Typing tool
|
|
|
|
|
|
Typing tool
|
Complete norovirus genomes
| MT537633 | GII.4 Sydney | |
|
|---|---|---|---|
| GII.P16 |
ORF1: 1..5095
ORF2: 5076..6698
ORF3: 6698..7504
LOCUS MT537633 7515 bp RNA linear VRL 31-JUL-2020
DEFINITION Norovirus GII isolate 259-2 nonstructural polyprotein (ORF1) gene,
partial cds; and VP1 (ORF2) and VP2 (ORF3) genes, complete cds.
ACCESSION MT537633
VERSION MT537633.1
DBLINK BioProject: PRJNA604000
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norovirus norwalkense.
REFERENCE 1 (bases 1 to 7515)
AUTHORS Silva,A., Wolfe,J., Ruelle,S., Hirneisen,K. and Yang,Z.
TITLE Application of whole-genome sequencing for Norovirus outbreak
tracking and surveillance efforts in Orange County, CA
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 7515)
AUTHORS Silva,A., Wolfe,J., Ruelle,S., Hirneisen,K. and Yang,Z.
TITLE Direct Submission
JOURNAL Submitted (29-MAY-2020) Schmid College of Science and Technology,
Chapman University, 1 University Drive, Orange, CA 94526, USA
COMMENT ##Assembly-Data-START##
Assembly Method :: CLC Genomics Workbench v. 11
Sequencing Technology :: Illumina
##Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..7515
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="259-2"
/isolation_source="stool"
/host="Homo sapiens"
/db_xref="taxon:122929"
/geo_loc_name="USA"
/collection_date="17-Dec-2018"
/note="genotype: GII.4[P16]"
gene <1..5095
/gene="ORF1"
CDS <1..5095
/gene="ORF1"
/codon_start=2
/product="nonstructural polyprotein"
/protein_id="QKE61142.1"
/translation="MASNDATVAVACNNNNDKEKSSGEGLFTNMSFTLKKALGARPKQ
PAPRDEPQKPPRPPTPELVKRIPPPPPNGEGEEEPVIRYEVKSGISGLPELTTVPQPD
VANTAFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAAIS
MARVELTPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLNDS
WLSRRMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLIGK
IKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED
LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
KKEEANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRLST
KSASPDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAREV
ARKVASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELADTC
PLTLNCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK
AKRDFPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA
SGLLHERMDEFELQGPTITTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVKTM
EELKQAIRNVTIKRCRIIYGGSTYDLESDGKGKVLVEKVKNTSVQTNNELAGALHHLK
HARIRYYVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEEAP
KSEDDEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKY
SIEEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLVTG
SEIRKRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSPSL
FITSTHVIPAGITEAFGVPIKQIQIHKSGEFCRFRFPRPIRPDVTGMILEEGAPEGTV
ATVLIKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDCG
CPYIYKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGYDKGTYCGAPILGPG
GAPKLSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPRG
KPPRPSVLEAAKQTVINVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFWNG
ETFTGKLADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYRKIKKRLLWGSDLST
MIRCARSFGGLMDEMKAHCISLPVRVGMNVNEDGPIIFEKHSRYKYHYDADYSRWDST
QQRAVLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCTSQ
WNSIAHWLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLKEY
GLKPTRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGPNH
EDPNETMIPHSQRPIQLMALLGEASLHGPSFYSRISKLVITELKEGGMDFYVPRQEPM
FRWMRFSDLSTWEGDRNLAPNFVNEDGVE"
mat_peptide <1..991
/gene="ORF1"
/product="p48"
mat_peptide 992..2089
/gene="ORF1"
/product="NTPase"
mat_peptide 2090..2620
/gene="ORF1"
/product="p22"
mat_peptide 2621..3019
/gene="ORF1"
/product="VPg"
mat_peptide 3020..3562
/gene="ORF1"
/product="Pro"
mat_peptide 3563..5092
/gene="ORF1"
/product="RdRp"
gene 5076..6698
/gene="ORF2"
CDS 5076..6698
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="QKE61143.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML
TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG
STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRVV"
gene 6698..7504
/gene="ORF3"
CDS 6698..7504
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="QKE61144.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRDAVPARGPSNKSS
NSSTATSVYSNQTISTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRV"
ORIGIN
1 gatggcgtct aacgacgcta ccgttgccgt tgcttgcaac aacaacaacg acaaggaaaa
61 atcttcaggt gaaggcttat tcacaaatat gtctttcacc ttaaagaaag ccctcggggc
121 taggcccaaa cagcctgccc cgagagacga accacaaaag cccccaagac caccaacccc
181 cgagttggtc aagaggatac cccctcctcc acctaatggc gaaggagaag aagaaccagt
241 cattaggtat gaggttaaga gtgggatctc tggcctgccc gagctcacaa cagtccccca
301 accggacgtg gccaacacag cattcagtgt tccaccactg agcttgagag aaaacaggga
361 ggccaaggaa ccgctaacag gggcaatatt agagatgtgg gatggagaga tataccacta
421 tggcctgtac gtggagaaag gcttagtgtt gggtgtgcac aaaccacctg cagccataag
481 catggcaaga gtggagctga cgccgctgtc attgtactgg cgtgtggtgt acactcccca
541 atacctcatc tcccctgaaa ctctcaggag gctcaacgga gaggcgttcc cttacaccgc
601 cttcgacaac aactgctacg ccttttgctg ctgggtgtta gacctcaatg actcatggct
661 tagcaggagg atggtgcaaa gaacaacggg cttcttcaga ccttaccaag agtggaacag
721 aaagcccctg cctaccatgg atgactccaa aattaagaag gtagcaaata tattcctatg
781 ttcattgtcc acattattca ccagacccat aaaagacctc atagggaaaa ttaaaccatt
841 aaacatattg aacatcctgg caacgtgtga ctggacgttt gccggaatag tggagtctct
901 gatattactt gctgaactct tcggagtttt ctggacgccc ccagatgtgt ctgctatgat
961 cgctccctta ctcggggact acgagttgca agggccagaa gacctcgccg ttgaactcgt
1021 acctgtggta atgggaggga ttggtttggt gttgggattc accaaagaga aaattggcaa
1081 aatgttgtcc tcagcagcat caacactcag ggcttgcaaa gatcttggtg cctatggctt
1141 agagatactc aagttggtca tgaagtggtt cttcccaaag aaagaggagg ccaatgagct
1201 agccatggtg agggccatag aggatgccgt gctagatctt gaggcaatag aaaataacca
1261 catgacaacc ctgttgaaag acaaagacag cttagcaaca tacatgaaaa cactggacat
1321 ggaggaggag aaagccagaa ggttgtccac aaaatctgca tcccctgaca tagttgggac
1381 aatcaacgcc ctgctggctc gaatagcagc ggccaggtca ttagtccaca gggccaagga
1441 agagctatct agcaggataa ggccagtagt tgttatgata tctggcaaac caggaatagg
1501 caaaactcat ctggccaggg aggtggcaag aaaggtggca tccactctca caggggacca
1561 aagagtcgga ctcataccaa gaaacggtgt ggaccattgg gatgcataca aaggtgagag
1621 agtcgtgctg tgggacgact atggcatgag taaccccatc catgatgctc ttcgcataca
1681 agaattggct gatacgtgtc cccttacctt aaattgtgac agaattgaaa ataagggaaa
1741 agtttttgac agtgaagtca taataattac aacaaacctt gccaatccag ccccacttga
1801 ttatgtcaac tttgaggcct gttccaggag aattgatttc ctggtgtacg ctgaggcacc
1861 agaagtagaa aaggcaaaac gggactttcc tggtcagcca gatatgtgga aggacgcctt
1921 caagccggac ttttcacaca tcaagctaca gcttgcacct cagggcggct ttgacaagaa
