Typing tool
|
|
|
|
|
|
Typing tool
|
Complete norovirus genomes
| MF140647 | GII.7 | |
|
|---|---|---|---|
| GII.P7 |
ORF1: 1..5080
ORF2: 5061..6683
ORF3: 6683..7456
LOCUS MF140647 7525 bp RNA linear VRL 24-OCT-2017
DEFINITION Norovirus GII strain
Norovirus/GII/Hu/NL/2013/GII.P7-GII.7/Rotterdam/E1300275_p12_d54
ORF1 gene, partial cds; and ORF2 and ORF3 genes, complete cds.
ACCESSION MF140647
VERSION MF140647.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norovirus norwalkense.
REFERENCE 1 (bases 1 to 7525)
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 7525)
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..7525
/organism="Norovirus GII"
/mol_type="genomic RNA"
/strain="Norovirus/GII/Hu/NL/2013/GII.P7-
GII.7/Rotterdam/E1300275_p12_d54"
/host="Homo sapiens"
/db_xref="taxon:122929"
/geo_loc_name="Netherlands"
/collection_date="17-Sep-2013"
/note="genotype: GII.P7-GII.7"
CDS <1..5080
/codon_start=2
/product="ORF1"
/protein_id="ATN23637.1"
/translation="NDATAAFGSQNSVNDSDNATPSNKEEVGAFSNIKVGFKKMLGAV
PKGTKAPSSGQHCPTVKVGSKTLTIPPEPPNGEDTVQFNAKSETIVGLPDLTTVQNEH
ENTPYTVPPLSEREHRPATEPLPGTILEMWDGEFYHYSVYVSDGRALGVHKPPAAISL
ATIELTPISLYWRPVYTPNYLVSPDTLKGLAGEKFPYTAFSNNCYNFCCWVLELNDTW
LNRRCISRTTGFFKPYQSWNRKPLPTVDDGKIKKVANAILCALGSLFSKPIKDLLGKL
KPLNLLHLLASCDWTFAGIVETVILMAELFNVFWTPPDVSNFIASLIGDFELQGPEDL
AMELVPVVMGGVGMVLGFTAEKIGRMLSSAASTLRACKDLGNYALDILKLVMKWFFPK
KEEKAEMETLRAIEDAVLDMEAIGNNHLTTLLKDKDSLTAFMKTLDLEEEKARKLSTK
SSSPDIVGTINAILARIAAARSLLHKAKEEMFSRIRPVVVMISGRPGIGKTHMARHLA
KSIANTMSGDQRVGLVPRNGVDHWDAYRGERVVLWDDYGMGSPVKDALTLQELADTCP
VTLNCDRIENKGKMFDSDVIIITTNLVNPAPLDYVNFEACSRRVDFLVYAESPEIEKV
KRDFPGQPDMWKDHFKPDFSHIKLTLAPQGGFDKNGNTPHGKGTMRSLTQGSLTARVA
GLVHERRDEFQLQGNDLQTYNFDTNRVSAFRKLAADNKYGIMETMRVGATLKNVKTLE
DLKIALRDVKFNECEIIYKNSKYRVSSNGKGSVSVDKVEDNASQTVNEVQSAILRLRQ
ARARYYISCFQDLVYTLMQVAGASFVVNRISRRFCWERWVKPAETQEVNESEKEVAQG
RWEIEPKDTEPEGKKGKNKKGRGKKHTAFSSKGLSDEEYDEFKRIREERNGKYSIEEY
LQDRDRYYEEVAVARATEEDFCEEEEAKIRQRIFRPTKKQRKEERGVLGLVTGSDIRK
RRPDDFQPKGNLWADDTRSVDYNERLDFEAPPSVWSRIVPLGTGWGFWVSSNLLITTT
HVLPKGVKELFGVEIKQIQVHKSGEFCRFRFPRPIRPDVTGLVLEEGAPEGTVCSILI
KRPTGEMIPLAVRMGTHASMKIQGRTVGGQMGMLLTGANAKNMDLGTGPGDCGCPYIY
KRGNDIVVAGVHTAAARGGNTVICATQGQDGEAVLEGNEDLGTYCGAPILGPGKAPKL
STKTKFWRSSPDALPPGTYEPAYLGGKDPRVEKGPSLQQVMRDQLRPFTEPRGKPPRP
AVLEEAKKTVMNVLEQTIDPAKPWSYSQACASLDKTTSSGSPHHVKKNDHWNGETFTG
PLADQASKANLMYEQAKHVQPVYTAALKDELVKTDKIYKKIKKRLLWGSDLGTMIRCA
RAFGGLMDSMKASCIALPCRVGMNMNEDGPIIFDKHSKYRYHYDADYSRWDSTQQRNI
LSAAMEVMVRFSAEPELAQVVAEDLLAPSQLDVGDFVISVQEGLPSGVPCTSQWNSIA
