Typing tool
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Typing tool
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Complete norovirus genomes
| MT729788 | GII.4 New Orleans | |
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| GII.P4 Yerseke |
ORF1: 5..5104
ORF2: 5085..6707
ORF3: 6707..7507
LOCUS MT729788 7564 bp RNA linear VRL 12-JUL-2020
DEFINITION Norovirus GII isolate Hu/US/2018/GII.4 New Orleans[P4
Yerseke]/CA-RGDS-1093, complete genome.
ACCESSION MT729788
VERSION MT729788.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7564)
AUTHORS Pan,C.-Y., Huynh,T., Padilla,T., Montmayeur,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..7564
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="Hu/US/2018/GII.4 New Orleans[P4
Yerseke]/CA-RGDS-1093"
/isolation_source="stool"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="USA: California"
/collection_date="Nov-2018"
/note="genotype: GII.4 New Orleans[P4 Yerseke]"
gene 5..5104
/gene="ORF1"
CDS 5..5104
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="QLD99654.1"
/translation="MKMASNDASAAAVANSNNDTAKSSSDGVLSSMAVTFKRALGARP
KQPPPREIPQRPPRPPTPELVKSIPPPPPNGEDDIVVSYSVKDGVSGLPDLSTVRQPE
EVNTAFSVPPLNQRENRDAKEPLVGTILEMWDGEIYHYGLYVDQGLVLGVHRPPSAVS
LARIELAPLSLYWRPVYTPQYLIPPDSLKKLHGETFPYIAFDNNCYAFCCWVLDLNDS
WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKLKKVANVFLCALASLITRPIKDIVGK
LKPLNILNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED
LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
KKEEANELAIVRSIEDAVLDLEAIENNHMTTLLKDRDSLATYMRTLDLEEEKARKLST
KSASPDIIGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREV
AKKIAASLTGDQRVGLVPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC
PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK
AKHDFPGQPDMWKNAFKPDFSHIKLSLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA
SGLLHERLDEFELQGPTLTTFNFDRNKVLAFRQLAAENKYGLMDTMKVGKQLKDVKTM
PELKAALKNISIKKCQIVYGGATYSLESDGKGNVRVDRVQSASVQTNNELAGVLHHLK
HARIRYYVKCFQEALYSIIQIAGAAFVTTRIAKRMNIQNLWSKPQVENTEETTSKDGC
PKPKDDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEFKRIREERNG
KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV
TGSEIRKRNPDDFKPKGKLWADDERSVDYNERLSFEAPPSIWSRIVNFGSGWGFWVSP
SLFITSTHVIPQGAKEFFGVPIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG
TVATLLIKRSTGELMPLAARMGTHATMRIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILG
PGSAPKLSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMREQLKPFTEP
RGKPPKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCW
NGESFTGKLADQASKANLMYEEGKNMTPVYTAALKDELVKTDKIYGKIRKRLLWGSDL
ATMIRCARAFGGLMDELKAHCITLPIRVGMSMNEDGPIIFERHSRYTYHYDADYSRWD
STQQRAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCT
SQWNSIAHWLLTLCALSEVTNLSPDTIQANSLFSFYGDDEIVSTDIKLDPEKLTTKLR
EYGLKPTRPDKTEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTKGS
NHEDPSETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQE
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="QLD99655.1"
/translation="MKMASSDANPSNGSTANLVPEVNNEVMALEPVAGAALAAPVAGQ
QNVIDPWIRSNFVQAAGGEFTVSPRNAPGEILWSAPLGPGLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIVFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLLPLPD
VRNNFYHYTQSNDPTLKLIAMLYTPLRANNAGDDVFTVSCRILTRPSPDFDFIFLVPP
