Typing tool
|
|
|
|
|
|
Typing tool
|
Complete norovirus genomes
| MF140679 | GII.6 | |
|
|---|---|---|---|
| GII.P7 |
ORF1: 1..5063
ORF2: 5044..6687
ORF3: 6687..7463
LOCUS MF140679 7480 bp RNA linear VRL 24-OCT-2017
DEFINITION Norovirus GII strain
Norovirus/GII/Hu/NL/2014/GII.P7-GII.6/Rotterdam/E1300314_p5_d328
ORF1 gene, partial cds; and ORF2 and ORF3 genes, complete cds.
ACCESSION MF140679
VERSION MF140679.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7480)
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 7480)
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..7480
/organism="Norovirus GII"
/mol_type="genomic RNA"
/strain="Norovirus/GII/Hu/NL/2014/GII.P7-
GII.6/Rotterdam/E1300314_p5_d328"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="Netherlands"
/collection_date="15-Apr-2014"
/note="genotype: GII.P7-GII.6"
CDS <1..5063
/codon_start=3
/product="ORF1"
/protein_id="ATN23733.1"
/translation="FGSQKSANDSTNTTPSNKEEAGAFSNIKVGFKKMLGAVPKGTKT
PSSAQHCPTVKIGDKTLTVPPEPPNGEDVVQYDAKSETVHGLPDLTTVQNEHENTPYS
VPPLSEREHRPATEPLPGTILEMWDGEFYHYSVYVSGGKALGVHKPPAAISLATIELT
PISLYWRPVYTPSYLVCPDTLKGLAGEKFPYTAFSNNCYNFCCWVLELNDTWLSRRSI
SRTTGFFKPYQSWNRKPLPTVDDGKIKKVANAILCALGSLFTKPIKDLLGKLKPLNLL
HLLASCDWTFAGVVETVILMAELFNIFWTPPDVSNFISSLVGDFELQGPEDLAVELVP
VVMGGVGMVLGFTAEKIGRMLSSAASTLRACKDLGNYALDILKLVMKWFFPKKEEKAE
METLRAIEDAVLDMEAIGNNHLTTLLKDKDSLSAYMKTLDLEEEKARKLSTKSSSPDI
VGTINAILARIAAARSLLHKAKEEMFSRARPVVVMISGKPGIGKTYMARHLAKGVANT
MSGDQRVGLVPRNGVDHWDAYRGERVVLWDDYGMGNPIKDALTLQELADTCPVTLNCD
RIENKGKMFDSDVIVITTNLVNPAPLDYVNFEACSRRIDFLVYAESPEIEKVKRDFPG
QPDMWKDHFKSDFSHIKLTLAPQGGFDKNGNTPHGRGTMRSLTQGSLIARVAGLVHER
KDEFQLQGNDLQTYNFDTNRVSAFRRLAADNKYGIMETMRVGAALKNVKTLEDLKVAL
RDVKFNECQIIYRSSKYRISSNGKGSVSIDKVGDQVSQTASEVGSAILRLRQARARYY
VSCFQDLIYTLIQVAGASFVVSRISKRFCWERWVKPTETQETNESEKEVVQGGWEIEP
KDTEPEGKKGKNKKGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEEYLQDRDR
YYEEVAVARATEEDFCEEEEAKIRQRIFRPTKKQRKEERGVLGLVTGSDIRKRRPDDF
QPKGKLWADDTRNVDYNERLDFEAPPSVWSRIVPLGTGWGFWVSSNLLITTTHVLPKG
IKELFGVELKQIQIHKSGEFCRFRFPRPIRPDVTGLVLEEGAPEGTVCSILVKRPTGE
MIPLAVRMGTHASMKIQGRTVGGQMGMLLTGANAKNMDLGTGPGDCGCPYIYKRGNDI
VVAGVHTAAARGGNTVICATQGQDGEAVLEGNEDLGTYCGAPILGPGKAPKLSAKTKF
WRSSPDALPPGTYEPAYLGGKDPRVEKGPSLQQVMRDQLKPFTEPRGKPPRPAILEEA
KKTVMNVLEQTIDPAKPWTYSQACASLDKTTSSGSPHHVRKNDHWNGESFTGPLADQA
SKANLMYEQAKHVQPVYTAALKDELVKTDKIYKKIKKRLLWGSDLGTMIRCARAFGGL
MDSMKASCIALPCRVGMNVNEDGPIIFDKHSKYKYHYDADYSRWDSTQQRCILSAAME
VMVRFSAEPELAQVVAEDLLAPSQLDVGDFVISVQEGLPSGVPCTSQWNSIAHWILTL
SAMAEVSGLSPDVVQAHSCFSFYGDDEIVSTDINLDPMKLTQKLREYGLVPTRPDKTE