HWILTLSAMAEVSGLSPDVVQAHSCFSFYGDDEIVSTDINLDPMKLTQKLREYGLVPT
RPDKTEGPLVITEDLTGLTFLRRSIARDPAGWFGKLDQDSILRQLYWTRGPNHENPYE
SMVPHSQRATQLMALLGEASLHGPQFYKKVSKMVINEIKSGGLEFYVPRQEAMFRWMR
FSDLSTWEGDRNLAPEGVNEDGVE"
CDS 5061..6683
/codon_start=1
/product="ORF2"
/protein_id="ATN23638.1"
/translation="MKMASNDAAPSNDGAAGLVPEINNEVMPLEPVAGASLATPVAGQ
HNIIDPWIRNNFVQAPAGEFTVSPRNSPGEILLDLELGPELNPYLAHLARMYNGHAGG
MEVQIVLAGNAFTAGKIIFAAIPPGFPYENLSPSQITMCPHVIIDVRQLEPVLLPMPD
IRNNFFHYNQGNDPKLRLIAMLYTPLRANNSGDDVFTVSCRVLTKPSPDFEFTFLVPP
TVESKTKQFSLPILKISEMTNSRFPVPVEMMYTARNENQVVQPQNGRVTLDGELLGTT
PLLAVNICKFKGEVIAKNGDVSSYRMDMEITNTDGTPIDPTEDTPGPIGSPDFQGVLF
GVASQRNKNEQNPPTRAHEANINTGGDQYAPKLAQVKFFSESQDFEVHQPTVFTPVGV
AGDPSHPFRQWVLPRYGGHLTNNTHLAPAVAPLFPGEQILFFRSQIPSSGGYESGNMD
CLVPQEWVQHFYQEAATAQSEVALIRFINPDTGRVLFEAKLHKQGFITVAHTGDNPIV
MPPNGYFRFEAWVNQFYSLAPVGTGNGRRRIQ"
CDS 6683..7456
/codon_start=1
/product="ORF3"
/protein_id="ATN23639.1"
/translation="MASAFFANLAGGVASNGISSLINAGANAINQKVEFDYNKQLQNA
SFSHDKEMLQAQIEATKRLQQEMIDIKQGVLTAAGFSPTDAARGSVGAPMTKLVDWSG
TRYWAPGAMRTTGYSGTFTHLPPVQSASYVNNQNRQSPKVDPPPPSSSGSSVSSVKTQ
STTLSGTSRVGSSSHLTLSTRPSTRTSDWVRSQNERLSPFMNGALQTTYVTPPSSRAS
SVSTVSTVPKEVLDSWTPMFNTHRQPLFAHLRRRGESQI"
ORIGIN
1 taacgacgct actgctgcct ttggcagtca aaactctgtc aatgacagtg acaacgccac
61 cccttctaat aaagaagagg ttggtgcatt ctccaacatc aaagttggat tcaagaaaat
121 gctgggtgcc gttcccaagg gcaccaaagc acccagcagt ggtcaacatt gccccacagt
181 taaggttggg tctaaaacat taacaatccc ccctgagccc ccgaatggtg aagacaccgt
241 acagtttaat gcaaagtcag aaactatagt tgggttgccg gacttgacaa cggtgcaaaa
301 tgaacatgaa aacaccccat acactgtccc tccattaagt gagagggagc acaggccggc
361 caccgaacca cttcctggca caatattaga gatgtgggat ggtgagtttt accattattc
421 cgtgtacgtc agcgacggca gagctctggg agtccacaaa ccaccggcgg ctataagcct
481 cgcgacgata gagctcaccc ccatatcact ttactggagg cccgtttata cccccaatta
541 cttggtctcc ccggacacat taaaaggtct cgctggtgag aagttcccct atacggcctt
601 cagtaacaac tgttataact tctgttgctg ggtgcttgag ctcaacgaca cgtggcttaa
661 cagaagatgc atttccagaa ccaccggctt cttcaagcca taccagtctt ggaacagaaa
721 acctctccca accgttgatg atggaaagat taagaaagtg gccaatgcaa tcctctgtgc
781 actcggctca ctgttctcaa aaccaatcaa agacctgtta ggcaaactca agccattgaa
841 tctactacac ttgcttgcgt cttgtgattg gacgtttgcg ggtatagtgg agacagtcat
901 cttgatggcg gagcttttca atgtcttctg gaccccccca gatgtctcta attttatagc
961 ctccctaata ggtgattttg aattgcaagg gcctgaggac ctggctatgg agctcgtccc
1021 cgtggtcatg ggcggcgtag ggatggttct cggttttacc gccgagaaga taggccgcat
1081 gctatcgtcc gctgcatcaa cactgcgggc gtgcaaagac ctagggaact atgcccttga
