Typing tool
|
|
|
|
|
|
Typing tool
|
Complete norovirus genomes
| MH218595 | GII.3 | |
|
|---|---|---|---|
| GII.P21 |
ORF1: 5..5104
ORF2: 5085..6731
ORF3: 6731..7495
LOCUS MH218595 7548 bp RNA linear VRL 11-JUN-2018
DEFINITION Norovirus GII isolate NORO_125_19_01_2015, complete genome.
ACCESSION MH218595
VERSION MH218595.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7548)
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 7548)
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..7548
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="NORO_125_19_01_2015"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="United Kingdom"
/collection_date="19-Jan-2015"
/note="genotype: GII.P21_GII.3"
gene 5..5104
/gene="ORF1"
CDS 5..5104
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="AWR17443.1"
/translation="MKMASNDASAAAAAKSNNDNAKSSSDGVLSNMAVTFKRALGARP
KQPPPSDKPPKPPRPPTPELVKAIPPPPPNGEDEPIISYNVKGGVSGLPELSTVTQLE
ENSTAFSVPPLSQRENKDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAVS
LAKIELTPLSLYWRPVYTPQYLISPDTLRKLHGETFPYTAFDNNCYAFCCWVLDLNDS
WLNRRMIQRTTGFFRPYQDWNRKPLPTMDDSKVKKVANVVLCALSSLFTRPIKDIIGK
LKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED
LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
KKEEKNELAMVRSIEDAVLDLEAIENNHMTALLKDKDSLATYMRTLDMEEEKARKLST
KSASPDIVGTINALLSRIAAARSLVHRAKEELSSRPRPVVVMISGKPGIGKTHLAREL
AKKIASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSSPVHDALRLQELADTC
PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYADAPEVEK
AKRDFPGQPDMWKDTFKPDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTAGSLVARA
SGLLHERLDEYELQGPTPTTFNFDRNKVLAFRQLAAENKYGLVDTMRVGSQLKNVKTM
TELKQALKNISVKKCQLVYGGGTYTLESDGKGNVHVEKVNNTSVQTNNELSGVLHHLK
CARIRYYVKCVQEALYSILQIAGAAFITTRIAKRTNIQNLWSKPQAENLEETNNEEGC
PKPKNDEEFVVSSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTKKQRKEERASLGLV
TGSEIRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP
SLFITSTHVIPQGAQEFFGVPIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG
TVATLLIKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGNEGEAMLEGGDNKGTYCGAPILG
PGNAPKLSTKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP
RGKPPKPSVLEAAKKTIINVLEQTIDPPQKWTYAQACASLDKTTSSGHPHHVRKNDCW
NGESFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGVVKKRLLWGSDL
STMIRCARAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWD
STQQRAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVMDVGDFKISINEGLPSGVPCT
SQWNSIAHWLLTLCALSEVTDLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLR
EYGLKPTRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGP
NHEDPFETMIPHSQRPIQLMSLLGEAALHGPSFYSKISKLVISELKEGGMDFYVPRQE
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..6731
/gene="ORF2"
CDS 5085..6731
/gene="ORF2"
/codon_start=1
/product="VP1"
/protein_id="AWR17444.1"
/translation="MKMASNDAAPSNDGAAGLVPEINNEAMALEPVAGAAIAAPLTGQ
QNIIDPWIMNNFVQAPGGEFTVSPRNSPGEVLLNLELGPEINPYLAHLARMYNGYAGG
FEVQVVLAGNAFTAGKIIFAAIPPNFPIDNLSAAQITMCPHVIVDVRQLEPVNLPMPD
VRNNFFHYNQGSDSRLRLIAMLYTPLRANNSGDDVFTVSCRVLTRPSPDFSFNFLVPP
TVESKTKPFSLPILTISEMSNSRFPVPIDSLHTSPTENIVVQCQNGRVTLDGELMGTT
QLLPSQICAFRGVLTRSTSRANDQADTATPRFFDHSWHIQLDNLNGTPYDPAEDIPGP
LGTPDFRGKVFGVASQRNPDTTTRAHEAKIDTSSPRFTPKLGSLEISTESDDFEHNQP
