Typing tool
|
|
|
|
|
|
Typing tool
|
Complete norovirus genomes
| MH218639 | GII.6 | |
|
|---|---|---|---|
| GII.P7 |
ORF1: 5..5098
ORF2: 5079..6722
ORF3: 6722..7498
LOCUS MH218639 7550 bp RNA linear VRL 11-JUN-2018
DEFINITION Norovirus GII isolate NORO_170_23_09_2014, complete genome.
ACCESSION MH218639
VERSION MH218639.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7550)
AUTHORS Brown,J.R., Roy,S., Shah,D., Williams,C.A., Williams,R., Dunn,H.,
Hartley,J., Harris,K. and Breuer,J.
TITLE Norovirus transmission dynamics in a paediatric hospital using full
genome sequences
JOURNAL Clin. Infect. Dis. (2018) In press
PUBMED 29800111
REMARK Publication Status: Available-Online prior to print
REFERENCE 2 (bases 1 to 7550)
AUTHORS Brown,J.R., Roy,S., Shah,D., Williams,C.A., Williams,R., Dunn,H.,
Hartley,J., Harris,K. and Breuer,J.
TITLE Direct Submission
JOURNAL Submitted (17-APR-2018) Division of Infection and Immunity,
University College London, 90 Gower St, London, London WC1E 6BT,
United Kingdom
COMMENT ##Assembly-Data-START##
Assembly Method :: CLC Genomics Workbench v. 10.1
Sequencing Technology :: Illumina
##Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..7550
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="NORO_170_23_09_2014"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="United Kingdom"
/collection_date="23-Sep-2014"
/note="genotype: GII.P7_GII.6"
gene 5..5098
/gene="ORF1"
CDS 5..5098
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="AWR17577.1"
/translation="MKMASNDATTAFGSQNSVNDSINTAPSNKEEVGAFSNIKVGFKK
MLGAVPKGTKAPSSDQHCPSVKIGTKTLTVPPEPPNGEDTVQFDAKSETVRGLPDLTT
VQNEHENTPYTVPPLSEREHRPATEPLPGTILEMWDGEFYHYSVYVSGGKALGVHKPP
AAISLATIELTPISLYWRPVYTPNYLVCPDTLKGLAGEKFPYTAFSNNCYNFCCWVLE
LNDTWLSRRSISRTTGFFKPYQSWNRKPLPTVDDGKIKKVANAILCALGSLFSKPIKD
LLGKLKPLNLLHLLASCDWTFAGIVETVILMAELFNIFWTPPDVSSFIASLIGDFELQ
GPEDLAVELVPVVMGGIGMVLGFTAEKIGRMLSSAASTLRACKDLGNYALDILKLVMK
WFFPKKEEKAEMETLRAIEDAVLDMEAIGNNHLTTLLKDKDSLTAFMKTLDLEEEKAR
KLSTKSSSPDIVGTINAILARIAAARSLLHKAKEEMFSRIRPVVVMISGRPGIGKTHM
ARHLAKSIANTMSGDQRVGLVPRNGVDHWDAYRGERVVLWDDYGMGNPVKDALTLQEL
ADTCPVTLNCDRIENKGKMFDSDVIIITTNLVNPAPLDYVNFEACSRRVDFLVYAESP
EVEKVKRDFPGQPDMWKDHFKPDFSHIKLTLAPQGGFDKNGNTPHGKGTMRSLTQGSL
TARVAGLVHERRDEFQLQGNDLQTYNFDTNRVSAFRKLAADNKYGIMETMRVGTALKS
VKTLEDLKVALRDVKFNECEIIYRNSKYRVSSNGKGSVSVDKVEDQTSQTANEVGAAL
LRLRQARARYYVSCFQDLIYTLIQVAGASFVVNRISKRFCWERWVKPTETQETSESEK
EVAQGRWEIEPKDTESEGKKGKNKKGRGKKHTAFSSKGLSDEEYDEFKRIREERNGKY
SIEEYLQDRDRYYEEVAVARATEEDFCEEEEAKIRQRIFRPTKKQRKEERGVLGLVTG
SDIRKRRPDDFQPKGNLWADDTRSVDYNERLDFEAPPSVWSRIVPLGTGWGFWVSSNL
LITTTHVLPKGIKELFGVEIKQIQIHKSGEFCRFRFPRPIRPDVTGLVLEEGAPEGTV
