Typing tool
|
|
|
|
|
|
Typing tool
|
Complete norovirus genomes
| MT725762 | GII.4 Sydney | |
|
|---|---|---|---|
| GII.P4 New Orleans |
ORF1: 5..5104
ORF2: 5085..6707
ORF3: 6707..7510
LOCUS MT725762 7566 bp RNA linear VRL 12-JUL-2020
DEFINITION Norovirus GII isolate Hu/US/2017/GII.4 Sydney[P4 New
Orleans]/CA-RGDS-1091, complete genome.
ACCESSION MT725762
VERSION MT725762.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norovirus norwalkense.
REFERENCE 1 (bases 1 to 7566)
AUTHORS Pan,C.-Y., Huynh,T., Padilla,T., Montmayear,A.M., Chhabra,P.,
Barclay,L., Vinje,J. and Morales,C.
TITLE Direct Submission
JOURNAL Submitted (07-JUL-2020) Viral and Rickettsial Disease Laboratory,
California Department of Public Health, 850 Marina Bay Parkway,
Richmond, CA 94804, USA
COMMENT ##Assembly-Data-START##
Assembly Method :: SPAdes v. 3.6; Geneious v. R10
Sequencing Technology :: Illumina
##Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..7566
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="Hu/US/2017/GII.4 Sydney[P4 New
Orleans]/CA-RGDS-1091"
/isolation_source="stool"
/host="Homo sapiens"
/db_xref="taxon:122929"
/geo_loc_name="USA: California"
/collection_date="Dec-2017"
/note="genotype: GII.4 Sydney[P4 New Orleans]"
gene 5..5104
/gene="ORF1"
CDS 5..5104
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="QLD97902.1"
/translation="MKMASNDASAAAVANSNNDTAKSSSDGVLSSMAVTFKRALGARP
KQPPPREKPQRPPRPPTPELVKNIPPPPPNGEDEIVVTYSVKDGVSGLPDLSTVRQPE
ESNTAFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS
LAKVELAPLSLYWRPVYTPQYLISPDTLKKLSGETFPYTAFDNNCYAFCCWVLDLNDS
WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKIKKVANIFLCALSSLFTRPIKDIIGK
IRPLNILNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED
LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
KKEEANELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST
KSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREV
AKRIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC
PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPDVEK
AKRDFPGQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA
SGLLHERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGKQLKDVKTM
PELKQALKNVSIKKCQIVYNGCTYMLESDGKGNVKVDRIQSAAVQTNNELAGALHHLR
CARIRYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQDLWSKPQVENIEETTSKDGC
PKPKDDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERVSLGLV
TGSEIRKRNPDDFKPKGRLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP
SLFITSTHVIPQDAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG
TVVTLLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILG
PGSAPTLSTKTKFWRSSTASLPPGTYEPAYLGGKDPRVKGGPSLQQVMREQLKPFTEP
RGKPPKPSVLEAAKKTIINVLEQTIDPPERWSFAQACASLDKTTSSGHPHHMRKNDCW
NGESFTGKLADQASKANLMFEEGKNMTPVYTAALKDELVKTDKIYGKIRKRLLWGSDL
ATMIRCARAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFERHSRYTYHYDADYSRWD
STQQRAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCT
SQWNSIAHWLLTLCALSEVTNLSPDTIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLK
EYGLKPTRPDKTEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP
NHGDPSETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQE
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..6707
/gene="ORF2"
CDS 5085..6707
