Typing tool
|
|
|
|
|
|
Typing tool
|
Complete norovirus genomes
| MH218733 | GII.2 | |
|
|---|---|---|---|
| GII.P31 |
ORF1: 5..5104
ORF2: 5085..6713
ORF3: 6713..7492
LOCUS MH218733 7550 bp RNA linear VRL 11-JUN-2018
DEFINITION Norovirus GII isolate NORO_94_23_10_2014, complete genome.
ACCESSION MH218733
VERSION MH218733.1
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_94_23_10_2014"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="United Kingdom"
/collection_date="23-Oct-2014"
/note="genotype: GII.Pe_GII.2"
gene 5..5104
/gene="ORF1"
CDS 5..5104
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="AWR17857.1"
/translation="MKMASNDASAAAAANSNNDIAKSSSDGMFSNMAVTFKRALGARP
KQPPPKEIPPRPPRPPTPELVKKIPPPPPNGEDELVVSYSARDGVSGLPELTTVRQPE
ETNTAFSVPPLNQRENRDAKEPLTGTIIEMWDGEIYHYGLYVERGLILGVHKPPAAIS
LAKVELTPLSLFWRPVYTPQYLISPDTLRRLHGESFPYTAFDNNCYAFCCWVLDLNDS
WLNRRMIQRTTGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCTLSSLFTRPIKDIIGK
LKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED
LAVELVPIVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
KKEEANELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYLRTLDLEEEKARKLST
KSASPDIVGTINSLLARIAAARSLVHRAKEELSSRPRPVVVMISGKPGIGKTHLAREL
AKKIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC
PLTLNCDRIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYADAPGVEK
AKRDFPGQPDMWKDAFNPDFSHIKLSLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA
SGLLHERLDEYELQGPALTTFNFDRNKILAFRQLAAENKYGMMDTMRVGRQLKDVKTM
SDLKQALKNIAIKKCQIVYGGSTYTLEADGKGSVRVDKVQSATVQTNNELAGALHHLR
CARIRYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQNLWSKPQVEDTEEMVNADGC
PKLKDDEEFVVSSDDIKTEGKKGKNKSGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV
TGSEIRKRNPEDFKPKGKLWADDDRSVDYNEKLNFEAPPSIWSRIVNFGSGWGFWVSP
SLFITSTHVIPQGAKEFFGVSIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG
TVATLLIKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILG
PGSAPKLSTKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP
RGKPPRPNVLEAAKKTIINVLEQTIDPPQKWSFAQACASLDKTTSSGYPHHMRKNDCW
NGDSFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDL
ATMIRCARAFGGLMDEFKAHCVTLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWD
STQQRDVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVMDVGDFQISISEGLPSGVPCT
SQWNSIAHWLLTLCALSEVTDLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLK
EYGLKPTRPDKTEGPLVISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP
NHEDPSETMIPHSQRPIQLMSLLGEAALHGPTFYSKISKLVIAELKEGGMDFYVPRQE
PMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE"
mat_peptide 5..994
/gene="ORF1"
/product="p48"