1141 catactcaaa ttggtcatga agtggttctt cccgaagaag gaagagaaag ctgagatgga
1201 aaccttgagg gcgattgagg atgccgtcct ggatatggaa gccataggga acaaccacct
1261 cacaaccctt cttaaggaca aagatagcct cacggctttc atgaagaccc tggatctgga
1321 agaggagaag gcaaggaaac tgtccactaa atcatcttca ccggacatag tcggcaccat
1381 caatgccata ctagctagga tagctgctgc tagatccctt ctacataagg ccaaagagga
1441 gatgttcagc aggatcaggc cagtggttgt tatgatatca ggcaggcctg gcattggaaa
1501 aacccacatg gcgagacatt tggctaagag catcgccaac accatgagtg gcgaccaaag
1561 agtcgggctc gttccgcgca acggcgtcga tcactgggat gcctacaggg gagagagggt
1621 ggtcttgtgg gatgactacg gcatggggag ccctgttaag gacgctctaa cactgcaaga
1681 gctggccgac acatgcccag tcactttaaa ttgtgacagg attgagaata aggggaagat
1741 gtttgacagt gatgtcatca taatcacgac caacctagtc aaccccgcgc ccctcgacta
1801 tgtgaacttc gaggcgtgtt ctaggagagt tgacttcctg gtctatgcag agtcaccaga
1861 aattgaaaag gtcaagagag acttcccagg ccagcctgac atgtggaaag accattttaa
1921 accagacttc tcccacatca agctgactct agccccccag ggtgggtttg acaaaaatgg
1981 caacacccca cacggtaagg gaaccatgcg gtccctaacc caggggtccc tgactgcgag
2041 agttgcaggc cttgtccatg agaggagaga tgaattccag ctccaaggaa atgacctcca
2101 aacatacaac tttgacacca acagagtctc cgcattcagg aaattggctg cagataacaa
2161 gtatgggatc atggagacga tgagagtggg tgcgacactc aagaatgtga agaccctgga
2221 agatcttaaa attgcattga gggatgtaaa attcaatgag tgtgaaataa tctacaagaa
2281 ctctaagtat cgagtctctt ccaacggtaa aggctcagtt tctgttgaca aagttgaaga
2341 caatgcatcc cagactgtaa acgaggtaca atccgcaatt ctcaggctca ggcaagcgag
2401 ggccagatat tacatcagct gcttccaaga cctcgtctat actctcatgc aggttgccgg
2461 agcatcattc gtagtcaaca ggatctccag aaggttctgc tgggaaaggt gggtcaaacc
2521 ggccgagacc caggaggtga atgagtccga aaaggaagtg gcacaaggca gatgggaaat
2581 tgagcccaag gatacagaac cagaaggcaa gaaaggtaag aacaagaaag gaagaggtaa
2641 gaaacacaca gctttctcta gcaaaggcct gagtgatgaa gagtatgacg agttcaagag
2701 aattagggaa gaaaggaacg gaaagtactc cattgaggaa tacctgcaag accgggaccg
2761 ctactatgaa gaagtggcag ttgcccgggc gacagaggag gacttctgtg aagaggaaga
2821 ggccaagata agacaaagga ttttccgccc gacaaagaaa cagaggaagg aggagagggg
2881 tgtgcttggc ttagtcaccg gctcagacat caggaagagg agaccagatg acttccaacc
2941 aaaaggcaac ctgtgggcag atgacaccag aagtgtggac tacaatgaga ggcttgattt
3001 tgaagcgccc ccgagtgttt ggtcaagaat agttccatta ggcactggtt ggggattctg
3061 ggtttcatcc aaccttctga tcacaacaac acacgtcctg cctaaagggg ttaaggagct
3121 ctttggagtt gaaatcaaac aaatccaagt tcacaagtct ggagagtttt gcaggttcag
3181 attcccaaga cctatcaggc cagatgtcac aggactcgtg ttggaggaag gcgccccaga
3241 aggcactgtc tgttctatac tcataaaaag gcccacaggt gagatgatcc ccttagcagt