CSILVKRPTGEMIPLAVRMGTHASMKIQGRTVGGQMGMLLTGANAKNMDLGTGPGDCG
CPYIYKRGNDIVVAGVHTAAARGGNTVICATQGQDGEAVLEGNENLGTYCGAPILGPG
KAPKLSTKTKFWRSSPDALPPGTYEPAYLGGKDPRVEKGPSLQQVMRDQLKPFTEPRG
KPPRPAVLEEAKKTVMNVLEQTIDPAKPWTYSQACASLDKTTSSGSPHHVRKNDHWNG
ESFTGPLADQASKANLMYEQAKHVQPVYTAALKDELVKTDKIYKKIKKRLLWGSDLGT
MIRCARAFGGLMDSMKASCIALPCRVGMNMNEDGPIIFDKHSKYRYHYDADYSRWDST
QQRSILSAAMEVMVRFSAEPELAQVVAEDLLAPSQLDVGDFVISVQEGLPSGVPCTSQ
WNSIAHWILTLSAMAEVSGLSPDVVQAHSCFSFYGDDEIVSTDINLDPMKLTQKLREY
GLVPTRPDKTEGPLVITEDLTGLTFLRRSIARDPAGWFGKLDQDSILRQLYWTRGPNH
ENPYESMVPHSQRATQLMALLGEASLHGPQFYKKVSKMVINEIKSGGLEFYVPRQEAM
FRWMRFSDLSTWEGDRNLAPEGVNEDGVE"
gene 5079..6722
/gene="ORF2"
CDS 5079..6722
/gene="ORF2"
/codon_start=1
/product="VP1"
/protein_id="AWR17575.1"
/translation="MKMASNDAAPSNDGAANLVPEATNEVMALEPVMGASIAAPVVGQ
QNIIDPWIRENFVQAPQGEFTVSPRNSPGEMLLNLELGPELNPYLSHLSRMYNGYAGG
MQVQVVLAGNAFTAGKIIFSAVPPHFPVENISAAQITMCPHVIVDVRQLEPVLLPLPD
IRNRFFHYNQENNPRMRLVAMLYTPLRANSGEDVFTVSCRVLTRPAPDFEFTFLVPPT
VESKTKPFTLPILTLGELSNSRFPAPIDMLYTDPNEAIVVQPQNGRCTLDGTLQGTTQ
LVPTQICSFRGTLISQTSRSADSTDSAPRVRNHPLHVQLKNLDGTPYDPTDEVPAVLG
AIDFKGTVFGVASQRNTTGGSIGATRAHEVHIDTTNPRYTPKLGSVLMYSESTDFDDG
QPTRFTPIGMGADDWHQWELPEYSGHLTLNMNLAPAVAPAFPGERILFFRSVVPSAGG
YGSGHIDCLIPQEWVQHFYQEAAPSQSAVALIRYVNPDTGRNIFEAKLHREGFITVAN
SGNNPIVVPPNGYFRFEAWVNQFYTLTPMGTGQGRRRVQ"
gene 6722..7498
/gene="ORF3"
CDS 6722..7498
/gene="ORF3"
/codon_start=1
/product="VP2"
/protein_id="AWR17576.1"
/translation="MAGAFLAGLAGDAITSGVGSLINAGANAINQKVEYDFNRQLQLA
SFKHDKEMLQSQVLATKQLQQEMMNIRQGVLSAGGFSPTDAARGAVNAPMTKILDWNG
TRHFAPNSMKTTSYSGQFSSNPVHRQPTSPRSDSPKIKVNSDSASVYSSASIAPSQST
HSTALTAGSSSSRTTPSSAVASTLSRTSDWVRGQNERLSPFMDGALQTTFVTPPSSKA
SSYGSVSTVPKAILDSWTPMFNTHRQPLFAHVRRRGESQI"
ORIGIN
1 gtgaatgaag atggcgtcta acgacgctac cactgccttt ggcagccaaa actctgtcaa
61 tgacagcatc aacaccgccc cttctaataa agaagaggtt ggtgcattct ccaacatcaa
121 agttggtttt aagaaaatgc tgggtgccgt tcctaagggg accaaagcac ccagtagtga
181 tcagcactgc ccatcagtta agatcgggac taagacatta acagttcccc ctgagccccc
241 aaatggtgaa gacaccgtgc agtttgatgc gaagtcggaa actgtgcgcg ggctaccaga
301 cttgacaacg gtgcagaatg aacacgaaaa cacaccatac actgtccccc cattgagtga
361 aagggagcac agaccagcca ctgagccgct tcctggcaca atactggaga tgtgggatgg
421 tgaattctac cattactctg tgtacgtcag cggtggcaaa gcccttgggg tccacaagcc
481 ccctgcagcg ataagcctcg cgacgataga gctcacaccc atatctcttt attggaggcc
541 cgtttacacc cccaactatc tggtctgccc agacacgttg aaaggccttg ctggtgagaa
601 gttcccctac acggccttca gcaacaactg ttacaacttc tgttgctggg tgcttgagct
661 caatgacacg tggcttagca ggaggagcat ctctaggact accggcttct tcaaaccata
721 tcagtcttgg aataggaaac cccttccaac cgttgatgat ggaaagatca aaaaggtggc
781 caacgcaatt ctctgcgcac ttggatcact gttttcaaaa ccaatcaagg acctattggg