TRFTPVGIGVDHEEDFKQWTLPNYAGQLTHNMNLAPAVAPNFPGEQLLFFRSHLPSSG
GRSNGILDCLVPQEWVQHFYQESAPSQSQVALVRYVNPDTGRVLFEAKLHKLGFMTIA
KNGDSPITVPPNGYFRFESWVNPFYTLAPMGTGNGRRRIQ"
gene 6731..7495
/gene="ORF3"
CDS 6731..7495
/gene="ORF3"
/codon_start=1
/product="VP2"
/protein_id="AWR17445.1"
/translation="MAGAFIAGLAGDMLTNTVGSLVNAGANAINQTIDFENNKYLQNA
SFNHDKEMLNAQVEATKKLQADMIAIKQGVLTAGGFSPTDAARGAINAPMTKVLDWNG
TRYWAPGATSTTSMSGGFTHQTVHRSTPNFKTNQAPKSTPSSGSSVRSNSTQITSLSS
HSSGSSRSSGSTVISSIPSSNRTRDWVNQQNFNLEPHMPGSLRTAFVTPPSSTASSSG
TVSTVPKNVLDSWTSAFNTRRQPLFAHLRRRGESNV"
ORIGIN
1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgct gctgccaaaa gcaacaacga
61 caacgcaaaa tcttcaagtg acggagtatt atctaatatg gctgtcactt ttaaacgagc
121 cctcggggcg cggcctaaac agccgccccc gagtgacaaa ccaccaaaac ccccaagacc
181 acccacacca gagttggtta aggcaattcc ccctccccca cccaacgggg aagacgaacc
241 aattatttct tacaacgtca aagggggtgt ttctggtttg cctgagctct caactgtcac
301 ccaactggaa gagaactcta cagcattcag cgttccccct cttagtcaga gggagaacaa
361 agatgcaaag gaaccattga ctggaaccat cctggagatg tgggacgggg agatctacca
421 ttatggctta tacgtagaac gagggttagt gctcggtgtg cacaaaccac cagcagcagt
481 cagccttgct aagattgagc tgaccccctt gtctttgtat tggagaccag tgtacacccc
541 acagtacctc atttcccctg acactctcag aaagttgcat ggggagacat tcccttatac
601 agcctttgac aacaactgtt atgccttctg ctgttgggtg cttgacttga atgattcatg
661 gctgaacaga aggatgatac agaggacaac aggcttcttc cgaccctacc aggattggaa
721 caggaaaccc ctccccacga tggatgactc caaagtgaaa aaggtggcca atgttgtcct
781 atgtgctctc tcatcattgt tcacaagacc aattaaggac attattggga agttaaaacc
841 cctaaacatc ctcaacatct tagccacatg tgattggact tttgcaggca tagtagaatc
901 cctgatcctt ttggctgaac tttttggagt tttctggaca cccccagatg tgtctgcgat
961 gatcgctccc ttactgggtg attatgaact acagggaccc gaggatctcg ctgtggaact
1021 cgtacccgta gtaatgggag ggataggttt ggtgctggga ttcaccaaag agaaaatcgg
1081 caagatgctt tcttctgctg cttcaaccct gagggcatgt aaagatcttg gtgcatatgg
1141 gttggagatc ctcaaattgg ttatgaaatg gtttttccca aagaaagaag agaaaaacga
1201 attggcaatg gtgagatcca tcgaggatgc agtgctagac cttgaagcca ttgagaacaa
1261 ccatatgaca gctctactta aggataaaga cagccttgca acctacatga ggactcttga
1321 catggaggag gagaaggcga gaaaactttc caccaagtct gcctctccgg atattgtggg
1381 tacgataaat gccctactgt caaggattgc agctgcccgg tctctagtgc acagggctaa
1441 ggaagagctg tcaagcaggc cccgaccggt cgttgtaatg atttcaggga aaccgggtat
1501 agggaagacc catctagcta gagagttggc aaagaagatc gcctccacac tcacaggtga
1561 ccagagggtg ggtcttatcc cacgtaacgg ggtcgaccac tgggatgcat acaaaggtga
1621 gagagtcgtt ctctgggacg actatgggat gagcagccct gtccacgacg ccctcagact
1681 ccaggagctc gctgacacct gtcctctcac actcaactgt gacaggattg agaacaaagg
1741 taaagtcttt gacagtgacg tcataataat aaccaccaat ttggccaacc cagcgccact
1801 ggattatgtc aactttgaag cttgctcgag acgcatagac ttcctcgtct atgctgatgc
1861 tcctgaagtt gagaaggcta agcgggactt cccaggccaa ccagacatgt ggaaagacac
1921 cttcaaaccc gacttctcac acataaaatt ggcattagcc ccgcaaggag gttttgacaa
1981 gaatggtaac actcctcatg ggaagggagt catgaagacc ctcactgctg gttccctcgt
2041 cgcccgagca tcagggctcc tccacgagag attagacgag tatgagctgc agggcccaac
2101 tcccacaaca ttcaacttcg accgcaacaa ggtgcttgct tttaggcagc ttgctgctga
2161 aaacaagtac ggtctagttg acacaatgag ggtcgggtca caactcaaga atgtcaaaac