1981 tggcaacacc ccacatggga aaggagtgat gaagaccctc actaccggtt ctctgattgc
2041 ccgtgcatca ggcctactac atgagaggat ggatgaattt gaactccaag gtcccacaat
2101 caccaccttc aatttcgacc gaaacagaat cacagcattc agacaattgg ctgcagaaaa
2161 caagtatgga ttggtggata ccatgaaagt tggcaatcaa ttaaaaggag tgaaaaccat
2221 ggaagaactc aaacaagcaa tcagaaatgt gaccatcaag aggtgccgga tcatctacgg
2281 tggctccacg tatgaccttg aatctgatgg caagggcaaa gttttggtgg aaaaggtcaa
2341 gaacacctct gtacagacca acaacgagtt ggccggggcc ctgcaccatc tcaaacacgc
2401 ccgaatcagg tactatgtca aatgtgtgca agaagcagtc tattccatca tacaaattgc
2461 cggcgctgcg tttgtcacca cgcgcattgc acgccgcatg aacatacaag aactctggtc
2521 gaagccacaa ttagatcaaa atgaatcaga gactaaggaa gaggccccca aatcagaaga
2581 tgacgagttc atcatatctt ctaaggacat caaggaggaa ggaaagaagg gcaaaaacaa
2641 aactggccgt ggcaagaaac acactgcatt ctccagcaag ggcttgagcg atgaggagta
2701 tgacgagtac aagaggataa gagaagagag aaatgggaag tactctatag aggagtatct
2761 tcaagacaga gacaggtact atgaggagct cgccattgcc aaggccacgg aagaagactt
2821 ctgtgaagag gaggagataa aaatccgtca gagaattttc cgtcccacca ggaaacaaag
2881 aaaggaagag agggccacat taggactggt aacaggttca gaaatcagaa aaagaaaccc
2941 tgatgacttc aaacccaaag ggaagctgtg ggccgatgac aacagaagtg ttgactataa
3001 tgagaaactg gactttgagg cccccccaag catatggtct aggattgtga gctttggttc
3061 tggctggggc ttctgggtat caccaagcct gttcataaca tcaactcatg taatccccgc
3121 aggcataaca gaagcatttg gagtccccat caaacaaatt cagatccaca aatcaggtga
3181 attttgccga ttcagattcc caagaccaat tagaccagac gtgacaggaa tgatcttgga
3241 agaaggtgcg cctgaaggca ccgtggcaac tgtgctcatc aaacgcccca ccggagagct
3301 catgcctctt gcagccagaa tgggaacaca cgcaaccatg aaaattcaag gccgcatggt
3361 tggcggacag atgggtatgt tgctcactgg atcaaatgct aaaggaatgg atttgggaac
3421 aactcctggt gactgtggct gtccttacat ctacaaaagg ggcaatgact atatagtcat
3481 tggggtgcac actgcagcag cccgtggtgg aaacaccgtc atctgtgcca cacagggaag
3541 tgagggtgag gcaactcttg agggtggata tgacaaagga acatactgtg gggcacccat
3601 tctaggccct gggggtgcac caaagttgag caccaaaacc aaattttgga ggtcatcgaa
3661 cacgcccctc ccaccaggga catatgagcc tgcctacctc ggtggccgtg atccgcgtgt
3721 taagggtggg ccctccttgc agcaggtaat gagagaccag ttgaagccat tcactgaacc
3781 caggggcaaa cctccaagac caagtgtatt ggaagcagcc aaacaaaccg ttatcaatgt
3841 cctcgaacaa accctggatc ctccacaaaa atggacatac gcacaggcgt gtgcctcact
3901 tgacaaaacc acttccagcg ggcatcctca tcacgtccga aagaatgaat tctggaatgg
3961 tgagaccttc accggcaaat tggcagacca agcatcaaaa gcaaacctaa tgtttgagga
4021 agggaaacac atgacaccag tgtatacagc agcactcaag gacgagctag tcaagactga
4081 gaaaatctat agaaagatca agaagagact gctctggggc tctgacttgt ccaccatgat
4141 ccggtgcgct aggtcatttg gtgggctcat ggacgagatg aaggcacact gcatatcact
4201 cccagtacga gttggcatga atgtgaatga agatggccca ataatatttg agaaacattc
4261 cagatacaaa taccactatg acgcagacta ctctcgttgg gattcaacac aacagagggc
4321 agtactagca gcagccttgg aaatcatggt cagattctct gcagaaccac aattggcaca
4381 aatagtcgct gaggatcttc tggcccctag cgtagtagat gtaggagact ttaaaatcac
4441 tataaatgaa gggctcccat ctggtgtgcc atgcacctcc caatggaact ccatcgcaca
4501 ctggctgcta actctctgtg ccttgtctga agtcaccaaa ctgtcccctg acattataca
4561 agcaaattcc atgttctcat tttacggtga tgacgagatt gtcagcaccg acataaaatt
4621 ggaccctgaa cagttaaccg ccaagttgaa ggagtatggc ctgaaaccaa cccgcccaga
4681 caagaccgag ggacccctga tcatcagtga agatttgaac ggactcactt tcctccgaag
