Typing tool
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Typing tool
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Complete norovirus genomes
| MT712157 | GII.4 Sydney | |
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| GII.P31 |
ORF1: 5..5104
ORF2: 5085..6707
ORF3: 6707..7513
LOCUS MT712157 7569 bp RNA linear VRL 12-JUL-2020
DEFINITION Norovirus GII isolate Hu/US/2016/GII.4 Sydney[P31]/CA-RGDS-1089,
complete genome.
ACCESSION MT712157
VERSION MT712157.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7569)
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 (06-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..7569
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="Hu/US/2016/GII.4 Sydney[P31]/CA-RGDS-1089"
/isolation_source="stool"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="USA: California"
/collection_date="Feb-2016"
/note="genotype: GII.4 Sydney[P31]"
gene 5..5104
/gene="ORF1"
CDS 5..5104
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="QLD66192.1"
/translation="MKMASNDASAAAVVNGNNDIAKSSSDGVFSNMAVTFKRALGARP
KQPPPKEIPPRPPRPPTPELVKKIPPPPPNGEDELVVSYSARDGVSGLPELTTVRQPE
ETNTAFSVPPLNQRESRDAKEPLTGTIIEMWDGEIYHYGLYVERGLILGVHKPPAAIS
LAKVELTPLSLFWRPVYTPQYLISPDTLRRLHGESFPYTAFDNNCYAFCCWVLDLNDS
WLSRRMIQRTTGFFRPYQDWNKKPLPTMDDSKLKKVANIFLCTLSSLFTRPIKNIIGK
LKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED
LAVELVPIVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
KKEEANELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST
KSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVVMISGRPGIGKTHLAREL
AKKIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC
PLTLNCDRIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK
AKRDFPGQPDMWKNAFSPDFSHIKLSLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA
SGLLHERLDEYELQGPALTTFNFDRNKILAFRQLAAENKYGLMDTMRVGKQLKDVKTM
SDLKQALKNIAIKKCQIVYNGGTYTLEADGKGSVKVDKVQSATVQTNNELAGALHHLR
CARIRYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNVQNLWSKPQVGDTEEMINKDGC
PKPKDDEEFVVSSDDIKTEGKKGKNKSGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
KYSIEEYLQDRDRYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV
TGSEIRKRNPEDFKPKGKLWADDDRSVDYNEKLNFEAPPSIWSRIVNFGSGWGFWVSP
SLFITSTHVIPQGAKEFFGVPIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG
TVVTLLIKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDSKGTYCGAPILG
PGSAPKLSTKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP
RGKPPKPNVLEAAKKTIINVLEQTIDPPQKWSFSQACASLDKTTSSGHPHHMRKNDCW
NGESFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKVYGKIKKRLLWGSDL
ATMIRCARAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFEKHSRYRYHYDADYSRWD
STQQRDVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVMDVGDFQISISEGLPSGVPCT
SQWNSIAHWLLTLCALSEVTDLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLK
EYGLKPTRPDKTEGPLVISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP
NHEDPFETMIPHSQRPIQLMSLLGEAALHGPVFYSKISKLVIAELKEGGMDFYVPRQE
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="QLD66193.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKVIFAAVPPNFPTEGLSPSQVTMFPHIVVDVRQLEPVLIPLPD
VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHITGSHNYTMNLASQNWNNYDPTEETPAPLGTPDFVGKIQGVL
TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTNHDFEANQNTKFTPVGVIQDG
STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAV"
gene 6707..7513
/gene="ORF3"
CDS 6707..7513
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="QLD66194.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMRVKQAMLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRDAIPARGSSSKSS
NSSVVTSVYSNQTTSTRLGSTAGSGASVSSLPSTARTRSWVEDQNRSLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRA"
ORIGIN
1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgct gttgtcaacg gcaacaacga
61 catcgcaaaa tcttcaagtg acggtgtgtt ttctaacatg gctgtcactt ttaagcgggc
121 cctcggggcg cggcctaaac agccgccccc gaaggagata ccacccagac ccccgcgacc
181 acccacacca gaactggtca aaaagatccc tcctccccca cccaacgggg aggatgaact
241 agtggtctct tacagcgcca gagatggcgt ttcagggctg cctgagctca ccactgtcag
301 gcaaccggaa gaaaccaaca cggcgttcag tgtcccccca ctcaaccaaa gggagagcag
361 ggacgccaag gagccactaa ctggaacaat tattgaaatg tgggatggag aaatctacca
421 ttacggcctg tacgtggaac gaggtcttat acttggtgtg cataagccac cggcagctat
481 tagccttgcc aaggtcgagc taacaccgct ctctttgttc tggagacctg tatacacccc
541 ccagtatctc atctctccag acactcttag gaggttgcat ggagagtcat tcccctacac
601 tgcatttgac aacaactgct atgccttttg ttgttgggta ttagacctaa acgactcatg
661 gctaagcagg agaatgattc agagaacaac aggtttcttc aggccgtacc aggattggaa
721 caagaaaccc ctccccacta tggatgactc caaattaaag aaggtagcca acatattctt
781 gtgcactttg tcttcactat tcaccagacc cattaagaac ataataggga agttgaaacc
841 tcttaacatc cttaacattc tggctacgtg tgattggacc ttcgcaggca tagtggaatc
901 tttaatactc ttagcagaac tctttggagt tttctggaca cccccagatg tgtctgcgat
961 gatcgccccc ttgctaggtg attatgagct gcaaggacct gaggaccttg cagtagaact
1021 ggtccctata gtgatggggg ggataggctt ggtgctagga tttaccaaag agaaaattgg
1081 aaagatgcta tcatccgctg catccacttt aagagcttgt aaagaccttg gtgcatacgg
1141 actggaaatc ttaaagttgg tcatgaagtg gttcttccca aagaaagagg aagcaaatga
1201 actggctatg gtgagatcca tcgaggatgc agtgctagac ctcgaggcaa ttgaaaacaa
1261 ccacatgacc accctactca aagacaaaga cagcttggcg acctacatga gaacccttga
1321 ccttgaggag gagaaagcca gaaaactctc aaccaaatct gcttcacccg atattgtggg
1381 cacaatcaac gctcttctgg caagaatcgc tgctgcacgc tccctagtgc atcgggcgaa
1441 agaagagctc tccagcaggc cgagacctgt cgttgtgatg atatcgggaa ggccagggat
1501 agggaaaact caccttgcca gggagctggc caagaaaatc gcggcctccc tcacagggga
1561 ccagcgtgtg ggtcttatcc cacgcaatgg tgtcgatcac tgggacgcat acaagggcga
1621 aagagttgtc ctatgggacg actatggaat gagcaacccc atccatgacg ccctcaggtt
1681 gcaggaactt gctgacactt gccccctaac gctaaattgt gacagaattg agaacaaagg
1741 gaaagtcttt gacagtgatg ccataattat caccaccaat ctggccaacc cagcaccact
1801 ggattatgtc aattttgaag catgctcgag gcgtattgac ttcctcgtgt acgcagaagc
1861 ccctgaggtg gagaaggcaa agcgtgactt cccaggtcaa cctgacatgt ggaagaacgc
1921 tttcagtcct gacttctcac acataaaact gtcattggct ccacagggtg gttttgacaa
1981 gaacggtaac accccgcatg ggaaaggagt catgaagacc ctcaccactg gctccctcat
2041 cgcccgagca tcagggttac tccatgagag gctagatgaa tatgaactgc aaggcccagc