841 caaacttaaa ccattgaact tgctgcactt gctcgcatca tgtgactgga catttgcggg
901 tatagtagag acagtcatcc taatggcgga acttttcaac atcttttgga caccgccaga
961 tgtttccagt ttcatagcct ccctgatagg tgattttgaa ttgcaagggc ctgaggacct
1021 ggctgttgag cttgtccccg tggtcatggg tggcatagga atggttctcg gctttactgc
1081 tgagaagata ggccgcatgc tgtcgtccgc tgcatcaaca ctacgggcat gcaaagactt
1141 ggggaattat gcccttgaca tattgaaact ggttatgaag tggttcttcc caaagaaaga
1201 agagaaagcc gagatggaaa ccctaagggc gattgaggat gccgtcctag acatggaagc
1261 tataggaaat aaccatctca caaccctcct caaggacaag gatagcctca cggctttcat
1321 gaagactcta gatctagaag aggagaaggc aaggaagctg tccaccaaat catcctcgcc
1381 agacatcgtt ggcactatta atgccatact ggccagaata gctgctgcca ggtccctctt
1441 gcacaaagcc aaagaagaaa tgtttagcag gatcagacct gtggttgtca tgatctcggg
1501 tagacctggt attggcaaaa cccacatggc aagacacttg gctaagagca tcgccaacac
1561 catgagcggc gaccagagag tagggctcgt cccacgcaac ggggtcgatc attgggacgc
1621 ctacagggga gagagggtgg tcttgtggga tgattatggc atgggaaacc ctgtcaaaga
1681 tgccctaaca ctgcaagagt tggccgacac ctgcccagta actctaaact gtgataggat
1741 tgagaacaag gggaagatgt ttgacagtga tgtcatcata atcacgacca acttagtcaa
1801 cccagcgccc ctcgattatg taaacttcga ggcgtgctcc agaagggtcg actttctagt
1861 ctatgcagag tcaccagaag ttgagaaggt taagagagac ttccccggcc aacctgacat
1921 gtggaaggac cattttaagc cagacttttc ccacataaaa ctgactctag ccccacaggg
1981 tggatttgac aagaatggca acaccccaca tggtaagggc accatgcgat ccctaaccca
2041 ggggtccctg actgcaaggg ttgcaggtct tgttcatgag aggagagacg agtttcagct
2101 ccaggggaac gaccttcaaa catacaactt tgacaccaac agggtctctg catttaggaa
2161 gctggccgca gacaacaagt atgggatcat ggagactatg agagtgggca cagcgcttaa
2221 gagtgtcaag accttggaag atttgaaagt tgcactgagg gatgtgaagt tcaatgagtg
2281 tgagataatt tacagaaact ccaaataccg agtctcttcc aatggtaaag gttctgtctc
2341 tgttgacaaa gttgaggacc aaacatccca gactgcaaac gaagtgggtg cagcactcct
2401 cagactcagg caggcaagag ccagatatta tgtcagctgc ttccaagatc tcatttacac
2461 cctaatacag gtcgccggag catcattcgt tgtcaacagg atctctaaaa ggttctgctg
2521 ggagagatgg gtcaaaccaa ccgagaccca ggaaacgagt gaatccgaaa aggaagtggc
2581 ccaaggcaga tgggagattg agcccaagga cacagaatca gaaggtaaga aaggtaagaa
2641 caagaaagga agaggcaaga aacacacagc tttctccagc aaaggcctga gtgatgagga
2701 atatgacgag ttcaagagaa ttagagaaga gaggaacgga aaatactcca ttgaggaata
2761 cctgcaagac cgggatcgct actatgagga agtggcagtt gcccgggcga cagaggagga
2821 cttctgtgaa gaggaggagg ccaagataag acaaagaatc tttcgcccca caaagaaaca
2881 gaggaaggaa gaaagggggg tgcttggttt ggtcactggc tcagacatca gaaagagaag
2941 accagacgat tttcaaccga agggtaacct gtgggcagac gacaccagga gtgtggacta
3001 caacgagaga cttgatttcg aggctccccc gagtgtctgg tcaagaatag tcccattggg