TVESRTKPFSVPILTVEEMTNSRFPIPLERLFTGPSSDFVVQPQNGRCTIDGVLLGTT
QLSPVNICNFRGGVTQIGSTQAYTMNLASQNWSNYDPTEEIPAPLGTPDFVGRIQGVL
TQTTKRDGSTRGHKATVSTGDAYFTPKLGKIRFSTDTSSDLEANENTKFTPVGVVQDG
STTHKNEPKQWMLPDYSGRDTHNVHLAPAVSPSFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHRQGFATVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGAGRRRAL"
gene 6707..7507
/gene="ORF3"
CDS 6707..7507
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="QLD99656.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKDMLQAQIEATKKLQRGMIETKQAILLEGGFSDTDAARGAIN
APMTKALDWSGTRYWAPDARTTTYNAGRFSTPSPSGAPPGRIRVAAPTRDSSSISSKS
STANSMYSNQTASTRLGSTAGSGTSVSTFPSTARTRSWVEDQNRNLSPFLRGAHNISF
VTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFANIRKRGESRA"
ORIGIN
1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgct gttgctaaca gcaacaacga
61 caccgcaaaa tcttcaagtg acggagtgct ttctagcatg gctgtcactt ttaaacgagc
121 cctcggggcg cggcctaaac agcccccccc gagggaaata ccacaaagac ccccacgacc
181 acctactcca gaactggtta aaagtatccc ccctcccccg cccaacggag aggatgatat
241 agtggtttct tacagtgtca aagatggtgt ctccggtttg cctgaccttt ccaccgtcag
301 gcaaccggaa gaagttaaca cggccttcag tgtcccccca cttaatcaga gggagaatag
361 agatgctaag gagccactgg ttggaactat cctggaaatg tgggatggag aaatctacca
421 ttatggcctg tatgtggatc aaggtcttgt actgggtgtg cacagaccac cgtctgccgt
481 cagcctcgcc aggatcgagc tggcaccact ctccttgtat tggagacctg tgtacactcc
541 ccagtacctc atccctccag actcactcaa gaagttgcat ggagaaacgt tcccctacat
601 agcctttgac aacaattgct atgccttttg ttgctgggtc ctggacctaa atgactcatg
661 gctgagcagg aggatgattc agagaacaac tggtttcttc aggccttacc aagattggaa
721 taggaaaccc cttcccacta tggatgactc caaattaaag aaggtagcta atgtattcct
781 gtgtgctctg gcttcactaa ttaccaggcc cattaaagat atagtaggga agctaaagcc
841 ccttaatatc ctcaacatct tagcttcctg tgattggact tttgcaggca tagtggaatc
901 cctgatactc ttggcagagc tctttggagt cttctggaca cccccagatg tgtctgcaat
961 gattgccccc ttactcggtg actacgagct gcaaggacct gaggaccttg cagtggagct
1021 cgtccccgtg gtgatggggg gaattggctt ggtgctagga ttcaccaaag agaagattgg
1081 gaagatgttg tcatctgctg catccacctt gagagcttgt aaagatcttg gtgcatatgg
1141 gctagagatt ctaaagttgg tcatgaagtg gttcttccca aagaaagaag aagcaaacga
1201 attggctata gtgagatcta ttgaggatgc ggtcctggat ctcgaggcaa ttgagaacaa
1261 tcacatgacc accttgctca aagacagaga cagcctggca acctacatga gaacccttga
1321 ccttgaggag gagaaagcca gaaaactttc aaccaagtct gcctcacctg atattatagg
1381 cacaatcaac gccctcctgg cgagaatcgc tgctgcacga tccctagtac atcgagccaa
1441 ggaggaactt tccagcagac caaggccagt agtgttgatg atatcaggca gaccaggaat
1501 agggaagacc caccttgcta gggaagtggc taaaaagatc gcagcttccc ttacaggaga
1561 ccagcgtgta ggccttgtcc cacgcaatgg cgtcgaccac tgggatgcgt acaaggggga
1621 gagagtcgtc ctatgggacg attatggaat gagcaatccc attcacgatg ccctcagatt
1681 gcaagagctt gctgacactt gtcccctcac tctaaactgt gataggattg agaacaaagg
1741 aaaggtcttt gacagcgatg tcatcattat caccactaat ctggccaacc cagcaccact
1801 agactatgtc aactttgaag catgctcgag gcgcattgac ttcctcgtgt acgcagaagc
1861 ccctgaagtc gagaaggcga agcatgactt cccaggtcaa cctgacatgt ggaagaacgc
1921 cttcaaacct gatttctcac acataaaact atcattggcc ccacagggtg gctttgacaa
1981 gaacgggaac actccacacg gaaagggcgt catgaagacc ctcaccactg gctcccttat
2041 tgcccgggcg tcggggctac tccatgagag gttagatgag tttgaactac agggcccaac
