Typing tool
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Typing tool
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Complete norovirus genomes
| MT028542 | GII.4 | |
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| GII.P31 |
ORF1: 5..5104
ORF2: 5085..6707
ORF3: 6707..7513
LOCUS MT028542 7560 bp RNA linear VRL 12-FEB-2020
DEFINITION Norovirus GII isolate Hu/US/2018/GII.4 Sydney[P31]/Allegany0230,
complete genome.
ACCESSION MT028542
VERSION MT028542.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7560)
AUTHORS Montmayeur,A.M., Johnston,J., Tatusov,R.L., Chhabra,P. and Vinje,J.
TITLE Direct Submission
JOURNAL Submitted (07-FEB-2020) Division of Viral Diseases, Centers for
Disease Control and Prevention, 1600 Clifton Road NE, Atlanta, GA
30329, USA
COMMENT ##Assembly-Data-START##
Assembly Method :: Geneious v. 11.1.2; SPAdes v. 3.6
Sequencing Technology :: Illumina
##Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..7560
/organism="Norovirus GII"
/mol_type="genomic RNA"
/strain="Allegany0230"
/isolate="Hu/US/2018/GII.4 Sydney[P31]/Allegany0230"
/isolation_source="stool"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="USA"
/collection_date="31-Oct-2018"
/note="genotype: GII.4 Sydney[P31]"
gene 5..5104
/gene="ORF1"
CDS 5..5104
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="QHW12510.1"
/translation="MKMASNDASAAAVANGNNDIVKSSSDNVLSSMAITFKRALGARP
KQPPPKEIPPRPPRPPTPELVKKIPPPPPNGEDELVVSYSAKDGISGLPDLTTVSQPE
ENNTAFSVPPLNQRENRDAKEPLTGTIIEMWDGEIYHYGLYVERGLILGVHKPPAAIS
LAKVELTPLSLFWRPVYTPQYLISPDTLRRLHGESFPYTAFDNNCYAFCCWVLDLNDS
WLSRRMIQRTTGFFRPYQEWNRKPLPTMDDSKLKKVANIFLCTLSSLFTRPIKDIIGK
VKPLNILNILASCDWTFPGIVESLILLAELFGIFWTPPDVSAMIAPLLGDYELQGPED
LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
KKEEANELAMVRSIEDAVLDLEAIENNHMTALLKDKDSLATYMRTLDLEEEKARKLST
KSASPDIVGTINALLARIAAARSLVHRAKEELSSRSRPVVVMISGKPGIGKTHLAREL
AKKIAASLAGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC
PLTLNCDRIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK
AKRDFPGQPDMWKNAFSSDFSHIKLTLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA
SGLLHERLDEYELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMRIGKQLKDVKTM
PDLKQALKNVAIKKCQIVYGGSTYTLEADGKGSVKVDKVQSATVQTNNELAGALHHLR
CARIRYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQNLWSKPQVEDTEETASKDGC
PKPKDDEEFVVSSDDIKTEGKKGKNKSGRGKKHTAFSSKGLSDEEYDEYKRIRDERNG
KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV
TGTEIRKRNPEDFKPKGKLWADDDRSVDYNEKLNFEAPPSIWSRIVNFGSGWGFWVSP
SLFITSTHVIPQGAKEFFGVPIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG
TVATLLIKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKNMDLGTTPGD
CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILG
PGSAPKLSTKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP
RGKPPRPNVLEAAKKTIINVLEQTIDPPQKWSFAQACASLDKTTSSGHPHHMRKNDCW
NGESFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGKVKKRLLWGSDL
ATMIRCARAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFEKHSRYRYHYDADYSRWD
STQQRDVLAAALEIMVKFSPEPHLAQIVAEDLLSPSVMDVGDFQISISEGLPSGVPCT
SQWNSIAHWLLTLCALSEVTDLSPDIVQANSLFSFYGDDEIVSTDIKLDPEKLTAKLK
EYGLKPTRPDKTEGPLVISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP
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="QHW12511.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPGLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKVIFAAVPPNFPTEGLSPSQVTMFPHIVVDVRQLDPVLIPLPD
VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKQFSVPILTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDLTHIANSHNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGVL
TQTTRADGSTRGHKATVLTGSADFAPKLGRIQFQTDTDRDFEAHQNTKFTPVGVIQDG
GTTHQNEPQQWVLPSYSGRDTPNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMNLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYALAPMGNGTGRRRVV"
gene 6707..7513
/gene="ORF3"
CDS 6707..7513
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="QHW12512.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSDTDAARGAIN
APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQTSVALPGRSNLRDTAPVRGPSSKSS
NSSTVTSVYSNQTASTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI
AFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRV"
ORIGIN
1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgct gttgccaatg gcaacaacga
61 catcgtaaaa tcttcaagtg acaatgtgct ttctagcatg gctatcactt ttaaacgagc
121 cctcggggcg cggcctaaac agccgccccc gaaggaaata ccacccagac ctccacgacc
181 acccacacca gaattggtca aaaagatccc ccctccccca cccaacggag aggatgaact
241 agtggtttct tacagcgcca aagatggcat ttccggattg cctgatctaa ccactgtcag
301 ccaaccggaa gaaaacaata cggcgttcag cgttcccccg ctcaatcaaa gggagaatag
361 ggacgccaag gaaccactaa ctggaacaat tatagagatg tgggatggag aaatctacca
421 ttacggtctg tacgtggaac gaggtcttat acttggtgtg cacaagccac cggcagccat
481 cagccttgcc aaggtcgagt taacaccact ctctttgttc tggagacctg tgtatacccc
541 tcagtacctc atctctccag acactcttag gagactacat ggagagtcat tcccctatac
601 tgcatttgac aacaattgct acgccttctg ctgttgggtg ttagacctaa acgactcatg
661 gctgagtagg agaatgattc agaggactac agggttcttc agaccatacc aggaatggaa
721 caggaaaccc ctccccacta tggatgattc caaactgaaa aaggtagcca acatattctt
781 gtgcacccta tcttcactgt tcaccagacc cattaaggac ataataggaa aagtgaaacc
841 tcttaacatc ctcaatatcc tggcctcatg tgattggact ttcccaggca tagtggaatc
901 cctaatactc ttggcagaac tctttggaat tttctggaca cccccagatg tgtctgcgat
961 gatcgccccc ttactaggtg attatgaact gcaaggacct gaggaccttg cagtagaact
1021 ggtcccagtg gtgatgggag ggataggttt ggtgctagga tttaccaaag agaaaattgg
1081 aaagatgctg tcgtccgccg catccacctt gagggcttgc aaagaccttg gtgcatacgg
1141 tctagaaatt ttgaaattgg tcatgaaatg gttcttccca aagaaagagg aagcaaatga
1201 gctggccatg gtgagatcca tcgaggacgc agtgctggac ctcgaggcaa ttgaaaacaa
1261 ccacatgacc gccctgctca aggataaaga cagcttggca acctacatga gaacccttga
1321 ccttgaagag gagaaagcca gaaaactctc aaccaaatct gcttcacctg acattgtggg
1381 tacaatcaac gctcttctgg cacgaatcgc cgctgcacgc tccctagtgc atcgggcgaa
1441 agaagagctc tccagcaggt cgaggcctgt tgttgtgatg atatcgggaa aaccagggat
1501 agggaaaact caccttgcta gggagttggc caagaagatc gcagcctccc tcgcagggga
1561 ccagcgtgtg ggtctgatcc cacgcaatgg cgtcgaccac tgggacgcat acaagggtga
1621 aagagttgtt ctatgggacg actatgggat gagcaacccc atacacgatg ccctcaggtt
1681 gcaagaactt gctgacactt gccccctcac gctaaattgt gacaggattg aaaacaaagg
1741 aaaagttttt gatagtgacg ccataattat taccaccaat ctggccaacc cagcaccact
1801 tgattatgtc aactttgaag cgtgctcgag gcgcattgac ttcctcgtgt acgcggaagc
1861 tcctgaggtg gagaaggcaa aacgcgactt cccaggccag cccgacatgt ggaagaacgc
1921 tttcagttct gacttctcac acataaaact gacactggct ccgcagggtg gctttgacaa
1981 gaacggcaac accccgcatg gaaaaggtgt catgaagacc ctcaccactg gctccctcat