4741 gacggtgact cgtgacccag ctggctggtt tggaaaactg gaccaaagtt caattttgag
4801 gcagatgtac tggactagag gaccaaatca cgaagatccc aatgagacaa tgatacccca
4861 ttctcaaaga cccatacagc tcatggcact gcttggtgaa gcctctcttc acggaccctc
4921 tttctacagt agaatcagta aattggtcat aactgaactc aaagaaggtg ggatggactt
4981 ttacgtgcca aggcaggaac ccatgttcag gtggatgagg ttttctgact tgagcacgtg
5041 ggagggcgat cgcaatctgg ctcccaattt tgtgaatgaa gatggcgtcg agtgacgcca
5101 acccatctga tgggtccgca gccaacctcg taccagaggt caacaatgag gttatggctt
5161 tggagcccgt tgtcggtgcc gctattgcgg cacctgtagc gggccaacaa aatgtaattg
5221 acccctggat tagaaataat tttgtacaag cccctggtgg ggagtttaca gtatccccca
5281 gaaacgctcc aggtgaaata ctatggagcg cgcccctagg ccctgaccta aatccctacc
5341 tatcccattt ggccagaatg tacaatggtt atgcaggtgg ttttgaagtg caggtaattc
5401 tcgcggggaa cgcgttcacc gccgggaaga tcatatttgc agcagtccca ccaaattttc
5461 caactgaagg cttaagtcct agccaggtca ctatgttccc ccatataata gtagatgtta
5521 gacagttaga acctgtgctg attcctttac ccgatgttag gaataatttc tatcattaca
5581 atcagtcaaa tgactccact attaagttga tagcaatgtt gtacacacca cttagggcta
5641 ataatgctgg ggatgatgtt ttcacagttt cgtgccgagt tctcacgaga ccatcccccg
5701 attttgattt catattttta gtgccaccca cagttgagtc aagaactaaa ccattctctg
5761 tcccagtttt aactgttgag gagatgacca attcaagatt ccccatccct ttggaaaagc
5821 tgttcacagg ccccagcagt gcctttgttg ttcaaccaca aaacggcagg tgcacaactg
5881 atggcgtgct cctaggcacc acccaacttt ctcctgtcaa catctgcacc ttcagagggg
5941 atgtcaccca catcacaggt agtcgcaact acacaatgaa tttggcttct caaaattgga
6001 acaactatga cccaacagaa gaaatcccag cccctctagg aactccagat tttgtgggga
6061 agattcaagg catgctcacc caaaccacaa ggacagatgg ttcaacacgc ggccacaaag
6121 ctacagtgta cactgggagc gccgactttg ctccaaaact gggtagagtt caatttgaaa
6181 ctgacacaga ccatgatttt gaagctaatc aaaacacaaa gttcacccca gtcggtgtca
6241 tccaagatgg tagcaccacc catcgaaacg aaccccaaca gtgggtgctc ccaagttact
6301 caggcagaaa tactcacaat gtacatctgg cccccgctgt agcccccacc tttccgggtg
6361 agcaacttct cttcttcaga tccaccatgc ccggatgcag cgggtacccc aacatggatt
6421 tggactgtct gctcccccag gaatgggtgc agtacttcta tcaagaggca gccccagcac
6481 aatctgatgt ggctctgcta agatttgtga atccagacac aggtagggtt ttgtttgagt
6541 gcaagcttca caaatcaggc tatgttacag tggctcacac tggccaacat gatttggtta
6601 tcccccccaa tggctacttt agatttgatt cctgggtcaa ccagttctat acgcttgccc
6661 ccatgggaaa tggaacgggg cgtagacgtg tagtataatg gctggagctt tctttgctgg
6721 attggcatct gatgtccttg gctctggact tggttccctc atcaatgctg gggctggggc
6781 catcaaccaa aaagttgagt ttgaaaataa cagaaaattg caacaagcat ccttccaatt
6841 tagcagcaat ctgcaacagg cttcctttca acatgataaa gagatgctcc aagcacaaat
6901 tgaggccact aaaaagctac aacaggaaat gatgaaagtt aagcaggcaa tgctcctaga
6961 gggtgggttc tctgagacag atgcagcccg cggggcaatt aacgccccca tgacaaaagc
7021 tttggactgg agtgggacaa ggtactgggc tcccgatgct aggactacaa catacaatgc
7081 aggccgcttt tccacccctc aaccatcggg ggcactgcca ggaagagcta atcttaggga
7141 tgctgtccct gctcggggac cctccaacaa atcttctaac tcttctactg ccacctctgt
7201 gtattcaaat caaactattt caacgagact tggttctaca gctggttctg gaaccagtgt
7261 ctcgagcctc ccgtcaactg caaggactag gagctgggtt gaggatcaaa ataggaattt
7321 gtcacctttc atgagggggg cccacaacat atcatttgtc accccaccat ctagcagatc
7381 ctctagccaa ggcacagtct caaccgtgcc taaagagatt ttggactcct ggactggcgc
7441 tttcaacacg cgcaggcagc ctctcttcgc tcacattcgt aagcgagggg agtcacgggt
7501 gtaatgtgaa aagac
//