2101 tctcaccacc ttcaatttcg accgcaacaa agtgcttgcc tttagacaac ttgctgctga
2161 aaataagtat gggttgatgg atacaatgaa ggttgggaaa cagctcaagg atgttaaaac
2221 catgccagag ctcaaagcag cactcaagaa tatctcaatt aagaagtgcc aaatagtgta
2281 tggtggtgcc acctacagcc ttgaatctga tggcaagggc aatgtgagag ttgacagagt
2341 tcagagcgcc tccgtgcaga ccaacaacga attggctggt gtccttcacc atttgaaaca
2401 cgccagaatc agatactatg ttaagtgttt ccaggaggcc ctgtattcca tcatccaaat
2461 tgctggggct gcgtttgtca ccacgcgcat cgccaagcgc atgaacattc aaaacctatg
2521 gtccaagcca caagtagaga acacagagga aaccaccagc aaggatgggt gcccaaaacc
2581 caaagatgat gaagagtttg tcatttcatc cgacgacatc aaaactgagg gtaagaaagg
2641 aaagaacaag actggccgcg gcaagaagca cacagccttt tcaagcaaag gtctcagtga
2701 tgaagagtat gatgagttca agaggattag agaagagaga aatggcaagt actccataga
2761 agagtacctt caggacaggg acaagtacta tgaggaagtg gccattgcta gggcgactga
2821 ggaagacttc tgtgaagagg aggaggccaa gattcggcaa aggatcttta ggccaacaag
2881 gaaacaacgc aaggaggaaa gagcttctct cggtctggtc acaggctctg aaatcaggaa
2941 aagaaaccca gatgatttca aacccaaggg gaaattgtgg gctgacgatg aaagaagtgt
3001 ggactacaat gagagactca gttttgaggc cccaccaagc atctggtcga gaatagtcaa
3061 ctttggctca ggttggggat tctgggtctc ccccagtctg tttataacat caacccatgt
3121 cataccccag ggtgcaaagg agttctttgg ggtccccatc aaacaaatcc aaatccacaa
3181 gtcaggcgag ttctgtcgct tgagattccc aaaaccaatc aggactgatg tgacaggcat
3241 gatcctagaa gaaggtgcac ccgaaggtac cgtggccaca ctactcatca aaaggtccac
3301 tggggaactc atgccactag cagctaggat ggggacccac gcaaccatga ggatccaagg
3361 gcgcaccgtt ggaggccaaa tgggtatgct tttgacagga tccaacgcca aaagcatgga
3421 cttaggcacc acacctggtg attgtggctg tccctacatc tacaagagag ggaatgacta
3481 tgtggtcatt ggggtccaca cggctgccgc ccgtggtgga aacactgtca tatgtgctac
3541 ccaggggagt gagggagaag ccacacttga aggtggtgac aacaagggga catactgtgg
3601 tgcaccaatc ctaggcccag gaagtgcccc aaaacttagc accaagacca aattctggag
3661 atcgtccacg gcaccactcc cacctggcac ctatgaacca gcctaccttg gaggtaaaga
3721 ccccagagtc aagggtggcc cttcactgca acaagtcatg agggaacagt taaagccatt
3781 cacagagcct aggggtaagc caccaaagcc aagtgtgtta gaagccgcca agaagaccat
3841 catcaatgtt cttgagcaaa caattgatcc acctgagaaa tggtcattcg cacaagcttg
3901 cgcatccctt gacaagacca cttccagtgg ccacccgcac cacatgcgga agaacgactg
3961 ctggaacggg gagtccttca caggcaagct agcggaccag gcctccaagg ctaatctgat
4021 gtatgaagaa ggaaagaaca tgaccccagt ctacacagct gcgctcaagg atgaattggt
4081 taaaactgac aaaatttatg gtaagatcag gaagaggctt ctctggggct cggacctggc
4141 gaccatgatc cggtgtgctc gagcattcgg aggcctaatg gatgaactca aagcacactg
4201 tatcacactt cccattagag taggtatgag catgaatgag gacggcccca tcatcttcga
4261 aaggcattcc aggtatacat atcactatga tgctgattac tctcgatggg attcaacaca
4321 acaaagagcc gtattggcag cggctctaga aatcatggtc aaattctccc cggaaccaca
4381 tttggctcag gtggtcgcgg aagaccttct ttcccctagc gtggtggatg tgggcgactt
4441 cacaatttca atcaacgagg gtctcccctc tggagtgccc tgcacctccc aatggaactc
4501 catcgcccac tggcttctca ccctctgtgc actctctgaa gttacaaact tgtcccctga
4561 caccatacaa gctaattccc tcttttcttt ttatggtgat gatgaaattg ttagcacaga
4621 cataaaattg gacccagaaa aattgacaac aaaacttaga gaatatgggt taaagccaac
4681 ccgccctgac aaaactgaag gtccccttgt catctctgaa gacctgaatg gcctgacttt
4741 tctgcggaga actgtgaccc gcgatccagc tggttggttt ggaaaactag agcagagttc
4801 aatactcagg caaatgtact ggactaaggg ttctaaccat gaagatccat ctgaaacaat