2041 tgcccgagca tcaggactac tccatgagag gctagatgaa tatgaattgc aaggtccagc
2101 tctcactacc ttcaactttg atcgcaacaa ggtacttgct tttagacagc ttgctgctga
2161 aaacaagtat gggctgatgg acacaatgag aattggaaaa cagcttaagg atgtcaagac
2221 catgccagac ctcaaacaag cactcaagaa tgttgcgatc aagaagtgcc agatagtgta
2281 tggtggtagc acctacacgc ttgaggccga tggcaagggt agtgtgaaag ttgacaaagt
2341 gcagagtgcc accgtgcaaa ctaacaatga actagccggc gccctgcacc acctgaggtg
2401 cgccagaatc aggtactatg ttaagtgtgt ccaggaggca ttgtattcca tcatccaaat
2461 cgctggggcc gcgtttgtca ccacgcgcat cgccaagcgc atgaacatac aaaacctctg
2521 gtccaagcca caggtggaag acacggaaga gacggccagc aaagatggtt gcccaaaacc
2581 caaagatgat gaagagttcg tcgtttcatc cgacgacatc aagactgagg gcaagaaagg
2641 gaagaacaag tccggccgtg gcaagaagca cacggccttc tcaagcaaag ggctcagtga
2701 tgaggagtac gatgagtaca agagaatcag agatgaaagg aatggcaagt actccataga
2761 agagtacctt caggacagag acaagtacta tgaggaggtg gccattgcca gggcaactga
2821 agaggacttc tgtgaagaag aagaggccaa aatccggcag agaattttta gaccaacaag
2881 gaaacagcgt aaagaagaga gggcctcttt aggcttggtc acaggcacag agatcaggaa
2941 gagaaaccca gaagacttca aacccaaggg aaagctgtgg gctgatgatg acagaagtgt
3001 tgactacaac gagaaactca actttgaggc cccaccaagc atctggtcgc ggatagtcaa
3061 ctttggttca ggttggggct tctgggtctc ccccagtttg ttcataacat caacccatgt
3121 cataccccaa ggtgcaaaag agttcttcgg agtccccatc aaacagatcc aaatacacaa
3181 atcaggtgaa ttctgccgat tgagattccc aaaaccaatc agaactgatg tgacgggcat
3241 gattctggaa gaaggtgcgc cagaaggaac cgtggccaca ctgctcatca agagaccaac
3301 tggggagctc atgcctttgg cagccaggat gggaacccat gcgaccatga agattcaggg
3361 gcgcacagtt ggaggacaaa tgggtatgct tttgacagga tccaacgcca agaatatgga
3421 cttgggcaca acaccaggcg attgcggttg cccctacatc tacaaaagag ggaacgacta
3481 tgtggtcata ggagtccaca cagccgctgc ccgtggggga aacactgtca tctgtgccac
3541 ccagggtagt gagggagaag ccacacttga aggaggtgac aacaaaggaa cgtactgtgg
3601 tgcaccaatc ttgggcccag ggagtgctcc gaaactcagc accaaaacta agttttggag
3661 atcatccaca acgccactcc caccaggcac ctacgaacca gcctacctcg gtggcaagga
3721 ccccagagtc aaaggtggcc cttcactgca acaggttatg agggaccagc taaaaccatt
3781 cacagaacct agaggcaaac caccaagacc aaatgtgttg gaagctgcca agaaaaccat
3841 cattaatgtt cttgagcaaa caattgaccc accccaaaaa tggtcattcg cgcaagcttg
3901 cgcatccctt gacaaaacca cctccagcgg ccacccacac cacatgcgga aaaacgattg
3961 ttggaatggg gagtccttta caggtaaatt ggcagatcag gcctccaagg ccaacctaat
4021 gtttgaagag ggaaagaaca tgactccagt ctacacaggt gcacttaagg atgaattggt
4081 gaagactgac aaaatttatg gcaaggtcaa gaagaggctc ctgtggggct cggacctggc
4141 gaccatgata cggtgcgccc gggcttttgg aggcctcatg gatgaactta aggcacactg
4201 tgttaccctt cctgtcagag ttggtatgaa catgaatgag gatggcccca taatctttga
4261 gaagcactcc aggtataggt atcactatga cgctgactac tccaggtggg actcaacaca
4321 acaaagggat gtgctagcag cagcactaga aattatggtt aagttttctc cagagccaca
4381 cttggcccag atagttgcag aagacctcct ctcccctagt gtaatggatg tgggtgactt
4441 ccaaatatca ataagtgagg gactcccctc cggggtgcct tgcacctccc agtggaactc
4501 catcgcccac tggctcctca ccctttgtgc actctcagaa gtcacagacc tgtcccctga
4561 catcgtccag gccaactccc ttttctcctt ctatggtgat gatgagattg tgagtacaga
4621 cataaaattg gacccagaga aactgacagc aaaactcaaa gagtacgggc tgaagccaac
4681 ccgccccgac aaaactgaag gaccccttgt tatctctgaa gatctggatg gcctgacctt
4741 cctccggagg actgtgaccc gtgacccagc tggttggttt ggaaaattgg aacagagctc