2221 tatgacagaa ctcaaacagg cactcaagaa catctcagtc aagaaatgtc agcttgtgta
2281 cggtgggggc acatacacac tcgaatctga tggcaaaggc aatgtgcatg tcgaaaaggt
2341 gaacaacacc agtgtgcaaa ctaacaacga gctctccggg gttttgcacc atctcaagtg
2401 tgctagaatc aggtactatg ttaagtgtgt tcaggaagct ctctactcca tcttacaaat
2461 tgccggggct gcattcatca ccacgcgcat tgctaagcgc acgaacatac aaaacctctg
2521 gtccaagcca caagcagaaa atctagagga gactaacaac gaggagggtt gtccaaaacc
2581 caaaaatgat gaagaatttg tcgtctcctc tgatgacatc aaaactgagg gtaagaaagg
2641 aaagaacaag actggccgtg gtaagaagca cacagccttt tccagcaaag gactcagtga
2701 tgaggagtac gatgagtata agaggatcag ggaagaaaga aatggtaagt actccataga
2761 ggaataccta caggacagag acaaatacta tgaggaggtg gccatagcca gggcaactga
2821 ggaagatttc tgtgaagaag aggaggccaa aatccggcag aggatattca gaccaacaaa
2881 gaaacaacgc aaagaggaaa gagcttctct tggtttggtt acaggttctg agattaggaa
2941 gagaaaccca gatgacttca agcccaaagg gaaactatgg gccgatgatg acaggagtgt
3001 tgactacaat gagaaactta gtttcgaggc tccaccaagc atttggtcac gaatagtcaa
3061 cttcggctca gggtggggct tttgggtctc gcccagcctc ttcataacat caacccatgt
3121 cattccccaa ggcgcgcagg agttctttgg agtgcccatc aaacaaatac aaattcacaa
3181 atcaggtgag ttctgccggc tcaggttccc aaaaccaatc aggacagatg ttacgggcat
3241 gattttggag gaaggtgctc cagaaggcac tgttgccaca cttctcatca agagaccaac
3301 tggggaactc atgcccttgg cagccaggat gggcacccac gctaccatga aaattcaggg
3361 tcgcactgtt ggtggacaga tgggcatgct actcacaggg tctaacgcta agagcatgga
3421 tttgggcaca actcctggcg attgtggttg tccctacatc tacaagagag ggaacgacta
3481 cgtggtcatt ggagttcaca ctgccgccgc tcgtggagga aacactgtca tctgtgcaac
3541 ccaaggaaac gagggtgagg ccatgctaga gggtggtgat aacaagggaa cttattgtgg
3601 agcaccaata ttaggccctg gaaatgcccc caaactcagc accaaaacca aattctggag
3661 gtcttccacc acccccctgc cacccggaac ctatgagcca gcctatctgg gtggcaagga
3721 ccccagagtg aaaggtggcc cctcactgca acaggtaatg agagaccaac taaaaccatt
3781 cactgagccc agaggaaaac cacccaaacc aagtgtgcta gaagctgcca agaagactat
3841 aatcaatgtg cttgaacaaa caatagaccc acctcaaaaa tggacatatg cacaagcgtg
3901 tgcatcacta gacaagacca cttccagcgg tcaccctcac catgtgcgga agaacgattg
3961 ctggaatggg gaatctttca caggaaaact ggcagaccaa gcatcaaagg ccaacctaat
4021 gtttgaggaa ggaaagaaca tgactccagt atacacagga gctctgaaag atgagctagt
4081 caagactgac aagatttatg gggtggtcaa gaagaggctc ctgtggggtt cagatctatc
4141 aaccatgata cggtgtgcac gagccttcgg tgggctaatg gacgagctca aggcccattg
4201 cgtcacacta ccagtcaggg ttggtatgaa catgaatgag gatggaccca taatatttga
4261 gaaacactcc agatacaagt accattatga tgcagattac tcccgctggg attcaacaca
4321 acaaagagca gtgctagccg cagccctgga aataatggtc aaattctcac cagaacctca
4381 tctggcccaa gtggttgcag aagacctttt gtcccccagt gtgatggatg tgggtgattt
4441 caagatatca atcaacgagg gactgccctc tggtgtccct tgcacttcac aatggaactc
4501 cattgctcac tggctcctca cactatgtgc actgtctgaa gtcacagacc tgtcccctga
4561 catcatccag gcgaattctc tgttctcctt ttatggtgat gatgaaatag tgagcacaga
4621 catcaaatta gacccagaga aattgacagc aaaactgagg gaatacgggc ttaaaccaac
4681 ccgccctgac aaaacagagg gacccttaat tatctctgaa gatctgaatg gcctgacctt
4741 cctgcggaga acagtgaccc gcgacccggc cggatggttt ggcaaactgg accaaagctc
4801 aatactcagg cagatgtact ggaccagggg gccaaaccat gaagacccct ttgaaacaat