4861 gattccacac tcccaaagac ccatacaatt gatgtcccta ctaggggaag ccgctctcca
4921 cggcccagca ttctacagca aaatcagcaa gttagttatt gcagagctaa aagaaggtgg
4981 catggatttt tacgtgccca gacaagagcc aatgttcaga tggatgagat tctcagatct
5041 gagcacgtgg gagggcgatc gcaatctggc tcccagtttt gtgaatgaag atggcgtcga
5101 gtgacgccaa cccatctaat gggtccacag ccaacctcgt cccagaggtc aacaatgagg
5161 ttatggcttt ggagcccgtt gctggtgccg ctcttgcggc acctgtagcg ggccaacaaa
5221 atgtaattga cccctggatt agaagtaatt ttgtacaagc cgctggtgga gagtttacag
5281 tatcccctag aaacgctcca ggtgaaatac tatggagcgc gcccttaggt cctggtttga
5341 atccctacct ttcccatttg gctagaatgt ataatggtta tgcaggtggc tttgaagtgc
5401 aagtcatcct cgcggggaat gcgttcaccg ccggaaaaat tgtatttgca gcagtcccac
5461 caaatttccc aactgaaggc ttgagcccca gccaggtcac tatgtttccc cacataatag
5521 tagatgttag gcaactggaa cctgtgttac ttcccttacc cgatgttagg aacaatttct
5581 accactacac tcaatcaaat gatcccaccc tcaaattgat agcaatgttg tatacaccac
5641 ttagggctaa taatgctggg gatgatgtct tcacagtttc ctgtcggatt cttacgagac
5701 catcccctga ttttgatttt atatttttag tgccacccac agttgagtca agaactaaac
5761 cgttctctgt cccaatatta actgttgagg agatgaccaa ttcaagattc ccaatccctt
5821 tggaaaggct gttcacgggt cccagcagtg attttgttgt tcaaccacaa aatggcagat
5881 gcacgattga tggcgtgctc ctaggcacca cccaactgtc tcctgtcaac atctgcaact
5941 tcagaggggg tgtcacccaa attggaagta ctcaagcata cacaatgaat ctggcctccc
6001 aaaattggag caattatgac ccaacagagg aaatcccagc ccccctgggt accccagact
6061 tcgtgggcag gatccaaggt gtgctcaccc aaaccacaaa gcgggatggc tcgacccgcg
6121 gtcacaaagc cacagtgagc actggagatg cctacttcac cccaaagctg ggcaaaattc
6181 gattctccac tgatacaagt agtgatcttg aggccaatga aaacacgaaa ttcaccccag
6241 tcggagttgt ccaggatggt agcaccaccc acaaaaatga acccaaacag tggatgctcc
6301 cagattattc aggtagggat acccacaatg tgcatttggc cccagccgtg tctccctcgt
6361 ttccaggtga acaactcctt ttcttcaggt ccactatgcc cggatgcagc gggtatccca
6421 acatggatct ggattgccta ctcccccagg agtgggtgca gcacttctat caagaggcag
6481 ccccagcaca atctgatgta gctctgctaa ggtttgtgaa tccagatacg ggtagggttc
6541 tgtttgagtg caagctccat agacaaggtt ttgccacagt ggctcacact ggccaacatg
6601 atttagttat cccccccaat ggttatttca gatttgattc ctgggtcaat cagttctaca
6661 cacttgcccc catgggaaat ggagcggggc gtagacgtgc actataatgg ctggagcttt
6721 ctttgctgga ttggcttctg atgttcttgg ctctggactt ggctccctaa tcaatgctgg
6781 ggctggggcc atcaaccaaa aagttgaatt tgaaaataac agaaaattgc aacaagcttc
6841 cttccaattt agcagcaacc tacaacaggc ttcttttcaa catgacaaag atatgctcca
6901 agcacaaatt gaggccacca aaaagttaca acggggaatg attgagacta aacaggcaat
6961 actcctagag ggtgggttct ctgacacaga cgcggcccgt ggggcaatca acgcccccat
7021 gacaaaggct ttggattgga gcgggacaag atactgggct cccgatgcta ggactacaac
7081 atacaatgca ggccgctttt ccaccccttc accctcgggg gcaccaccag gaagaattag
7141 ggttgctgct cccactcggg attcctctag tatatcttct aaatcttcta ctgctaattc
7201 tatgtattca aatcaaactg cttcaacgag acttggttct acagctggtt ctggcaccag
7261 tgtctcgact ttcccgtcaa ctgcaaggac taggagctgg gttgaggatc aaaataggaa
7321 tttgtcacct ttcttgaggg gggcccacaa catatcgttt gtcaccccac catctagcag
7381 atcctctagc caaggcacag tctcaaccgt gcctaaagaa gttttggact cctggactgg
7441 cgctttcaac acgcgcaggc agcctctctt cgctaacatt cgtaagcgag gggagtcacg
7501 ggcgtaatgt gaaaagacaa aattgattac ttttcttttc tttagtgtct tttaaaaaaa
7561 aaaa
//