4801 aattctcagg caaatgtatt ggaccagggg ccccaaccat gaagatccat ctgaaacaat
4861 gataccacac tcccaaagac ccatacaatt gatgtccttg ctgggcgagg ctgcactcca
4921 cggcccagca ttttacagca aaattagcaa attggtcatt gcagaattga aagaaggtgg
4981 catggatttt tacgtgccca ggcaagagcc aatgttcaga tggatgagat tctcagatct
5041 gagcacgtgg gagggcgatc gcaatctggc tcccagtttt gtgaatgaag atggcgtcga
5101 gtgacgccaa cccatctgat gggtccgcag ccaacctcgt cccagaggtc aacaatgagg
5161 ttatggctct ggagcccgtt gttggtgccg ctatcgcggc acctgtagcg ggccaacaaa
5221 atgtaattga cccctggatt agaaataatt ttgtgcaagc ccctggtgga gagtttacag
5281 tatcccctag aaacgctcca ggtgaaatac tatggagcgc gcccttaggc cccggtctaa
5341 atccctacct atcccatttg gccagaatgt acaatggtta tgcaggtggt tttgaagtgc
5401 aggtaatcct cgcggggaac gcgttcaccg ctgggaaggt catatttgca gcagtcccac
5461 caaattttcc aactgaaggc ttgagcccca gccaggtcac catgttcccc catatagtag
5521 tggatgttag gcaattagac cctgtgttga ttcccttacc cgacgttagg aacaatttct
5581 atcactacaa tcaatcaaat gaccccacta ttaagttgat agcaatgctt tatacaccac
5641 ttagggctaa taatgctggg gacgatgtct tcacagtctc ttgccgggtc ctcacgagac
5701 cgtcccccga ttttgatttt atattcctag tgccacccac agttgagtca agaactaagc
5761 aattctctgt cccaatctta actgttgagg agatgaccaa ttcaagattc cccattcctt
5821 tggaaaagtt gttcacgggt cccagcagtg cttttgttgt tcaaccacaa aacggcaggt
5881 gcacgactga tggcgtgctc ctaggcacta cccaactgtc tcctgtcaac atctgcacct
5941 tcagaggaga tctcactcac atcgcaaata gtcataatta tacaatgaat ttggcttctc
6001 aaaattggaa caattatgac ccaacagaag aaatcccagc ccccctagga actccagatt
6061 ttgtagggaa gatacaagga gtgctcaccc aaaccacaag ggcagatggc tcaacacgcg
6121 gccacaaagc cacagtgctc actgggagcg ccgattttgc tccaaaactg ggtagaattc
6181 aatttcaaac tgacacagat cgtgattttg aagctcacca aaacacaaag ttcaccccag
6241 tcggtgtcat ccaagatggt ggcaccaccc atcaaaatga accccaacag tgggtgctcc
6301 caagttactc aggcagggac acccccaatg tgcatttggc ccccgctgta gcccccactt
6361 ttccgggtga acaacttctc ttcttcagat ctaccatgcc cggatgcagc gggtacccca
6421 atatgaatct ggactgcctg ctcccccagg aatgggtgca gtacttctac caagaggcag
6481 ccccagcaca atctgatgta gctctgctga gatttgtgaa tccagataca ggtagggttt
6541 tgtttgagtg taagcttcat aaatcaggct atgttacagt ggcccacact ggccagcatg
6601 atttggttat cccccccaat ggttatttta ggtttgattc ctgggtcaac cagttctacg
6661 cgcttgcccc catgggaaat ggaacggggc gtagacgtgt ggtataatgg ctggagcttt
6721 ctttgctgga ttggcatctg atgtccttgg ctctggactt ggttctctta tcaatgctgg
6781 ggctggggcc atcaaccaaa aagttgaatt tgaaaataac agaaaattgc aacaagcatc
6841 cttccaattt agcagtaacc tacaacaggc ttcctttcaa catgataaag agatgctcca
6901 ggcacaaatt gaggccacca aaaagttaca acaggaaatg atgaaagtta aacaggcaat
6961 gctcctagag ggtgggttct ctgatacaga tgcagcccgc ggggcaatca acgcccccat
7021 gacaaaagct ttggactgga gcgggacaag gtactgggct cccgatgcta ggactacaac
7081 atacaatgca ggccgctttt ccacccctca aacatcggtg gcactgccag gaagatctaa
7141 tcttagggat actgcccctg tccggggccc ctctagcaaa tcttctaact cttctactgt
7201 tacttctgtg tattcaaatc aaactgcttc aacgagactt ggttctacag ctggttctgg
7261 caccagtgtc tcgagcctcc cgtcaactgc aaggactagg agctgggttg aggatcaaaa
7321 caggaatttg tcacctttca tgaggggggc ccacaacata gcgtttgtca ccccaccatc
7381 tagcagatcc tctagccaag gcacagtctc aaccgtgcct aaagagattt tggactcctg
7441 gactggcgct ttcaacacgc gcaggcagcc tctcttcgct cacattcgta agcgagggga
7501 gtcacgggtg taatgtgaaa aggcaaaatt gattatcttt ctttttcttt agtgtctttt
//