4861 gataccacac tcccagagac ccatacaact gatgtcatta cttggtgaag ctgcattgca
4921 tggtccgtca ttctacagta aaatcagcaa attggtcatt tcggaactga aagagggtgg
4981 aatggatttt tacgtgccca gacaagaacc aatgttcagg tggatgaggt tctcagactt
5041 gagcacgtgg gagggcgatc gcaatctggc tcccagtttt gtgaatgaag atggcgtcga
5101 atgacgccgc tccatctaac gatggtgccg ccggcctcgt cccagagatc aacaatgagg
5161 caatggcgct agagccagtg gcgggtgcag caatagcagc acccctcact ggtcagcaaa
5221 atataattga tccctggatt atgaataatt ttgtgcaagc acctggtggt gagtttacag
5281 tgtcccccag aaattcccct ggtgaagtcc ttcttaattt ggaactgggc ccagaaataa
5341 atccctattt ggcccatctt gctagaatgt acaatggtta tgcaggtgga tttgaagtgc
5401 aggtggtcct agctggaaat gcgtttacag caggaaagat aatctttgca gccatccccc
5461 ccaattttcc aattgacaat ttaagtgcag cacagatcac aatgtgccca catgtgattg
5521 tggatgtcag acagttggaa ccagtcaacc tcccgatgcc tgacgttcgc aataacttct
5581 ttcattataa tcaagggtct gattcgaggt tacgcctaat tgcaatgcta tacacacctc
5641 ttagggcaaa caattctggg gatgatgttt ttactgtgtc ttgtagagtg ctaactagac
5701 ctagtcctga tttctcattc aatttccttg tgccacccac tgtggagtca aagacaaaac
5761 ctttttccct ccctatcctg actatctctg aaatgtccaa ttctaggttc ccagtaccaa
5821 ttgattccct acacaccagt cccactgaga atattgttgt tcagtgccaa aatgggcgcg
5881 tcacccttga tggtgagctg atgggcacca cccaactctt gcctagccaa atctgtgctt
5941 tcaggggcgt tctcaccaga tcaacaagca gagccaatga ccaggccgat acagcaaccc
6001 ctagattctt tgatcattct tggcatatac aattggataa tctaaatgga accccttatg
6061 atcctgcaga agacatacca ggccccctag ggacaccaga tttccgtggc aaagtctttg
6121 gcgtggccag ccagagaaat cctgatacca cgactagggc gcatgaagca aagatagaca
6181 cctcatctcc ccgcttcacc ccaaagctag gctcattaga gatatccact gaatctgatg
6241 attttgaaca taaccaacca acaagattca ccccagttgg cattggagtt gaccatgagg
6301 aagactttaa acagtggacc ctacccaact acgctggtca gctcacacat aacatgaact
6361 tagccccagc tgttgctccc aacttccctg gtgagcagct ccttttcttc cgctcacatt
6421 tgccatcttc tggtgggcga tccaacggga ttctagactg cctagttccc caagaatggg
6481 tacagcactt ctaccaagag tcagccccct ctcagtctca agtggccctg gttaggtatg
6541 ttaatcctga cactggtaga gtgttatttg aggccaaact acataaatta ggtttcatga
6601 ctatagccaa gaatggtgat tctccaataa ctgtccctcc aaatggatac tttaggtttg
6661 aatcttgggt gaaccccttt tacacacttg cccccatggg aactgggaat gggcgtagaa
6721 ggattcaata atggctggag cttttatagc aggattggct ggtgacatgc tcacaaatac
6781 tgtaggatct ttagttaatg caggggctaa tgctattaat caaacaattg attttgaaaa
6841 taataaatat ttgcaaaatg cttcttttaa tcatgataag gagatgttga atgcacaagt
6901 tgaggcaaca aagaagttac aggctgacat gattgctatc aaacaagggg ttttgaccgc
6961 tggcggcttc tcccctactg atgcagcccg tggggcaatt aatgccccca tgacaaaagt
7021 cctagattgg aatggaacga gatactgggc accaggtgcc acctccacaa cctcgatgtc
7081 gggtggcttt acacaccaaa ctgtgcacag atccacacca aattttaaaa cgaaccaggc
7141 ccccaaatcc acacccagta gtgggtcttc agtgaggtca aactcaaccc aaatcactag
7201 cctgagctca cactcgtccg ggtcgtctcg atccagcgga tctacagtta tcagctcaat
7261 accatcctct aacaggacta gggactgggt caaccaacaa aattttaatt tggaaccaca
7321 catgcctgga tctcttagga cagcttttgt cactccacca tctagtacag cctctagctc
7381 aggcacagtc tcaactgtgc ccaaaaatgt tttggactcc tggacatctg cgtttaacac
7441 gcgcagacag ccgctattcg cacaccttcg cagaaggggg gagtcaaatg tttagtgaaa
7501 agattatttt aaatttggtt taaaattagg tttaatttgg aatctttt
//