GPLVITEDLTGLTFLRRSIVRDPAGWFGKLDQDSILRQLYWTRGPNHENPYESMVPHN
QRATQLMALLGEAALHGPQFYKKVSKMVINEIKSGGLEFYVPRHEAMFRWMRFSDLST
WEGDRNLAPEGVNEDGVE"
CDS 5044..6687
/codon_start=1
/product="ORF2"
/protein_id="ATN23734.1"
/translation="MKMASNDAAPSNDGAANLVPEVNNEVMALEPVAGASIAAPVVGQ
QNIIDPWIRENFVQAPQGEFTVSSRNTTGEVLLNLELGPELNPYLRHLSRMYNGYAGG
MQVQVILAGNAFAAGKIIFAAVPPHFPVENISAAQITMFPHVVIDVRQLEPVLLPLPD
IRNRFFHYNQENTSRMRLVAMLYTPLRANSGEDMFTVSCRVLTRPAPDFEFTFLVPPT
VESKTKPFTLPILTLGELSNSRFPAPIDMLYINPSETIVVRSQNGRCLLDGTLQGTTQ
LAPTQICSFRGTLVRQESRSADSVDSARRAMNHPLYVQLRNLDGTSYDPTDEVPAVLG
AIDFKGTVYGVASQRDTKGSVGATRAHEVTINTRDAKYSPKLGSVLMHSESTDFFSDQ
PIRFTPIGMGEENDWSQWDLPDYSGALTLNMHLAPAVAPAFPGERILFFRSVVPAAGG
YGKGEIDCLIPQEWIQHFYQEAAPTQSAVALIRYVNPDTGRSLFEAKLHREGFITVAS
SGDNPIVVPSNGYFRFEAWVNQFYTLTPMGAGQGRKRAQ"
CDS 6687..7463
/codon_start=1
/product="ORF3"
/protein_id="ATN23735.1"
/translation="MAGAFLAGLAGDAITNGVGSLINAGANAINQKVEYDFNKQLQLA
SFQHDKEMLQSQVLATKQLQQEMMNIKQGVLTAGGFSPTDAARGAVNAPMTKILDWNG
TRYFAPNSMKTTSYSGQLSSNPVHKQSTLPRPSPSKTNVSSGSSSVYSSLSSASSQST
HSTVLTAGSGSSRTAPSSSTASTLSRTSDWVRGQNERLSPFMNGALQTTFVTPPSSRA
SSYGSVSTVPKAVLDSWTPMFNTNRQPLFAHIRRRGESQI"
ORIGIN
1 ccttcggcag ccaaaaatct gccaatgaca gtactaacac caccccttct aataaagaag
61 aggctggtgc attctccaac attaaagttg gttttaagaa gatgctgggt gccgttccta
121 aggggaccaa aacacccagt agtgctcagc actgccccac agtcaagatc ggggacaaaa
181 cattaacagt tccacccgag cccccaaatg gtgaggacgt tgtgcagtat gatgcgaagt
241 cagaaactgt gcatggacta ccagacttga cgacggtgca gaatgagcac gaaaacacac
301 cgtactctgt ccccccattg agtgaaagag aacacagacc agccactgaa ccgcttcctg
361 gcacaatact ggagatgtgg gatggtgaat tttatcacta ctccgtgtat gtcagtggcg
421 gcaaagccct aggagttcac aaaccccctg cagcaataag cctcgcaact atagagctca
481 cacccatatc tctttactgg aggcccgttt acacccccag ctacttagtc tgcccagaca
541 cgctgaaagg cctcgctggt gagaagtttc cctacacagc tttcagtaac aactgttaca
601 acttttgttg ctgggtgctt gagctcaacg atacgtggct tagcaggaga agcatctcca
661 gaaccaccgg tttcttcaaa ccataccagt cttggaacag gaaacccctt ccaaccgttg
721 atgatggaaa gattaagaag gtggccaacg caatcctctg tgcgcttgga tcactgttta
781 caaaaccaat caaagaccta ttgggaaagc tcaaaccact aaatttgctg cacctgctcg
841 catcatgtga ttggacgttt gcgggtgtag tagagacagt catcctaatg gcggaacttt
901 tcaacatctt ttggacaccg ccagatgttt ccaacttcat atcctccttg gtgggcgact
961 ttgaactgca agggcctgag gacctggctg tggagcttgt ccccgtggtc atgggtggcg
1021 tagggatggt tctcggcttc actgctgaga agataggccg tatgctgtct tccgccgcat
1081 caacgctgcg agcatgcaaa gacctgggga attacgccct tgacatacta aagctggtta