3301 gaggatgggc acacatgcat ccatgaaaat acagggcaga accgttggtg gccagatggg
3361 aatgcttctc acaggagcga acgcgaagaa catggacctc ggcactggtc ctggtgactg
3421 cggttgccct tacatctaca aacgtggcaa cgacattgtt gtcgcgggtg ttcacaccgc
3481 agcagccaga ggaggcaaca ctgttatatg tgccacccaa gggcaagatg gggaagcagt
3541 ccttgaggga aatgaggacc ttggcaccta ttgtggcgcc ccaattctgg gccctggcaa
3601 ggcgcctaaa ctcagcacga agactaagtt ctggcgttca tcaccagatg ccttgccacc
3661 tggcacatat gagcctgctt acctaggagg caaagaccct agagtggaaa aaggtccttc
3721 ccttcaacaa gtcatgaggg accagttgag acccttcaca gaacccaggg gcaaaccacc
3781 tagacctgca gtcttggagg aagccaaaaa gacagtgatg aatgttctag aacaaaccat
3841 tgaccccgcc aagccatggt cctattcgca ggcgtgtgcc tcattggaca aaaccacctc
3901 cagtggtagt ccccatcatg ttaagaaaaa tgaccactgg aatggggaga ccttcactgg
3961 tccacttgca gatcaggcat ctaaagccaa tctcatgtat gagcaggcta aacatgtgca
4021 gcccgtgtat acggccgcgc tcaaagatga gcttgttaag actgacaaga tctacaagaa
4081 aataaagaag aggctcctat gggggtcgga ccttggcaca atgatcaggt gcgccagggc
4141 ctttggtggt ctcatggaca gcatgaaggc aagttgtata gctcttcctt gcagggtagg
4201 gatgaacatg aatgaagatg gccctattat atttgacaaa cattctaagt acaggtacca
4261 ctatgatgct gactattcta ggtgggactc aacccaacaa aggaacattc tttctgccgc
4321 tatggaagtg atggtgcggt tctctgctga accagaattg gcacaagtgg ttgcagagga
4381 ccttttagca cctagccagc ttgatgttgg cgattttgtc atctcagtcc aggagggtct
4441 gccatcagga gtcccatgca catcacaatg gaattcaata gcacactgga tcctaacttt
4501 gagtgcaatg gcagaagtgt caggtctctc accagatgtt gtccaagccc actcttgttt
4561 ttccttttat ggggacgatg agatcgtcag tactgacatc aatcttgacc ccatgaagtt
4621 gacacagaaa ctcagggagt atggtctggt tcccacccgg cctgataaaa ctgaaggtcc
4681 cctcgtcata actgaagacc tcaccggcct gacgttcctc cgtaggtcga ttgctcggga
4741 cccagctggt tggtttggaa agctggacca agactcaatc cttaggcagc tgtactggac
4801 aagggggcct aaccatgaga acccgtacga gagcatggtt cctcattctc agcgggccac
4861 acaactcatg gcccttcttg gtgaggcctc actacatggc ccccagtttt ataagaaagt
4921 tagcaagatg gtcatcaatg agattaagag tggtggtctg gagttttatg tgcccagaca
4981 agaggccatg ttcaggtgga tgagattctc tgacctcagc acatgggagg gcgatcgcaa
5041 tcttgctccc gaaggtgtga atgaagatgg cgtcgaatga cgcagctcca tctaatgatg
5101 gtgcagcagg cctcgtacca gagatcaaca atgaggtcat gccccttgag cccgtagctg
5161 gtgcatcgct ggcgacacca gttgccgggc aacataatat aattgatccc tggataagaa
5221 ataattttgt acaagctcct gcaggtgagt ttacagtttc ccctagaaat tcccctggtg
5281 aaattttgct cgatttggag ttgggaccag aactaaaccc ctatctcgct catctggccc
5341 gtatgtataa tgggcacgct ggtggcatgg aagtgcaaat tgtgttagct gggaatgcgt