2101 cctcaccact ttcaactttg accgcaacaa gatacttgct tttagacagc ttgctgctga
2161 aaacaagtat gggctgatgg acacaatgag agttggaaaa cagctcaagg atgtcaagac
2221 catgtcagac ctcaaacaag cactcaagaa catcgcgatc aagaagtgcc agatagtgta
2281 taatggtggc acctacacac ttgaggccga tggcaagggt agtgtgaaag ttgacaaagt
2341 gcaaagtgcc actgtgcaga ccaacaacga actagccggc gccctacatc acctgaggtg
2401 cgctagaatc agatactatg ttaagtgcgt ccaggaggcg ctgtattcca tcatccaaat
2461 cgctggggct gcattcgtca ccacgcgcat cgctaaacgc atgaatgtac agaatctctg
2521 gtccaagcca caggtgggag acacagaaga gatgatcaac aaagatggtt gcccaaaacc
2581 caaagatgat gaagagtttg tcgtctcatc cgacgacatc aaaactgagg gcaagaaagg
2641 gaagaacaag tccggccgtg gcaagaagca cacagccttt tcaagcaaag ggctcagtga
2701 tgaggagtac gatgagtaca agagaatcag agaagaaagg aatggtaagt actccataga
2761 agaatacctt caggatagag acaggtacta cgaggaggtg gccattgcca gggcaaccga
2821 agaggacttc tgtgaagaag aagaggccaa aatccggcag agaattttta gaccaacaag
2881 gaaacaacgc aaagaagaga gggcctctct cggcttggtc acaggctctg aaatcaggaa
2941 gagaaaccca gaagacttca aacccaaggg gaagctgtgg gctgatgatg acagaagtgt
3001 tgactacaat gagaaactca actttgaggc cccaccaagc atttggtcgc ggatagtcaa
3061 ttttggttca ggctggggct tctgggtctc ccccagtcta tttataacat caacccatgt
3121 cataccccaa ggtgcaaaag agttcttcgg agtccctatt aagcaaatcc aaatacacaa
3181 atcaggtgaa ttctgccggt tgaggttccc taagccaatc agaactgatg tgacgggcat
3241 gattctagaa gaaggtgcgc ccgaggggac cgtggtcaca ctgctcatca agagaccaac
3301 tggagagctc atgcctctgg cagccagaat ggggacccat gcaaccatga aaattcaggg
3361 gcgcacagtt ggagggcaaa tgggtatgct actgacagga tccaacgcca agagtatgga
3421 cctaggcaca acaccaggcg actgcggctg cccctacatc tacaagaggg ggaatgacta
3481 cgtggtcata ggagtccata cggccgccgc ccgtggagga aacaccgtca tatgtgccac
3541 ccaggggagt gagggagaag ccacacttga aggaggtgac agtaaaggga catactgtgg
3601 tgcaccaatc ttgggcccag ggagcgctcc gaagctcagt accaagacta agttttggag
3661 atcatccaca acaccactcc cacctggcac ctacgaacca gcctacctcg gtggcaaaga
3721 ccccagagtc aaaggtggcc cctcattgca acaagttatg agggaccagc taaaaccatt
3781 cacagaaccc agaggcaaac caccaaaacc aaatgtgttg gaagctgcca agaaaaccat
3841 catcaatgtc cttgagcaaa caattgatcc accccagaaa tggtcatttt cacaagcttg
3901 cgcgtccctt gacaaaacca cttccagcgg ccacccgcac cacatgcgga aaaacgattg
3961 ttggaatggg gagtccttta caggaaaatt ggctgatcaa gcctccaagg ccaacctaat
4021 gtttgaagag ggaaagaaca tgactccagt ctacacaggc gcacttaaag atgagttagt
4081 taagaccgac aaagtttatg gtaagatcaa gaagaggctt ctgtggggtt cagatctggc
4141 gaccatgata cggtgcgccc gagcttttgg aggcctcatg gatgaactca aggcgcactg
4201 tgtcacactt cctgtcagag ttggcatgaa catgaatgag gatggcccca tcatctttga
4261 gaagcactcc aggtacaggt atcactatga tgctgattat tcccggtggg actcaacaca
4321 acaaagggat gtgctagcag cagcactaga aatcatggtt aagttctccc cggaaccaca
4381 cctggcccag gtagttgcag aagacctcct ttcccctagc gtaatggatg taggtgactt
4441 tcaaatatca ataagtgagg gtcttccctc tggggtgcct tgtacctccc agtggaattc
4501 catcgcccac tggctcctca ctctttgtgc actctctgaa gtcacggacc tgtcccctga
4561 catcattcag gccaactccc ttttctcctt ctatggtgat gatgagattg tgagcacaga
4621 tataaagttg gacccagaga agctgacagc aaaactcaag gagtacgggc tgaaaccaac
4681 ccgccccgac aaaactgaag gaccccttgt tatatctgaa gacctagatg gcctaacatt