mat_peptide 995..2092
/gene="ORF1"
/product="NTPase"
mat_peptide 2093..2629
/gene="ORF1"
/product="p22"
mat_peptide 2630..3028
/gene="ORF1"
/product="VPg"
mat_peptide 3029..3571
/gene="ORF1"
/product="Pro"
mat_peptide 3572..5101
/gene="ORF1"
/product="RdRp"
gene 5085..6713
/gene="ORF2"
CDS 5085..6713
/gene="ORF2"
/codon_start=1
/product="VP1"
/protein_id="AWR17858.1"
/translation="MKMASNDAAPSTDGAAGLVPESNNEVMALEPVAGAALAAPVTGQ
TNIIDPWIRANFVQAPNGEFTVSPRNAPGEVLLNLELGPELNPYLAHLARMYNGYAGG
MEVQVMLAGNAFTAGKLVFAAVPPHFPVENLSPQQITMFPHMIIDVRTLEPVLLPLPD
VRNNFFHYNQKDDPKMRIVAMLYTPLRSNGSGDDVFTVSCRVLTRPSPDFDFTYLVPP
TVESKTKPFTLPILTLGELSNSRFPVSIDQMYTSPNEVISVQCQNGRCTLDGELQGTT
QLQVSGICAFKGEVTAHLHDNDHLYNVTITNLNGSPFDPSEDIPAPLGVPDFQGRVFG
IISQRDKHNSPGHNEPANRGHDAVVPTYTAQYTPKLGQIQIGTWQTDDLTVNQPVKFT
PVGLNDTEHFNQWVVPRYAGALNLNTNLAPSVAPVFPGERLLFFRSYIPLKGGYGNPA
IDCLLPQEWVQHFYQEAAPSMSEVALVRYINPDTGRALFEAKLHRAGFMTVSSNTSAP
VVVPANGYFRFDSWVNQFYSLAPMGTGNGRRRVQ"
gene 6713..7492
/gene="ORF3"
CDS 6713..7492
/gene="ORF3"
/codon_start=1
/product="VP2"
/protein_id="AWR17859.1"
/translation="MAGAFVAGLAGDVLSNGLSSLINAGANAINQRAEFDFNQRLQQN
SFNHDKEMLQAQIQATKQLQADMMAIKQGVLTAGGFSPADAARGAVNAPMTQALDWNG
TRYWAPGSMRTTSYSGRFTSTAPVRQADFQHTQSRPSSGSSVSSFTTQSSRPTLTTTT
GSSHSTVSSNSTRSTNLSQSTVSRATSRTGEWVRDQNKNLEPYMHGALQTAFVTPPSS
RASDGTVSTVPKGVLDSWTPAFNTRRQPLFAHLRKRGESQA"
ORIGIN
1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgct gctgccaaca gcaacaacga
61 catcgcaaaa tcttcaagtg acggtatgtt ctctaacatg gctgtcactt ttaaacgggc
121 cctcggggcg cggcctaaac agccgccccc gaaggaaata ccacccagac ccccacgacc
181 gcccacccca gaattggtca aaaagatccc tcctccccca cccaacgggg aggatgaact
241 agtggtctcc tacagcgcca gagatggcgt ttccggactg cctgagctca ccactgtcag
301 acaaccggaa gaaaccaaca cggcgttcag tgttccccca ctcaaccaaa gggagaacag
361 ggacgccaag gaaccactaa ctggaacaat tattgaaatg tgggatggag aaatctacca
421 ttatggcctg tacgtggaac gaggccttat actcggtgtg cacaagccac cggcagctat
481 cagccttgcc aaggtcgagc taacaccact ctctttgttc tggagacctg tatacacccc
541 ccagtatctc atctctccag acactctcag gagattacat ggagagtcat tcccctacac
601 tgcttttgac aacaattgct acgccttttg ttgttgggta ttagacctaa acgactcatg
661 gctaaacagg agaatgattc agagaacaac aggtttcttc aggccgtacc aggattggaa
721 caggaaaccc ctccccacta tggatgattc taaattaaag aaggtagcca acatattctt
781 gtgcacctta tcttcactat tcaccagacc cattaaggac ataataggaa aattgaaacc
841 tctcaacatc cttaacattc tggctacatg tgattggacc ttcgcaggca tagtggaatc
901 cttaatactc ttggcagaac tctttggagt tttctggaca cccccagatg tgtctgcgat
961 gatcgccccc ttactaggtg attatgaact gcaagggcct gaggaccttg cagtggaact
