Typing tool
|
|
|
|
|
|
Typing tool
|
Complete norovirus genomes
| MF140669 | GII.4 New Orleans | |
|
|---|---|---|---|
| GII.P4 New Orleans |
ORF1: 1..5088
ORF2: 5069..6691
ORF3: 6691..7497
LOCUS MF140669 7523 bp RNA linear VRL 24-OCT-2017
DEFINITION Norovirus GII strain
Norovirus/GII/Hu/NL/2012/GII.P4-GII.4/Rotterdam/E1300296_p2_d0 ORF1
gene, partial cds; and ORF2 and ORF3 genes, complete cds.
ACCESSION MF140669
VERSION MF140669.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7523)
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 7523)
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..7523
/organism="Norovirus GII"
/mol_type="genomic RNA"
/strain="Norovirus/GII/Hu/NL/2012/GII.P4-
GII.4/Rotterdam/E1300296_p2_d0"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="Netherlands"
/collection_date="06-Mar-2012"
/note="genotype: GII.P4-GII.4"
CDS <1..5088
/codon_start=1
/product="ORF1"
/protein_id="ATN23703.1"
/translation="SNDASAAAVANSNNDTAKSSSDGVLSSMAVTFKRALGARPKQPP
PREKPQRPPRPPTPELVKNIPPPPPNGEDEIVVSYSVKGGVSGLPDLSTVRQPEESNT
AFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAISLAKV
ELAPLSLYWRPVYTPQYLISPDTLKKLSGETFPYTAFDNNCYAFCCWVLDLNDSWLSR
RMIQRTTGFFRPYQDWNKKPLPTMDDSKIKKVANIFLCALSSLFTRPIKDIIGKIRPL
NILNILASCDWTFAGIVESLILLAELFGVLWTPPDVSAMIAPLLGDYELQGPEDLAVE
LVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEE
ANELAIVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLSTKSAS
PDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREVAKRI
AASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCPLTL
NCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRD
FPGQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLL
HERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGKQLKDVRTMPELK
QALKNVSIKKCQIVYSGCTYILESDGKGNVKVDRIQSAAVQTNNELAGALHHLRCARI
RYYVKCVQEALYSIIQIAGAAFVTTRIVKRMNIQDLWSKPQVENTEETTSKDGCPKPK
DDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSI
EEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLVTGSE
IRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSPSLFI
TSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVVT
LLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCGCP
YIYKRGNDYVVIGVHTAAARGGNTVICATQGGEGEATLEGGDNKGTYCGAPILGPGSA
PTLSTKTKFWRSSTASLPPGTYEPAYLGGKDPRVKGGPSLQQVMREQLKPFTEPRGKP
PKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGYPHHVRKNDCWNGES
FTGKLADQASKANLMFEEGKNMTPVYTAALKDELVKTDKIYGKIKKRLLWGSDLATMI
RCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFERHSRYTYHYDADYSRWDSTQQ
RAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCTSQWN
SIAHWLLTLCALSEVTNLSPDTIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLREYGL
KPTRPDKTEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHGD
PSETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQEPMFR
WMRFSDLSTWEGDRNLAPSFVNEDGVE"
CDS 5069..6691
/codon_start=1
/product="ORF2"
/protein_id="ATN23704.1"
/translation="MKMASSDANPSDGSTANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHTPGSHNYTMNLASQNWNSYDPTEEIPAPLGTPDFVGKIQGVL
TQTTRTNGSTRGHKATVYTGSADFSPKLGRVQFATDTDNDFETNQNTKFTPVGVIQDG