3061 cactggctgg ggcttctggg tctcatcaaa cctcctgatc acaacaacac acgtcctgcc
3121 caagggaatt aaggaacttt ttggggttga aatcaaacag attcaaattc ataagtctgg
3181 agagttctgc aggttcagat tcccgagacc aattagacca gatgtcacag ggctcgtgtt
3241 ggaggaaggc gctccagaag gcactgtctg ctccatactc gtaaagagac ctacaggtga
3301 gatgatcccc ctagcagtga ggatgggcac gcatgcgtcc atgaaaatac agggtaggac
3361 cgtcggtggc cagatgggaa tgctcctcac aggggcaaat gcgaagaaca tggaccttgg
3421 caccggtccc ggtgactgcg gttgccctta catctacaaa cgtggcaatg atatagttgt
3481 cgcgggtgtc cacaccgcag cagcccgggg aggcaatact gtcatatgtg ccactcaagg
3541 gcaagatggg gaagcagtcc ttgagggaaa tgagaacctt ggcacttact gcggtgcccc
3601 aatcctgggt ccaggcaagg cgcccaaact tagcacgaag accaagttct ggcgctcatc
3661 accagacgct ttgccgccag gcacttatga gcctgcctac ttgggaggta aggaccccag
3721 agtggaaaaa ggaccatccc tgcagcaagt catgagggac cagctaaaac ctttcacgga
3781 acccagaggc aagccaccta gacctgcagt cttagaagaa gctaaaaaga cagtgatgaa
3841 tgttctagag caaaccattg accccgctaa gccgtggacc tattcccaag catgtgcctc
3901 actggacaag accacttcca gtggtagccc ccatcatgtt aggaaaaatg accattggaa
3961 tggggaatcc ttcactggtc cccttgcaga ccaagcatcc aaagccaacc tcatgtacga
4021 gcaggccaaa catgtgcagc ccgtgtacac ggccgcactc aaagatgaac tagttaaaac
4081 tgacaagatc tacaagaaga taaagaaaag gctcttatgg gggtcggatc ttggtacaat
4141 gatcaggtgt gccagggcct tcggcggtct catggatagc atgaaggcaa gttgcatagc
4201 cctcccatgt agggtaggta tgaacatgaa tgaagatggt cccatcatat ttgacaaaca
4261 ttctaagtat aggtaccatt atgatgctga ctactccagg tgggactcaa cccagcaaag
4321 gagcattctc tcggccgcta tggaagtgat ggtgcggttc tctgccgagc cagagctggc
4381 acaagtggtt gcagaggacc tcctggcacc cagtcaactc gatgttggag atttcgtcat
4441 ctcagtccag gagggtctgc catcgggggt tccatgcaca tcacaatgga attcaatagc
4501 acactggatc ctaaccttga gtgcaatggc agaagtgtcg ggtctctcac cagatgttgt
4561 tcaagcccac tcctgtttct cattctacgg tgatgatgag atcgtcagca ctgacatcaa
4621 ccttgatccc atgaagttga cacagaaact cagagagtat ggcctggtcc ccactcgacc
4681 tgacaaaact gagggtcccc tcgtaataac tgaagatctc accggcctaa cgttcctgcg
4741 taggtcaatt gcacgggacc cagctgggtg gtttggaaaa ttggaccagg actcaatcct
4801 cagacagttg tattggacaa ggggccccaa tcatgagaac ccatatgaga gcatggtccc
4861 tcattcccag cgggccacac agcttatggc ccttctcggt gaggcttcac tgcatggccc
4921 ccagttttac aagaaggtta gcaagatggt cattaatgag atcaaaagtg gtggtctgga
4981 attctatgtg cccagacaag aggccatgtt cagatggatg agattctctg acctcagcac
5041 atgggagggc gatcgcaatc ttgctcccga gggtgtgaat gaagatggcg tcgaatgacg
5101 ctgctccatc gaatgatggt gctgccaacc tcgtaccaga ggccaccaat gaggttatgg
5161 cacttgagcc ggtgatggga gcctcaattg ctgctcctgt cgtcggccaa caaaatataa
5221 ttgacccctg gattagagaa aattttgttc aggcaccaca gggtgagttt actgtttcac
5281 caaggaactc acctggtgag atgcttctaa atcttgaatt aggtcctgag ctcaaccctt
