat gctaggacta caacatacaa tgcaggccgc
7081 ttttccaccc ctcaaccatc gggggcactg tcaggaagag ccaatcttag ggatgctgcc
7141 cctgctcggg gttcctccag taaatcttct aactcttcta ctgctacttc tgtgtactca
7201 aatcaaacca cttcaacgag acttggttct acagctggtt ctggtaccag tgtctcgagc
7261 atcccgtcaa ctgcaaggac taggagctgg gttgaggatc aaagtaggaa tttgtctccc
7321 ttcatgaggg gggcccacaa catatcgttt gtcaccccac catctagcag atcctctagc
7381 caaggcacag tctcaaccgt gcctaaagag gttttggact cctggactgg cgctttcaac
7441 acgcacaggc agcctctctt cgcttacatt cgtagtcgag gggagtcacg ggtgtaatgt
7501 gaaaagacaa aattgattat
//