STTPRNEPQQWVLPSYSGRNIHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL"
CDS 6691..7497
/codon_start=1
/product="ORF3"
/protein_id="ATN23705.1"
/translation="MAGAFFAGLASDVLGSGLSSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMRVKQAMLLEGGFSETDAARGAIN
APMTKTLDWSGTRYWAPDARTTTYSAGRFSTPQPSGVLPGRANLRAIVPARGSSSTSS
NSSFATSVYSNQTTSTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRKRGESRV"
ORIGIN
1 tctaacgacg cttccgctgc cgctgttgct aacagcaaca acgacaccgc aaaatcttca
61 agtgacggag tgctttctag catggctgtc acttttaaac gagccctcgg ggcgcggcct
121 aaacaacctc ccccgaggga aaaaccacaa agacccccac gaccacctac tccagaactg
181 gtcaaaaata ttccccctcc cccacccaac ggggaggatg aaatagtggt ttcttatagt
241 gtcaaaggtg gtgtttccgg cttgcctgac ctttccaccg tcaggcaacc ggaagaatct
301 aacacggcct tcagtgtccc tccactcaac cagagggaga atagagatgc taaggagcca
361 ctcactggaa caattctgga aatgtgggat ggggaaatct accattatgg cctgtatgtg
421 gaacgaggtc ttgtactagg tgtgcacaaa ccaccagctg ccatcagcct cgctaaggtt
481 gagctagcac cactctcctt gtactggagg cctgtgtaca ctcctcagta cctcatctct
541 ccagacactc tcaagaaatt atccggagaa acgttcccct acacagcctt tgacaacaac
601 tgttatgcct tttgttgctg ggtcctggac ctaaatgact cgtggctgag caggagaatg
661 atccagagaa caactggttt cttcaggccc taccaagact ggaataagaa accccttccc
721 accatggatg actccaaaat aaagaaggta gccaacatat tcctgtgtgc tctgtcctcg
781 ctgttcacca gacccataaa agacataata gggaagataa ggcctctcaa catcctcaac
841 atcttagcct catgtgattg gacttttgca ggcatagtgg agtccctgat actcttggca
901 gaactctttg gagttctctg gacaccccca gatgtgtctg cgatgattgc ccccttactt
961 ggtgactacg agctacaagg acctgaggac cttgcagtgg agctcgtccc cgtggtgatg
1021 gggggaattg gtttggtgct aggattcacc aaagagaaga ttgggaaaat gttgtcatct
1081 gctgcgtcca ccctgagagc ttgtaaagac cttggtgcat atgggctaga gatcctaaag
1141 ttggtcatga aatggttctt cccgaagaag gaggaggcaa atgagctggc tatagtgagg
1201 tctatcgagg atgcagttct ggatctcgag gcaattgaaa acaaccatat gaccaccttg
1261 ctcaaagaca aagacagtct ggcaacctat atgagaacac ttgaccttga ggaggagaaa
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 tgtaggcctc
1561 atcccacgca atggcgtcga ccattgggat gcgtacaagg gggagagggt cgtcctatgg
1621 gacgattatg gaatgagcaa ccctattcac gacgccctca ggctgcaaga acttgctgac
1681 acttgccccc tcactctgaa ctgtgacagg atcgaaaaca aaggaaaggt ctttgacagc
1741 gatgtcatca ttatcactac caatctggct aacccagcac cactggatta tgtcaatttt
1801 gaagcatgct cgaggcgcat cgacttcctc gtgtatgcag aagcccctga agtcgaaaag
1861 gcgaagcgtg acttcccagg ccagcctgac atgtggaaga acgccttcag ttctgatttc
1921 tcacacataa aactagcact ggccccacag ggtggtttcg acaagaacgg gaatacccca
1981 cacggaaaag gcgtcatgaa gactctcacc actggctccc ttatcgcccg ggcatcaggg
2041 ctactccatg agaggttaga tgaatttgaa ctacagggcc cagctctcac caccttcaat
2101 ttcgatcgca ataaagtgct tgcctttaga cagcttgctg ctgaaaataa atatggattg
2161 atggacacaa tgagagttgg gaaacagctc aaggatgtca gaaccatgcc agaactcaaa
2221 caagcactca aaaatgtctc aatcaagaaa tgtcaaatag tgtatagtgg ttgcacctac
2281 atacttgagt ctgatggcaa gggcaatgtg aaagttgaca gaatccaaag cgccgccgtg
2341 cagaccaaca atgagctggc tggtgccctg caccatttga ggtgcgccag aatcagatat