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="QLD97903.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKVIFAAVPPNFPTEGLSPSQVTMFPHIVVDVRQLEPVLIPLPD
VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGAPDFVGKIQGML
TQTTRADGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG
NTTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRVV"
gene 6707..7510
/gene="ORF3"
CDS 6707..7510
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="QLD97904.1"
/translation="MAGAFFAELASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQVEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARTTTYNAGRFSAPQPSGVLPGRTNLRDAAPARGSSKSSN
SSTATSVYSNQTTSTRLGSTAGSGTSVSSLPSTARTRSWVEDQSRNLSPFMRGAHNIS
FVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRKRGESRA"
ORIGIN
1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgct gttgctaaca gcaacaacga
61 caccgcaaaa tcttcaagtg acggagtgct ttctagcatg gctgtcactt ttaaacgagc
121 cctcggggcg cggcctaaac agcccccccc gagggaaaaa ccacaaagac ccccacgacc
181 acccacacca gaactggtta aaaatattcc ccccccccca cccaacggag aggatgaaat
241 agtggttact tatagtgtta aggatggtgt ttccggcttg cctgaccttt ccaccgtcag
301 acagccggaa gaatccaaca cggccttcag tgtccctcca ctcaatcaga gggagaacag
361 agatgctaag gaaccactca ctggaacaat tctggaaatg tgggacgggg aaatctacca
421 ttatggcctg tatgtggagc gaggtcttgt actaggcgta cacaagccac cagctgccat
481 cagcctcgct aaggttgagt tggcaccact ctccttatac tggaggcctg tgtacactcc
541 tcagtacctc atctctccag acactctcaa gaaattgtct ggggaaacgt tcccctacac
601 agcatttgac aacaactgct atgccttttg ttgctgggtt ctggacctaa atgactcgtg
661 gctgagcagg agaatgatcc agaggacaac tggtttcttc aggccctacc aagactggaa
721 taggaaaccc cttcccacta tggatgactc caaaataaag aaggtggcca atatatttct
781 gtgtgccctg tcctcgctat ttaccaggcc cataaaagac ataataggga aaataaggcc
841 tcttaacatc ctcaacatct tggcctcatg tgattggacc tttgcgggca tagtagagtc
901 cctgatactc ttagcagagc tctttggagt tttctggaca cccccagatg tgtctgcaat
961 gattgccccc ttacttggtg actacgagct acaaggacct gaggaccttg cagtggagct
1021 cgtccccgtg gtgatggggg gaattggttt ggtgctagga ttcaccaaag aaaaaattgg
1081 gaaaatgttg tcatcagctg cgtccacctt gagagcttgc aaagaccttg gtgcatatgg
1141 gctagagatc ctaaagctag tcatgaagtg gttcttcccg aagaaggagg aggcaaatga
1201 gctggctatg gtgaggtcca tcgaggatgc agtcctggat ctcgaagcaa ttgaaaacaa
1261 tcatatgacc accttgctta aagataaaga cagtctggca acctacatga gaacactcga
1321 ccttgaagag gagaaagcca ggaaactctc aaccaagtct gcctcacctg acatcgtggg
1381 cacaatcaac gccctcctgg cgagaatcgc tgccgcacgt tctctggtgc atcgagcgaa
1441 ggaggagctt tccagcagac caagacctgt ggtgttgatg atatcaggta ggccaggaat
1501 agggaagacc cacctcgcta gggaagtggc taagagaatc gcagcctccc ttacaggtga
1561 ccagcgtgtt ggtctcatcc cacgcaatgg cgtcgaccac tgggatgcgt ataaggggga
1621 gagggtcgtc ctatgggacg attatggaat gagcaaccct attcacgatg ccctcaggct
1681 gcaagaactc gctgacactt gccccctcac tctgaactgt gacaggattg aaaataaggg
1741 gaaggtcttt gacagcgatg tcatcattat caccactaat ctggccaacc cagccccact
1801 ggactatgtc aactttgaag catgctcgag gcgcattgac ttcctcgtat atgcagaagc
1861 ccctgatgtc gaaaaggcga agcgtgactt cccaggccag cctgacatgt ggaagaacgc
1921 tttcagttcc gatttctcac acataaaact agcactggcc ccacagggtg gtttcgacaa
1981 gaacgggaac accccacacg ggaagggcgt catgaagact ctcaccactg gctcccttat
2041 tgcccgggca tcagggctac tccatgagag gttagatgaa tttgaactgc agggcccagc