5341 atttgagtca cttgtcccgc atgtataatg gctatgctgg tggtatgcag gttcaggtgg
5401 tcctagctgg gaatgcgttc acagctggta aaatcatctt ttccgccgtc ccaccacatt
5461 tccctgttga gaacattagt gcagcccaaa ttacaatgtg cccccatgta attgttgatg
5521 taagacagct tgagccagtg cttttgcccc tccctgacat aaggaataga ttcttccatt
5581 ataaccagga aaacaacccc cggatgagac ttgtggctat gttgtataca ccccttagag
5641 caaattctgg tgaggatgtg tttacggtgt cttgtagagt cctgacccgc cctgcccccg
5701 actttgagtt cacgtttttg gtgccaccaa ctgtggagtc aaagactaag ccctttacac
5761 tccctattct gactcttgga gagctatcca actccagatt ccccgctccg atagacatgt
5821 tgtacaccga ccccaatgag gcaattgtgg tgcaaccaca aaatggcagg tgcactctag
5881 atggaacact tcaagggact acccaactgg tgcccaccca aatttgctcc ttcaggggca
5941 cgctaattag ccagacgtcg aggtctgcag attcaacaga ttcagcccca cgggtgagga
6001 accaccctct ccacgttcag ctgaagaacc tcgatgggac accatatgac ccaacagatg
6061 aggtgccagc agttttgggt gccatagatt tcaaaggaac tgtgtttggg gtcgctagtc
6121 aaagaaacac cacagggggc tctataggag caacccgcgc ccatgaagtg cacatagaca
6181 ccacaaaccc tagatatacc ccaaagcttg gctctgtgtt gatgtattct gaatccactg
6241 attttgatga tggacaaccc acccgcttta cccctattgg catgggagcc gatgattggc
6301 accaatggga attgcccgaa tattctggtc acctcactct caacatgaat ttggcccctg
6361 cagttgctcc tgctttccct ggtgagcgca ttctcttctt cagatcagtg gtgccgtctg
6421 ctggtggcta tggatcaggt cacatagatt gcctcatccc acaggagtgg gttcaacatt
6481 tctaccagga ggccgcccca tcacagtctg cggtggctct tatcagatat gtcaaccctg
6541 acactggaag aaacatcttt gaggcaaaac tgcatagaga agggttcatc actgtggcaa
6601 attctggaaa taaccccata gttgtgcccc caaatggtta cttcaggttt gaggcctggg
6661 tcaatcaatt ctatacactc acccccatgg gaactggaca ggggcgcaga agagttcaat
6721 aatggcggga gctttcttag ctggattggc aggtgacgcc ataacaagtg gtgtcgggtc
6781 cctaatcaat gctggggcca atgcaattaa ccaaaaggta gagtatgact ttaatagaca
6841 gctccaattg gcatccttca aacatgacaa agagatgttg cagtcacaag tactggccac
6901 taaacagctc cagcaggaaa tgatgaatat acggcaaggg gttttgtccg ctggcggctt
6961 ttcccctaca gatgccgcga gaggtgctgt gaacgcaccg atgacaaaaa ttttggactg
7021 gaatggaaca aggcactttg ccccaaatag tatgaagaca accagttatt cgggccagtt
7081 ttccagcaac cctgtacaca ggcaacccac ttcaccccgt tctgattccc caaaaatcaa
7141 agttaatagt gattctgcta gtgtgtatag ttctgcatct attgctcctt cacaatcaac
7201 ccactcaacg gctctgactg cggggtccag ctcatctagg acaacaccct cttctgcagt
7261 agcttccact ctatctagga ctagtgattg ggtgagagga caaaatgaga ggcttagccc
7321 gtttatggat ggtgctctcc aaacaacttt tgtcacacca ccatcgagca aggcttcatc
7381 atatgggtcg gtctcgaccg ttcccaaagc tattttggac tcctggactc ctatgtttaa
7441 tacccatagg cagcctctct tcgctcatgt gcgcaggcga ggggagtcac agatttagtg
7501 aaaagattga ttaggttttc tttctttctt cttttccttt tctttctttt
//