5401 tcacagctgg caagatcata tttgctgcca tccctccagg gttcccatat gaaaacttgt
5461 caccttcaca aatcacaatg tgccctcatg ttataattga tgttagacaa ttagaaccag
5521 ttctattacc tatgccagat attagaaaca acttcttcca ttacaatcag ggcaatgacc
5581 caaaattgag attgatagct atgctctaca cccctttaag ggctaataat tctggtgatg
5641 atgtgttcac agtttcttgt agggtcctca ctaaaccgtc acctgatttt gaattcacat
5701 ttttggtccc ccctacggtt gaatctaaaa ccaaacagtt ctcactgccc atcctcaaaa
5761 tatcagagat gaccaactca agattcccag tgccagtgga aatgatgtac acagccagga
5821 atgagaacca agttgtccag ccacagaatg gtagggtcac acttgatggc gagctactag
5881 gcaccacacc cttgttggct gtcaacatct gcaaattcaa gggggaggtt atagctaaga
5941 atggagatgt gagttcctat aggatggaca tggaaattac caacactgat ggcaccccaa
6001 ttgaccccac agaagataca cctggtccca ttggttcacc tgactttcaa ggtgtactct
6061 ttggcgttgc cagccaacgc aacaagaatg agcaaaaccc ccccacgaga gcccatgaag
6121 ccaacattaa cactggtgga gaccaatacg cccccaaatt ggcccaagtg aaattcttct
6181 cagagtccca ggatttcgag gtgcaccagc ccacagtttt caccccagtt ggtgtggcag
6241 gcgacccctc ccatcctttc agacagtggg tcctgcctcg atacggtgga catctcacca
6301 acaacaccca cctggctcca gcagtggccc ccctattccc aggtgagcag atcctattct
6361 ttagatcaca aatacccagc tcaggcggct atgaatcggg taacatggac tgccttgtcc
6421 cccaagaatg ggtccaacac ttctatcaag aagctgccac agctcagtct gaggtggcac
6481 tcataaggtt catcaaccca gacactggca gagtcctctt tgaggccaag ctgcacaagc
6541 aaggctttat aactgtggct cacactggtg ataacccaat tgtcatgcca ccaaatgggt
6601 actttagatt tgaagcttgg gttaatcagt tttactcact cgcccccgtg ggaactggga
6661 atgggcgcag gaggatccaa taatggccag tgctttcttt gcaaatttgg caggaggcgt
6721 tgcctccaat ggaattagtt cactcataaa tgctggggct aatgctatta accaaaaagt
6781 tgagtttgat tataataaac aactccaaaa tgcatccttc tcccatgata aggaaatgct
6841 ccaagcccaa attgaagcca ccaaacgtct gcaacaagag atgattgaca taaaacaagg
6901 ggtgctgaca gctgcgggat tctctcctac ggatgccgcg aggggttctg tcggcgcacc
6961 aatgacaaaa ttagttgatt ggagtggcac tagatattgg gcgcctggtg ccatgaggac
7021 aacaggctat tcaggaactt ttactcactt gccccctgtg cagtctgctt catatgttaa
7081 taatcagaat agacaatctc ctaaagtaga tccccctcct ccttcttcga gtggttcttc
7141 tgtttcttct gttaaaacac aatcgactac cctctcaggc acttcaaggg tgggctcctc
7201 atcccattta accctgtcaa ccaggccgag cacaaggaca tctgattggg tgcgcagcca
7261 gaatgaaagg ttgagtccct tcatgaatgg agcgttgcaa acaacatatg taacgccacc
7321 atccagtagg gcgtcaagtg tcagcacagt ctcgaccgtg ccgaaagagg ttttggactc
7381 ctggacgcct atgtttaaca ctcacaggca gccactcttc gcccatctgc gtaggcgagg
7441 ggagtcacag atttagtgaa aagattggtt aggaaagttg attagtttgc tcttcttttc
7501 cactattcct ttaattcttt ctttt
//