2401 tatgtcaagt gtgtccagga ggccctgtat tccatcattc aaattgctgg ggctgcattt
2461 gtcaccacgc gcattgtcaa gcgcatgaac atacaagacc tatggtccaa gccacaagtg
2521 gaaaacacag aggagactac cagcaaggac gggtgtccaa aacctaagga tgatgaggag
2581 tttgtcattt catccgacga catcaaaact gagggtaaga aagggaagaa caagactggt
2641 cgcggcaaga agcacacagc attttcaagc aaaggcctca gtgatgaaga gtacgatgag
2701 tacaagagga ttagagaaga aaggaatggc aagtactcca tagaagagta ccttcaggac
2761 agggacaaat actatgagga ggtggccatt gccagggcga ctgaggaaga cttctgtgaa
2821 gaggaagagg ccaagatccg gcaaaggatc tttaggccaa caaggaaaca acgcaaggag
2881 gaaagagcct ctctcggtct ggtcacaggc tctgaaatta ggaaaagaaa cccagatgac
2941 ttcaaaccca aggggaaatt gtgggctgac gatgacagaa gtgtggacta caatgagaaa
3001 ctcagttttg aggccccacc aagcatctgg tcgagaatag tcaactttgg ttcaggctgg
3061 ggattctggg tctcccccag tctgtttata acatcaaccc atgtcatacc ccagggtgca
3121 aaggagttct ttggagtccc catcaaacaa atacaggtgc acaagtcagg cgagttctgt
3181 cgcttgagat tcccaaaacc aatcaggact gatgtaacag gcatgatctt agaagaaggc
3241 gcacctgagg gcaccgtggt cacactactc atcaaaaggt ccactggaga actcatgccc
3301 ctagcagcta ggatggggac ccatgcgacc atgaagatcc aagggcgcac cgttggaggc
3361 cagatgggca tgcttctgac aggatccaac gccaagagca tggacctggg taccacacca
3421 ggtgattgtg gctgccccta tatctacaag agaggtaatg actatgtggt cattggagtc
3481 cacacggctg ccgcacgtgg gggaaacact gtcatatgtg ccacccaggg gggtgaagga
3541 gaggctacac ttgaaggtgg tgacaacaag gggacatact gtggtgcacc aatcctaggc
3601 ccagggagtg ccccaacact tagcaccaag accaaattct ggagatcgtc cacagcatca
3661 ctcccacctg gcacctatga accagcctat cttggtggca aggaccctag agtcaagggt
3721 ggcccttcac tacagcaagt catgagggaa cagttgaagc cattcacaga gccaaggggc
3781 aagccaccaa aaccaagtgt attagaagct gccaagaaga ccatcatcaa tgtccttgag
3841 caaacaattg atccacctga gaaatggtcg ttcgcacaag cctgcgcgtc ccttgacaag
3901 accacttcca gtggttatcc gcaccacgtg cggaaaaatg actgctggaa cggggagtcc
3961 ttcacaggca agctggcaga ccaggcttcc aaggccaacc tgatgtttga agaagggaag
4021 aacatgaccc cagtctacac agctgcgctc aaggatgagt tggtcaaaac tgacaaaatt
4081 tatggtaaga tcaagaagag gcttctctgg ggctcggact tggcgaccat gatccggtgt
4141 gctcgagcat tcggaggcct aatggatgaa ctcaaagcac actgtgtcac acttcccatt
4201 agagttggca tgaatatgaa tgaggatggc cccatcatct tcgagaggca ttccaggtac
4261 acatatcact atgatgctga ttactctcgg tgggattcaa cacaacagag agccgtgttg
4321 gcagcagctc tagaaatcat ggttaaattc tccccagaac cacatttggc tcaggtagtc
4381 gcggaagacc ttctctctcc tagcgtggtg gacgtgggcg acttcacaat atcaatcaac
4441 gagggtcttc cctctggggt gccttgcacc tcccaatgga actccatcgc ccactggctt
4501 ctcactctct gtgcgctctc tgaagtcaca aatctatccc ccgataccat acaggctaac
4561 tccctcttct ctttttatgg tgatgatgaa attgttagca cagacataaa attggaccca
4621 gagaaattga cagcaaagct cagagaatat gggctaaaac caacccgccc tgacaaaact
4681 gaaggacccc ttgtcatctc tgaagacctg aatggcctaa cttttctgcg gagaactgtg
4741 acccgcgacc cagctggttg gtttggaaaa ctggagcaga gttcaatact caggcaaatg
4801 tactggacta ggggtcccaa ccatggagac ccatctgaaa caatgattcc acactcccaa
4861 agacccatac aattaatgtc cctactgggg gaggccgctc tccacggccc tgcattttac
4921 agcaaaatca gcaaattggt cattgcagag ctaaaagaag gtggcatgga tttttacgtg