2101 tctcaccacc ttcaatttcg atcgcaataa agtgcttgcc tttagacagc ttgctgctga
2161 aaacaaatat ggactgatgg acacaatgag ggttgggaaa cagctcaagg acgtcaaaac
2221 catgccagaa ctcaaacaag cactcaaaaa tgtctcaatc aagaagtgtc aaatagtgta
2281 taatggttgc acctacatgc ttgagtctga tggcaagggc aatgtgaaag ttgacaggat
2341 ccagagcgcc gccgtgcaga ccaacaatga gctggctggt gccctgcacc acttgaggtg
2401 cgccagaatc agatactatg tcaagtgtgt ccaggaagcc ctgtattcca tcattcaaat
2461 tgctggggct gcatttgtca ccacgcgcat tgccaagcgc atgaacatac aggatctatg
2521 gtccaagcca caagtggaaa acatagagga aactaccagc aaggacgggt gcccaaaacc
2581 caaggatgat gaggagtttg tcatttcatc cgacgacatc aaaactgagg gcaagaaagg
2641 gaagaacaag actggccgtg gcaagaagca cacagcattt tcaagcaaag gcctcagtga
2701 tgaagagtac gatgaataca agaggatcag agaagaaagg aatggcaagt actctataga
2761 agagtacctc caggacaggg acaaatatta tgaggaggtg gccattgcca gagcgactga
2821 ggaagacttc tgtgaagagg aggaagccaa gatccggcaa aggatcttta ggccaacaag
2881 gaaacaacgc aaggaggaaa gagtctctct cggtttagtc acgggctctg aaattaggaa
2941 aagaaaccca gatgacttca aacccaaagg gagattgtgg gctgacgatg acaggagtgt
3001 ggactacaat gagaaactca gttttgaggc cccgccaagc atttggtcaa gaatagtcaa
3061 ctttggttca ggctggggat tctgggtctc ccccagcttg ttcataacat caacccatgt
3121 tataccccag gacgcaaagg agttctttgg agtccccatc aaacaaatac aggtacacaa
3181 gtcaggcgag ttctgtcgct tgagattccc taaaccaatc aggactgatg tgacgggcat
3241 gatcttagaa gaaggcgcac ctgagggcac cgtggttaca ctactcatca aaaggtccac
3301 cggggaactt atgcccctag cagctaggat ggggacccat gcgaccatga agatccaagg
3361 gcgcactgtt gggggccaga tgggcatgct tctgacagga tccaacgcca agagtatgga
3421 cctgggtact acaccaggtg attgtggctg cccctacatc tacaagagag gtaatgacta
3481 tgtggtcatt ggagtccaca cggctgccgc acgtgggggg aacactgtca tatgtgccac
3541 ccaggggagt gaaggagagg ccacacttga gggtggtgac aacaagggga cttactgtgg
3601 tgcaccaatc ctaggcccag ggagtgcccc aacacttagc accaagacca aattctggag
3661 atcgtccaca gcatcactcc cacctggcac ctatgaacca gcctaccttg gtggcaagga
3721 ccctagagtc aagggtggcc cttcactaca gcaagtcatg agggaacagt tgaagccatt
3781 cacagagccc agaggtaagc caccaaaacc aagtgtgtta gaagctgcca agaaaaccat
3841 catcaatgtt cttgagcaaa caattgatcc acctgagaga tggtcgttcg cacaagcttg
3901 cgcgtctctt gacaagacca cttccagtgg tcatccgcat cacatgcgga aaaacgactg
3961 ctggaacggg gagtccttca caggcaagct ggcagaccag gcttctaagg ccaacctgat
4021 gtttgaagaa ggaaagaaca tgaccccagt ctacacagct gcgctcaagg atgagctagt
4081 taaaactgac aaaatttatg gtaagatcag gaagagactt ctttggggct cggacttggc
4141 gaccatgatc cggtgtgctc gggcattcgg aggcctaatg gatgaactca aagcacactg
4201 tgtcacactt cccgttagag ttggcatgaa tatgaatgag gatggcccca tcatcttcga
4261 gaggcattcc aggtacacgt accactatga tgctgattac tctcgatggg attcaacaca
4321 acagagagcc gtgttggcgg cagctctaga aatcatggta aaattctccc cagaaccaca
4381 tttggcccag gtagtcgctg aagaccttct ttctcctagc gtggtggacg tgggcgactt
4441 cacaatatca atcaacgagg gtcttccctc tggggtgccc tgcacctccc aatggaactc
4501 catcgcccac tggcttctca ctctctgcgc gctctccgaa gtcacaaacc tgtctcctga
4561 taccatacag gctaattctc tcttttcttt ttatggcgat gatgaaattg ttagcacaga
4621 cataaaattg gacccagaga aattgacagc aaaactcaaa gaatacgggt taaaaccaac
4681 ccgccctgac aaaactgaag gaccccttgt catctctgaa gacctgaatg gcctaacttt
4741 cctgcggaga actgtgaccc gcgacccagc tggttggttt ggaaaactgg agcagagttc
4801 aatactcagg caaatgtact ggactagggg acccaaccat ggagacccat ctgaaacaat