1141 tgaagtggtt cttcccaaag aaagaagaga aggccgagat ggaaacttta agggcaattg
1201 aggacgccgt cctggacatg gaagctatag ggaacaatca tcttacaacc ctcctcaagg
1261 acaaggatag cctctcggcc tacatgaaga ctctggacct ggaagaagaa aaggcaagga
1321 agctgtccac caagtcatcc tcgccagaca ttgtcggcac tatcaatgcc atactggcca
1381 gaatagctgc tgccagatcc ctcctacaca aggctaaaga agaaatgttt agtagggcca
1441 gacccgtggt tgttatgatt tcgggcaaac ctggcattgg caaaacttac atggcaagac
1501 acctagctaa gggcgtcgcc aacaccatga gtggcgacca aagagttggg ctcgttccgc
1561 gcaacggggt cgaccattgg gacgcctaca ggggggagag ggtggtcttg tgggatgact
1621 acggcatggg gaaccctatc aaggatgctc taacattaca agaattggcc gacacttgtc
1681 cagtcactct aaactgtgat aggattgaaa acaaagggaa gatgttcgac agtgatgtca
1741 ttgtaatcac gaccaattta gtcaacccag cgcccctcga ttatgtaaac ttcgaggcgt
1801 gctccaggag gattgacttt ctggtctatg cagagtcacc agagattgag aaagttaaga
1861 gagacttccc tggccaacct gacatgtgga aagaccattt caaatcagac ttctcccaca
1921 taaagctgac tctggctccc cagggcggat ttgacaagaa tggcaacacc ccacatggta
1981 ggggcaccat gcgatccctg acccaggggt ccctgatcgc aagggtcgcg ggtcttgttc
2041 atgagaggaa agatgagttc cagctccaag ggaacgacct ccaaacatac aactttgaca
2101 ccaacagggt ctccgcattt aggagactag ccgcagacaa caaatatggg atcatggaaa
2161 caatgagagt gggtgcggcg cttaagaatg tcaagacctt ggaagatcta aaggttgccc
2221 tgagggatgt gaagttcaac gagtgtcaga taatttacag gagctccaaa tatcgaatct
2281 cttccaatgg caaaggctct gtctctattg ataaagttgg ggatcaggtg tcccagactg
2341 caagtgaagt gggttcagca atccttagac tcaggcaggc aagggccaga tactatgtca
2401 gctgcttcca agacctcatc tacactttga tacaggttgc cggagcatca ttcgttgtta
2461 gcagaatctc caagaggttt tgttgggaga ggtgggtcaa accaaccgag acccaggaaa
2521 cgaatgaatc cgagaaggaa gtagtccaag gtggatggga gattgaaccc aaggacacag
2581 aaccagaagg caagaagggc aagaacaaga aaggaagagg caagaaacac acggctttct
2641 ccagcaaagg cctgagtgat gaggagtatg acgagtacaa gagaatcagg gaagagagga
2701 acggaaagta ctccattgag gaatacctgc aagaccggga tcgctactat gaggaagtgg
2761 cagttgcccg ggcaacagag gaggactttt gtgaggaaga ggaggccaag ataagacaaa
2821 gaatcttccg ccccacaaag aaacagagga aggaagaaag gggggtgctt ggtttggtca
2881 ccggctcaga catcaggaag aggagaccag acgatttcca accaaagggc aaactgtggg
2941 cagacgacac cagaaatgtg gactataacg agagacttga ctttgaggct cccccgagcg
3001 tctggtcgag aatagttcca ttgggcactg gatggggctt ctgggtttcg tccaatctcc
3061 tgatcacaac aacacacgtc ctgcctaagg ggatcaagga actttttgga gttgaactca
3121 aacagatcca aattcataag tctggagaat tttgcaggtt caggttccca agaccaatta
3181 ggccagatgt cacagggctc gtgctggagg aaggcgctcc agaaggcacc gtctgttcca