4981 cccagacaag agccaatgtt cagatggatg agattctcag atctgagcac gtgggagggc
5041 gatcgcaatc tggctcccag ttttgtgaat gaagatggcg tcgagtgacg ccaacccatc
5101 tgatgggtcc acagccaacc tcgtcccaga ggtcaacaat gaggttatgg ctttggagcc
5161 cgtagttggt gccgccattg cggcacctgt ggcgggccaa caaaatgtaa ttgacccctg
5221 gattagaaac aattttgtac aagcccctgg tggagagttt acagtatccc ctaggaacgc
5281 tccaggtgaa atactatgga gcgcgccctt aggccctgat ttgaatccct acctttccca
5341 cttggccaga atgtacaatg gttatgcagg tggttttgaa gtgcaggtaa tcctcgcggg
5401 gaacgcgttc accgccggga agatcatatt tgcagcagtc ccaccaaatt tcccgactga
5461 aggtttgagc cccagccagg tcactatgtt cccccacata atagtagatg ttaggcaatt
5521 ggaacccgtg ttgatcccct tacccgatgt taggaataat ttctaccatt ataaccaatc
5581 aaatgacccc accatcaaat tgatagcaat gttgtacaca ccacttaggg ctaataatgc
5641 cggggacgat gtcttcacag tttcttgtcg tgttctcacg agaccatccc ccgattttga
5701 tttcatattt ttggtgccac ccacagttga atcaagaact aaaccattct ctgtcccagt
5761 tttaactgtt gaggagatga ccaattcaag gttccccatc cctctggaaa agttgttcac
5821 gggccccagc agtgcctttg ttgttcaacc acaaaacggc aggtgcacga ctgatggcgt
5881 gctcctaggt actacccaac tgtctcctgt caacatctgc accttcagag gggatgtcac
5941 ccatactcca ggcagtcata actacacaat gaatttggcc tcccaaaatt ggaacagtta
6001 cgatccaaca gaagaaatcc cagcccctct aggaactcca gatttcgtgg ggaagatcca
6061 aggtgtgctc actcaaacca caaggacaaa tggctcgacc cgcggccaca aagctacagt
6121 gtatactggg agcgccgact tttctccaaa actgggtaga gttcaatttg ccactgacac
6181 agacaatgat tttgaaacta accaaaacac aaagttcacc ccagtcggtg tcatccagga
6241 tggtagtact accccccgaa atgaacccca acagtgggtg ctcccaagtt actcaggcag
6301 aaacattcat aacgtacacc tggcccccgc tgtagccccc actttcccgg gcgagcagct
6361 cctcttcttc aggtctacta tgcccggttg cagcgggtac cccaacatgg atttggactg
6421 tctgctcccc caggagtggg tgcaatactt ctaccaggag gcagccccag cacaatctga
6481 tgtggctctg ttaagatttg tgaatccaga cacaggtagg gttttgtttg agtgtaagct
6541 tcataaatca ggctatgtta cagtggctca tactggccag catgatttgg ttatccctcc
6601 caatggttat tttagatttg attcctgggt caaccagttc tacacacttg cccccatggg
6661 aaatgggacg gggcgtagac gtgcattata atggctggag ctttctttgc tggattggca
6721 tctgacgtcc ttggctctgg acttagttcc ctaatcaatg ctggggctgg ggccatcaac
6781 caaaaagttg aatttgaaaa taacagaaag ctgcaacagg cttccttcca atttagtagc
6841 aatctacaac aggcctcctt tcaacatgac aaagagatgc tccaagcaca aattgaggcc
6901 accaaaaagt tgcaacagga aatgatgaga gttaaacaag caatgctcct agagggtgga
6961 ttctctgaga cagatgcagc ccgtggagca atcaacgccc ccatgacaaa aactttggac
7021 tggagcggga caaggtactg ggctcccgat gctaggacta caacatatag tgcaggccgc
7081 ttttccaccc ctcaaccctc gggggtatta ccaggaagag ctaatcttag ggctattgtc
7141 cccgcccggg gttcctccag cacgtcttct aactcttctt ttgctacttc tgtgtattca
7201 aatcaaacca cctcaacgag acttggttct acagctggtt ctggtaccag tgtctcgagc
7261 ctcccgtcaa ctgcaaggac taggagctgg gttgaggatc aaaataggaa tttgtcacct
7321 ttcatgaggg gggcccacaa catctcgttt gtcaccccac catctagcag atcctctagc
7381 caaggcacag tctcaaccgt gcccaaagaa gttttggact cctggactgg cgctttcaac
7441 acgcgcaggc agcctctctt cgctcacatt cgcaagcgag gggagtcacg ggtgtaatgt
7501 gaaaagacaa aattgattat ctt
//