1021 ggtcccaata gtgatggggg ggataggttt ggtgctagga tttaccaaag agaaaattgg
1081 aaagatgcta tcatccgccg catccacttt aagagcttgt aaagaccttg gtgcatacgg
1141 actggaaatt ttgaaattgg tcatgaagtg gttcttccca aagaaagagg aagcgaatga
1201 actggctatg gtgagatcca tcgaggatgc agtgctggac ctcgaggcaa ttgaaaacaa
1261 ccacatgacc actctgctca aagacaaaga cagcttggca acctacttga gaacccttga
1321 ccttgaggag gagaaagcca ggaaactctc aaccaaatct gcttcacccg acatcgtggg
1381 cacaatcaac tctctactgg caagaatcgc tgctgcacgc tctctagtgc atcgggcgaa
1441 agaagagctc tccagcaggc caagacccgt tgttgtgatg atatcgggaa aaccagggat
1501 agggaaaact caccttgcca gggagctggc caaaaagatc gcggcctccc tcacggggga
1561 ccagcgtgtg ggtcttatcc cgcgcaatgg tgtcgaccac tgggacgcat acaaaggtga
1621 aagagttgtc ctatgggacg actatggaat gagcaacccc atccatgatg ccctcaggct
1681 gcaggaactt gctgacactt gccccctcac gctaaattgt gatagaattg agaacaaagg
1741 gaaagtcttt gacagtgatg ccataattat caccaccaat ctggccaacc cagcaccact
1801 ggattatgtc aactttgaag cgtgctcgag acgcattgac ttcctcgtgt acgcagatgc
1861 tcctggggtg gagaaggcga agcgcgactt cccaggccaa cctgacatgt ggaaggacgc
1921 tttcaatcct gacttctcac acataaaact gtcgttggct ccacagggtg gttttgacaa
1981 gaacggcaac accccgcatg ggaaaggtgt catgaagacc ctcaccaccg gctccctcat
2041 cgcccgggct tcagggttac tccatgagag gctagatgaa tatgaactgc aaggcccagc
2101 cctcaccact ttcaactttg accgcaacaa gatacttgct tttaggcagc ttgctgctga
2161 aaacaagtat gggatgatgg acacaatgag agttggaaga cagctcaagg atgtcaagac
2221 catgtcggac ctcaaacaag cactcaagaa catcgcgatc aagaagtgcc agatagtgta
2281 tggtggtagc acctacacac ttgaggccga tggcaagggt agtgtgagag ttgacaaagt
2341 acaaagtgcc actgtgcaaa ccaataatga attagccggt gccctacacc acctaaggtg
2401 cgccagaatt agatactatg ttaagtgtgt ccaggaggca ctgtattcca tcatccaaat
2461 cgctggggct gcattcgtca ccacgcgcat cgctaagcgc atgaatatac agaacctctg
2521 gtccaagcca caagtggaag acacagaaga gatggttaac gcagatggtt gcccaaaact
2581 caaagatgat gaagagtttg tcgtctcatc cgacgacatc aaaactgagg gtaagaaagg
2641 gaagaacaag tccggccgtg gcaagaagca cacagccttc tcaagcaaag gactcagtga
2701 tgaggagtac gacgagtaca agagaatcag agaggaaagg aatggtaagt attccataga
2761 agagtacctt caggacagag acaagtacta cgaggaggtg gccattgcta gggcaaccga
2821 agaggacttc tgtgaagaag aagaggccaa aatccgacag agaattttta gaccaacaag
2881 aaaacaacgc aaagaagaga gggcctctct cggcttggtc acaggttctg aaatcaggaa
2941 aagaaaccca gaagatttca aacccaaggg aaagctgtgg gccgatgatg acagaagtgt
3001 tgattacaat gagaaactta actttgaggc cccaccaagc atctggtcgc ggatagtcaa
3061 ctttggttct ggttggggct tctgggtgtc ccccagcctg tttataactt caacccatgt
3121 catacctcaa ggtgcaaaag agttcttcgg agtctctatc aagcaaatcc agatacacaa
3181 atcaggtgaa ttctgccgac tgagattccc aaaaccaatc agaactgatg tgacgggcat