3241 tactcgtgaa gagacctaca ggtgaaatga tccccctagc agtgaggatg ggcacacatg
3301 cgtccatgaa gatacagggt aggaccgtcg gtggccagat gggaatgctt ctcacaggag
3361 caaacgcgaa gaacatggat cttggcaccg gccctggtga ctgcggttgt ccttacatct
3421 acaaacgtgg caacgacata gttgtcgcgg gtgtccacac cgcagcagcc cgggggggca
3481 acactgtcat atgtgccacc cagggacaag atggggaggc agtccttgag ggaaatgagg
3541 accttggcac ttactgcggt gccccaattc tgggcccagg caaagcaccc aaactcagtg
3601 cgaagaccaa gttctggcgc tcatcaccag acgctttgcc accaggcacc tatgagcctg
3661 cctatctggg gggtaaggac cccagagtgg agaaaggacc atctctgcaa caagtcatga
3721 gggatcagct aaaacctttc acagaaccca ggggtaaacc tcctagacct gcaatcttag
3781 aagaagccaa aaagacagtt atgaatgtac tagaacaaac cattgatcct gctaaaccat
3841 ggacctattc ccaagcatgt gcttcactgg acaagaccac ttccagtggt agcccccacc
3901 atgtcaggaa aaatgaccat tggaatggag aatctttcac tggccccctt gcagaccaag
3961 catccaaagc caacctcatg tatgaacagg ccaaacatgt gcagcccgtg tacacggccg
4021 cgctcaaaga cgagcttgtt aagactgata agatctataa aaagataaag aagagactct
4081 tgtgggggtc ggaccttggc acgatgatca ggtgcgccag ggcttttggt ggtctcatgg
4141 atagcatgaa ggcaagttgc atagccctcc catgtagagt ggggatgaac gtgaatgagg
4201 atggtcctat catatttgac aagcactcta agtacaagta ccactatgat gctgactatt
4261 ctagatggga ttccacccag caaaggtgca ttctctcggc cgctatggaa gtgatggtgc
4321 ggttttctgc cgagccagag ctggcgcaag tggttgcaga ggatctacta gcacccagcc
4381 aactagacgt tggcgatttt gtcatctcag tccaggaggg tctgccatca ggggtcccgt
4441 gcacatcaca gtggaactca atagcacatt ggatcctaac cttgagtgca atggcagaag
4501 tgtcaggtct ctcaccagat gttgtccaag cccactcttg tttttccttt tacggcgatg
4561 atgagatcgt cagcactgac atcaaccttg accccatgaa gttgacacag aaactcagag
4621 aatatggtct ggtccccacc cgacctgaca aaactgaagg tccccttgta atcactgaag
4681 acctcaccgg cctgacgttc ttgcgtaggt caattgtgag agatccagct gggtggtttg
4741 gaaaattgga ccaagactca atcctcaggc agctatattg gacaaggggc cccaatcatg
4801 agaatccata cgagagcatg gtccctcata accagcgggc aacacagctc atggcccttc
4861 taggtgaggc tgcactgcat ggccctcagt tttacaagaa agttagcaaa atggtcatca
4921 atgaaattaa aagtggtggt ctggaatttt atgtgcccag acatgaggcc atgttcagat
4981 ggatgagatt ctctgacctc agcacatggg agggcgatcg caatcttgct cccgaaggtg
5041 tgaatgaaga tggcgtcgaa tgacgctgct ccatcgaatg atggtgctgc caacctcgta
5101 ccagaggtca acaatgaggt tatggcactt gaaccggtgg cgggagcctc aattgcagct
5161 cctgtcgtcg gccaacaaaa tataattgac ccctggatta gagaaaattt tgttcaggca
5221 ccacagggtg agttcactgt ttcatcaagg aacacaaccg gtgaggtact tctgaatctt
5281 gaattaggcc ctgagctcaa cccttatctg agacatttgt cccgcatgta caacggttat
5341 gctggtggta tgcaggttca ggtgatccta gctgggaatg cgttcgcagc tggtaaaatc