4741 tctccggaga actgtgaccc gtgacccagc tggttggttt ggaaaattgg aacaaagttc
4801 aattcttaga caaatgtact ggaccagggg tcccaaccat gaagatccat tcgaaacaat
4861 gataccgcac tcccaaagac ccatacaatt gatgtccttg ctgggcgagg ctgcactcca
4921 cggcccggta ttttatagca aaattagcaa attagtcatt gcagagttga aggaaggtgg
4981 catggatttt 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 tatcccctag aaacgctcca ggtgaaatac tatggagcgc gcccttgggc cctgatctaa
5341 acccttacct atcccatttg gccagaatgt acaatggtta tgcaggtggt tttgaagtgc
5401 aggtaattct cgcggggaac gcgttcaccg ccgggaaggt catatttgca gcagtcccac
5461 caaattttcc aactgaaggc ttgagcccta gccaggtcac tatgttcccc catatagtag
5521 tagatgttag gcaactagag cctgtactga ttcccttacc cgatgttagg aacaatttct
5581 atcactacaa tcaatcaaat gaccccacca ttaagttgat agcaatgttg tatacaccac
5641 ttagggctaa taatgctggg gatgatgtct tcacagtttc ttgccgagtt ctcacgagac
5701 catctcccga ttttgatttc atattcctag tgccacccac agttgagtcg agaactaaac
5761 cattctctgt cccagtttta actgttgagg agatgaccaa ttcaagattc cccattcctt
5821 tggaaaagct gttcactggc cccagcagtg cctttgttgt ccaaccacaa aacggcaggt
5881 gcacgactga tggcgtgctc ctaggcacca cccaactgtc tcctgtcaat atctgcacct
5941 tcagaggaga tgtcacccac atcacaggca gtcacaacta cacaatgaat ttagcttctc
6001 aaaattggaa taattatgac ccaacagaag aaaccccagc ccctctagga actccagact
6061 ttgtggggaa gattcaaggt gtgctcaccc aaaccacaag gacagatggc tcaacacgcg
6121 gccacaaagc cacagtgtac actgggagcg ccgactttgc tccaaaactg ggtagagttc
6181 aatttgaaac tgacacaaac cacgattttg aagctaacca aaacacaaag ttcaccccag
6241 tcggtgtcat ccaagatggt agtaccaccc accgaaatga accccaacag tgggtgctcc
6301 caagttactc aggcagaaat actcataatg tgcatctggc ccccgctgta gcccccactt
6361 ttccgggtga gcaacttctc ttcttcagat ccaccatgcc cggctgcagc gggtacccca
6421 acatggattt ggattgtctg ctcccccagg aatgggtgca gtacttctac caagaggcag
6481 ccccagcgca atctgatgtg gctctgctaa gatttgtgaa tccagacaca ggtagggttt
6541 tgtttgagtg taagctccat aaatcaggct atgtcacagt ggctcacact ggccaacatg
6601 atttggtcat tccccccaat ggttatttta gatttgattc ctgggtcaac cagttctaca
6661 cgcttgcccc catgggaaat ggaacggggc gtagacgtgc agtataatgg ctggagcttt
6721 cttcgctgga ttggcatctg atgtccttgg ctctggactt ggttccctta tcaatgctgg
6781 ggctggggcc atcaaccaaa aagttgagtt tgaaaacaac agaaaattgc aacaagcatc
6841 cttccaattt agcagcaacc tacaacaggc ttcctttcaa catgacaaag agatgctcca
6901 agcacaaatt gaggccacca aaaagttaca acaggaaatg atgagagtta agcaggcaat
6961 gctcctagag ggtgggttct ctgagacgga tgcagcccgt ggggcaatca acgcccccat
7021 gacaaaagct ctggattgga gcgggacaag gtactgggct cccgatgcta ggactacaac
7081 atacaatgca ggccgctttt ctacccctca accatcgggg gcactgccag gaagagctaa
7141 tcttagggat gctatccctg ctcggggttc ctccagtaaa tcttctaact cttctgtagt
7201 tacttctgtg tactcaaatc aaaccacttc aacgagactt ggttctacag ctggttctgg
7261 cgccagtgtc tcgagcctcc cgtcaactgc aaggactagg agttgggttg aggatcaaaa
7321 taggagtttg tcacctttca tgaggggggc ccacaatata tcgttcgtca ccccaccgtc
7381 tagcagatcc tctagccaag gcacagtctc aaccgtgccc aaagagattt tggactcctg
7441 gactggcgct ttcaacacgc gcaggcagcc actcttcgct cacattcgta agcgagggga
7501 gtcacgggcg taaagtgaaa agacaaaatt gattatcttt ctctttcttt agtgtctttt
7561 aaaaaaaaa
//