3241 gattctagaa gaaggcgcgc ccgaagggac cgtggccaca ctgctcatca agagaccgac
3301 tggagagctc atgcctctgg cagccagaat ggggacccac gcaaccatga agattcaggg
3361 gcgcacagtt ggagggcaaa tgggtatgct cctgacagga tccaacgcca agagcatgga
3421 cctaggcaca acaccaggtg actgcggctg tccctacatc tacaagagag ggaatgacta
3481 cgtggtcata ggagtccata cggccgctgc ccgtggagga aacactgtca tatgtgccac
3541 ccaggggagt gagggagaag ccacacttga aggaggtgac aataaaggaa catactgtgg
3601 tgcaccaatc ttgggcccag ggagcgctcc gaagctcagt accaagacta agttttggag
3661 gtcatccaca acaccactcc cgcctggcac ctacgaacca gcatacctcg gtggcaaaga
3721 tcccagagtt aaaggtggcc cttcattgca acaagttatg agggaccagt tgaagccatt
3781 cacagaaccc agaggcaaac caccaagacc aaatgttcta gaagctgcca agaaaaccat
3841 catcaatgtt cttgagcaaa caattgaccc accccaaaaa tggtcattcg cgcaggcctg
3901 cgcatccctt gacaaaacca cctccagtgg ctacccgcac catatgcgga agaacgactg
3961 ttggaatggg gattccttca caggaaaatt ggcagaccag gcctccaagg ctaatctaat
4021 gtttgaagag ggaaagaaca tgaccccagt ctacacaggt gcacttaaag atgagttggt
4081 gaagactgat aaaatttatg gtaagatcaa gaagagactt ctgtggggct cagatctggc
4141 gaccatgata cggtgtgccc gggctttcgg aggccttatg gatgaattca aggcacactg
4201 tgtcacactt cctgtcagag ttggtatgaa catgaatgag gatggcccca tcatctttga
4261 gaagcactcc agatataaat accactatga tgctgattat tcccggtggg actcaacaca
4321 acaaagggat gtgctggcag cagcactaga aatcatggta aaattctctc cagaaccaca
4381 cctggcccag gtagttgcag aagatctcct ttcccctagc gttatggatg taggtgactt
4441 tcaaatatca ataagtgagg ggctcccctc cggggtacct tgtacctccc agtggaattc
4501 catcgcccac tggctcctca ctctttgtgc actctctgaa gtcacggacc tgtcccctga
4561 catcattcag gccaattccc ttttctcctt ctatggtgat gatgagattg tgagcacaga
4621 cataaagttg gatccggaga agctgacagc aaaactcaag gagtacgggc tgaaaccaac
4681 ccgccccgac aaaactgaag gacctcttgt tatctctgaa gatctggatg gtctaacatt
4741 ccttcggagg actgtgaccc gtgacccagc tggctggttt ggaaaactgg aacaaagctc
4801 aattctcagg caaatgtact ggaccagggg tcccaaccat gaagacccat ctgaaacaat
4861 gataccacac tcccaaagac ccatacaatt gatgtccttg ctgggcgagg ctgcactcca
4921 cggcccgaca ttttatagca aaattagcaa attagtcatt gcagagctga aggaaggtgg
4981 catggatttt tacgtgccca gacaagagcc aatgttcaga tggatgagat tctcagatct
5041 gagcacgtgg gagggcgatc gcaatctggc tcccagtttt gtgaatgaag atggcgtcga
5101 atgacgccgc tccatctact gatggtgcag ccggcctcgt gccagaaagt aataatgagg
5161 tcatggctct tgaacccgtg gctggtgccg ccttggcagc cccagtcacc ggacaaacaa
5221 atattataga cccttggatt agagcaaatt ttgtccaggc ccctaatggt gaatttacag
5281 tttctccccg taatgcccct ggtgaagtgt tattgaatct agagttgggt ccagagttaa
5341 atccttatct ggcacattta gcaagaatgt acaacgggta tgctggtggg atggaggtgc