5401 atctttgccg ccgtcccacc acatttccct gtagaaaata ttagtgcagc ccaaatcaca
5461 atgttccccc atgtagttat tgatgtaaga cagcttgagc cagtgctttt acccctccct
5521 gacataagga ataggttctt tcattacaat caggaaaaca cttctagaat gagacttgtg
5581 gctatgttgt acacacccct tagggcaaat tctggtgagg atatgtttac ggtgtcttgc
5641 agagtcctga cccgtccagc ccctgacttt gagttcacgt ttctggtgcc gccaactgta
5701 gaatcaaaga ctaagccctt tacactccca attctaactc ttggagaact atctaattct
5761 agattccctg ccccaataga catgctgtac ataaatccca gtgagacaat tgtggtgagg
5821 tcacaaaatg gccggtgtct tctggacgga acacttcaag ggaccaccca gctggcgccc
5881 acccaaattt gctccttcag gggcacgctg gttcgccagg agtcgaggtc tgcagattca
5941 gtagactcag ctagacgagc aatgaaccat cctctctacg ttcagctgag gaacctcgat
6001 gggacatcat atgatccaac agatgaggtg ccagcggttc tgggtgccat agattttaaa
6061 ggaactgtgt atggggtcgc tagtcaaagg gacaccaaag gctctgtagg agcgacccgc
6121 gcccatgaag tgacaataaa caccagagat gctaaatact ctccaaaact tggctctgtg
6181 ttgatgcatt ctgaatccac tgatttcttc agtgaccagc ccatccgctt tactcctatt
6241 ggtatggggg aggaaaatga ttggagccaa tgggatttgc ctgattattc tggtgccctc
6301 accctcaaca tgcacctagc ccccgcagtt gcccctgctt tccctggtga gcgcattctc
6361 ttctttagat cagtggtgcc agctgctggt ggttatggaa aaggtgaaat agactgtctc
6421 atcccacagg aatggattca gcatttctac caggaggccg ccccaacaca atccgcggtg
6481 gcccttatta gatatgttaa tcctgacact gggagaagcc tctttgaggc aaagctacat
6541 agagaagggt tcatcactgt ggcaagttct ggagacaacc ccatagttgt gccatcaaat
6601 ggctacttca gatttgaggc ttgggttaat caattctata cactcacccc catgggagct
6661 ggacaggggc gcaaaagagc ccagtaatgg caggagcttt cttagctgga ttggcaggtg
6721 acgccataac aaatggtgtc gggtccctga tcaacgctgg ggccaatgca atcaaccaaa
6781 aggtagagta tgacttcaat aaacaactcc aattggcatc ctttcaacat gacaaagaga
6841 tgttgcagtc acaagttctg gccactaaac agctccaaca ggagatgatg aacataaagc
6901 aaggggtctt gaccgctggc ggcttttccc ctacagatgc tgcaagaggc gctgtgaacg
6961 cgccgatgac aaaaattctg gattggaatg gaacgaggta ttttgcccca aacagtatga
7021 agacaaccag ttattcaggc cagctctcca gtaaccctgt acataagcaa tccacactac
7081 cccgtcccag cccttcaaaa actaatgtta gtagtggttc ttctagtgtg tatagttctt
7141 tatcttctgc ttcctcacaa tcaactcatt caacggtttt gactgcggga tccgggtcgt
7201 ctaggacagc tccctcctcc tcaacagctt ccaccttgtc tagaactagt gattgggtaa
7261 gaggacaaaa tgagagactc agcccgttta tgaatggtgc tctccaaaca acttttgtca
7321 caccaccatc gagcagggct tcatcatatg ggtcggtctc aaccgtcccc aaagctgttt
7381 tggactcctg gactcctatg ttcaatacca ataggcagcc tctcttcgct cacattcgta
7441 ggcgagggga gtcacagatt tagtgaaaag attgattagg
//