4861 gattccacat tcccaaagac ccatacaatt gatgtcccta ctgggggagg ccgctctcca
4921 cggcccagca ttttacagta agattagcaa attggtcatt gcagagctaa aagaaggtgg
4981 tatggatttt tacgtgccca gacaagagcc aatgttcaga tggatgagat tctcagatct
5041 gagcacgtgg gagggcgatc gcaatctggc tcccagtttt gtgaatgaag atggcgtcga
5101 gtgacgccaa cccatctgat gggtccgcag ccaacctcgt cccagaggtc aacaatgagg
5161 ttatggctct ggagcccgtt gttggtgccg ctattgcggc acctgtagcg ggccaacaaa
5221 atgtaattga cccctggatt agaaacaatt ttgtacaagc ccctggtgga gagtttacag
5281 tgtcccccag aaacgctcca ggtgaaatac tatggagcgc gcccttaggc cctgatttaa
5341 atccctacct atcccacttg gccagaatgt ataatggtta tgcaggtggt tttgaagtgc
5401 aggtgattct cgcggggaac gcgttcaccg ccgggaaggt catatttgca gcagtcccac
5461 caaattttcc aactgaaggc ttgagcccca gccaggtcac tatgttcccc catatagtag
5521 tggatgttag gcaactagaa cctgtgttga ttcccttacc cgatgttagg aataatttct
5581 accattacaa tcaatcaaat gaccccacca ttaagttgat agcaatgtta tatacaccac
5641 ttagggctaa taatgctggg gatgatgtct tcacagtttc ttgccgagtt ctcacgaggc
5701 catcccccga ttttgatttc atatttctag tgccacccac agttgagtct agaaccaaac
5761 cattttccgt cccagttttg actgttgagg agatgaccaa ttcaagattc cccattcctt
5821 tggaaaagtt gttcacgggc cccagtagtg cctttgttgt tcaaccacaa aacggtaggt
5881 gcacgactga cggcgtgctc ctaggcacca cccaattgtc tcctgtcaac atctgcacct
5941 tcagagggga tgtcacccac attacaggta gtcgtaacta cacaatgaat ttggcttctc
6001 aaaactggaa caattatgat ccaacagaag aaatcccagc ccctctagga gctccagatt
6061 ttgtggggaa gattcaaggc atgctcaccc aaaccacaag ggcagatggc tcaacacgcg
6121 gccacaaggc tacggtgtac actgggagcg ccgacttcgc tccaaaactg ggcagagttc
6181 aatttgaaac tgacacagac catgattttg aagctaacca aaacacaaag ttcactccag
6241 tcggtgtcat ccaagatggc aacaccaccc accgaaatga accccaacag tgggtgctcc
6301 caagttactc aggcagaaat actcataatg ttcatctggc ccccgctgtg gcccccactt
6361 ttccgggtga acaacttctc ttctttagat ccaccatgcc cggatgtagc gggtatccca
6421 acatggattt ggactgtttg ctcccccagg aatgggtgca gtacttctac caagaggcag
6481 ccccagcgca atctgatgtg gccctgctaa gatttgtgaa tccagacaca ggtagggttt
6541 tgtttgaatg caaacttcat aaatcaggct atgttacagt ggctcacact ggccaacatg
6601 atttggtcat cccccccaat ggttatttta ggtttgattc ctgggtcaac cagttctaca
6661 cgcttgcccc catgggaaat ggaacggggc gtagacgcgt agtataatgg ctggagcttt
6721 ctttgctgag ttagcatctg atgtcctcgg ctctggactt ggttccctta tcaatgctgg
6781 ggctggggcc atcaaccaaa aagttgagtt tgaaaataac agaaaattgc aacaagcatc
6841 cttccaattt agcagcaatt tacaacaggc ttcctttcaa catgacaaag aaatgcttca
6901 agcacaagtt gaggccacca aaaagctaca acaggaaatg atgaaagtta agcaggcaat
6961 gcttctagag ggtgggttct ctgaaacaga tgcagcccgc ggggcaatca acgcccccat
7021 gacaaaagct ttggactgga gcgggacaag gtactgggct cctgatgcta ggactacaac
7081 ttataatgca ggccgctttt ccgcccctca accatcgggg gtactaccag gaaggactaa
7141 tcttagggat gctgcccctg ctcggggttc ctctaaatct tctaactctt ctactgctac
7201 ttctgtgtac tcaaatcaaa ccacttcaac gagacttggt tctacagctg gttctggcac
7261 cagtgtctcg agtctcccgt caactgcaag gaccaggagc tgggttgagg atcaaagtag
7321 gaatttgtct cctttcatga ggggggccca caacatatcg tttgtcaccc caccatctag
7381 cagatcctct agccaaggca cagtctcaac cgtgcctaaa gaggttttgg actcctggac
7441 tggcgctttc aacacgcgca ggcagcctct cttcgctcac attcgtaaac gaggggagtc
7501 acgggcgtaa tgtgaaaaga caaaattgat tatctttctt tttctttagt gtcttttaaa
7561 aaaaaa
//