5401 aggtcatgtt ggctgggaac gcgttcacag ccggcaagtt ggtctttgcc gccgtaccac
5461 ctcacttccc ggttgaaaac cttagtccac agcaaattac catgtttccc catatgatta
5521 tagatgtgag aactttggaa cctgttttat taccactccc tgatgttaga aataatttct
5581 tccattacaa tcagaaggat gatcctaaga tgagaattgt ggctatgctt tatactcccc
5641 ttagatctaa tggctcaggt gatgacgtgt ttacagtctc atgcagggtg ttgactagac
5701 cctcccctga ttttgacttc acatatttgg tgccaccaac agtggaatct aagactaaac
5761 cattcaccct cccaatcctc acgcttgggg agctctccaa ttctagattt ccagtgtcca
5821 tagatcagat gtataccagc cccaatgaag ttatatcagt gcaatgtcaa aatggtaggt
5881 gcacactgga tggggaactc caaggaacaa cacaactcca agtcagtggc atttgtgcct
5941 tcaagggaga ggtgaccgcc catttgcatg acaatgacca tctatataat gtcaccatca
6001 caaacttgaa cgggtcccct tttgacccct ccgaggacat ccctgcccct ttgggcgtac
6061 ctgattttca gggaagggtc tttggtatca tctcccaaag agacaaacac aacagccctg
6121 ggcataatga accagcaaac aggggacacg acgctgtggt ccctacttac acagcacagt
6181 acaccccaaa attgggtcaa attcaaattg gcacatggca gaccgatgat cttacagtca
6241 accaaccagt caaattcacc ccagttggac ttaatgacac tgaacatttt aaccaatggg
6301 tggtccccag atatgctggt gctctaaacc tcaacacaaa tcttgcccct tctgttgctc
6361 cagtttttcc aggggagcgc ctgctctttt tcagatcata tatccccctc aagggtggtt
6421 atggaaatcc agctattgat tgtctgctac cacaagagtg ggtgcaacat ttctatcagg
6481 aagcagcccc ttcaatgagt gaggtggccc ttgtcagata catcaacccg gacactggtc
6541 gagcactgtt tgaggccaag ctccacagag ctggtttcat gacggtctcg agcaacacca
6601 gtgccccggt ggttgtgcct gccaacggat acttcagatt tgattcttgg gtgaaccaat
6661 tctattctct cgcccccatg ggaactggaa atgggcgtag aagggttcaa taatggctgg
6721 agcttttgta gctggtcttg caggggacgt gctcagcaat gggctcagtt cactaattaa
6781 tgcaggtgct aatgcaataa atcagagggc agaatttgat tttaatcaga gattacaaca
6841 aaattctttc aatcatgata aggagatgtt acaggctcag attcaggcaa ccaagcagct
6901 gcaggcagac atgatggcta taaagcaggg agtcttgacc gctggcggct tctcccccgc
6961 tgacgcagcc agaggtgctg tgaatgcacc catgacacag gcgctggatt ggaacggcac
7021 aaggtattgg gcaccaggct ccatgaggac cacatcttac tctggaagat tcacatcaac
7081 cgccccagtg aggcaggccg acttccaaca cacccagagc cggccttcga gtggctcttc
7141 tgtgtcctcc ttcactactc agtcttcaag gccaactctg actacaacca ctgggtcctc
7201 acatagtaca gtttcatcaa attcaactcg cagcacaaac ctctcccaat caacggtttc
7261 cagggctaca tctaggacag gtgagtgggt tagagatcaa aataaaaatt tggaacctta
7321 catgcatggt gccttacaga cagcctttgt caccccacct tccagcaggg cttctgatgg
7381 gacagtctca accgtcccaa aaggtgtttt ggactcctgg acacctgcgt tcaacacccg
7441 caggcagccg ctttttgcac acctccgtaa gaggggggag tcacaagcct agtgaaaagg
7501 taaatttatt tagaatgaaa tgattttatc ttttaaaaaa aaaaaaaaaa
//