Typing tool
|
|
|
|
|
|
Typing tool
|
Complete norovirus genomes
| MT726225 | GII.4 Sydney | |
|
|---|---|---|---|
| GII.P31 |
ORF1: 5..5104
ORF2: 5085..6707
ORF3: 6707..7513
LOCUS MT726225 7568 bp RNA linear VRL 12-JUL-2020
DEFINITION Norovirus GII isolate Hu/US/2018/GII.4 Sydney[P31]/CA-RGDS-1092,
complete genome.
ACCESSION MT726225
VERSION MT726225.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7568)
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..7568
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="Hu/US/2018/GII.4 Sydney[P31]/CA-RGDS-1092"
/isolation_source="stool"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="USA: California"
/collection_date="Mar-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="QLD98119.1"
/translation="MKMASNDASAAAVANSNNDIAKSSSDGVLSNMAVTFKRALGARP
KQPPPKEIPPRPPRPPTPELVKKIPPPPPNGEDELVVSYSARDGVSGLPELTTVRQPE
EANTAFSVPPLNQRESRDAKEPLTGTIIEMWDGEIYHYGLYVERGLVLGVHKPPAAIS
LAKVELTPLSLFWRPVYTPQYLISPDTLRRLHGESFPYTAFDNNCYAFCCWVLDLNDS
WLSRRMIQRTTGFFRPYQDWNKKPLPTMDDSKLKKVANIFLCTLSSLFTRPIKDIIGK
LKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED
LAVELVPIVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
KKEEANELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST
KSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVVMISGRPGIGKTHLAREL
AKKIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC
PLTLNCDRIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK
AKRDFPGQPDMWKNAFSPDFSHIKLSLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA
SGLLHERLDEYELQGPALTTFNFDRNKILAFRQLAAENKYGLMDTMRVGKQLKDVKTM
SDLKQALKNIAIKRCQIVYNGGTYTLEADGKGSVKVDKVQSATVQTNNELAGALHHLR
CARIRYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQNLWSKPQVEDTEEMTNKDGC
LKPKDDEEFVVSSDDIKTEGKKGKNKSGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
KYSIEEYLQDRDRYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV
TGSEIRKRNPEDFKPKGKLWADDDRSVDYNEKLNFEAPPSIWSRIVNFGSGWGFWVSP
SLFITTTHVIPQGAKEFFGVPIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG
TVVTLLIKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDSKGTYCGAPILG
PGSAPKLSTKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP
RGKPPRPNVLEAAKKTIINVLEQTIDPPQKWSFAQACASLDKTTSSGHPHHMRKNDGW
NGESFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKVYGKIKKRLLWGSDL
ATMIRCARAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFEKHSRYRYHYDADYSRWD
STQQRDVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVMDVGDFQISISEGLPSGVPCT
SQWNSIAHWLLTLCALSEVTDLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLK
EYGLKPTRPDKTEGPLVISENLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP
NHEDPFETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQE
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="QLD98120.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKVIFAAVPPNFPTEGLSPSQVTMFPHIVVDVRQLEPVLIPLPD
VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHITGSHNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGVL
TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTNHDFEANQNTKFTPVGVIQDG
GTTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRVV"
gene 6707..7513
/gene="ORF3"
CDS 6707..7513
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="QLD98121.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMRVKQAMLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDAGITTYNAGRFSTPQPSGALPGRANLRDAVPARGSSSKSP
NSSVATSVYSNQTTSTRLGSTAGSGASVSSLPSTARTRSWVEDQNRSLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRRRGESRV"
ORIGIN
1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgct gttgccaaca gcaacaacga
61 catcgcaaaa tcttcaagtg acggtgtgtt atctaacatg gctgtcactt ttaagcgggc
121 cctcggggcg cggcctaaac agccgccccc gaaggagata ccacccagac ccccgcgacc
181 acccacacca gaactggtca aaaagatccc ccctccccca cccaacgggg aggatgaatt
241 agtggtctct tacagcgcca gagatggcgt ttccggactg cctgagctca ccactgtcag
301 gcaaccggaa gaagccaaca cggcgttcag tgtcccccca ctcaaccaaa gggagagcag
361 ggacgccaag gagccactaa ctggaacaat tattgaaatg tgggatggag aaatctacca
421 ttacggtctg tacgtggaac gaggtcttgt acttggtgtg cataagccac cggcagctat
481 cagccttgcc aaggtcgagc taacaccgct ctctttgttc tggagacctg tatacacccc
541 ccagtatctc atctccccag acactcttag gaggttgcac ggagagtcat tcccctacac
601 tgcatttgac aacaattgct acgccttttg ttgttgggta ttagacctaa acgactcatg
661 gctaagcagg agaatgatcc agagaacaac aggtttcttc aggccatacc aggattggaa
721 caagaaaccc ctccccacta tggatgactc caaattaaag aaggtagcca acatattctt
781 gtgcactttg tcttcgctat tcaccagacc cattaaggac ataataggga agttgaaacc
841 tcttaacatc ctcaacattc tggctacatg tgattggact ttcgcaggca tagtggaatc
901 tttaatactc ttagcagaac tctttggagt tttctggaca cccccagatg tgtctgcgat
961 gatcgccccc ttgctaggtg attatgaact gcaaggacct gaggaccttg cagtggaact
1021 ggtccctata gtgatggggg ggataggttt ggtgttagga tttaccaaag agaagattgg
1081 aaagatgcta tcatccgctg catccacttt aagagcttgt aaagaccttg gtgcatacgg
1141 actggaaatc ttaaaattgg tcatgaagtg gttcttccca aagaaagagg aggcaaatga
1201 actggctatg gtgagatcca tcgaggatgc agtgctagac ctcgaggcaa ttgaaaacaa
1261 ccacatgacc accctactca aagacaaaga cagtttggca acttacatga gaacccttga
1321 ccttgaggag gagaaagcca gaaaactctc aaccaaatct gcttcacccg atattgtggg
1381 cacaatcaac gctcttctgg caagaatcgc tgctgcacgc tccctagtgc atcgggcgaa
1441 agaagagctc tccagcaggc cgagacctgt cgttgtgatg atatcgggaa gaccagggat
1501 agggaaaacc cacctcgcca gggagcttgc caagaaaatc gcggcctccc tcacagggga
1561 ccagcgtgtg ggtcttatcc cacgcaatgg tgtcgatcac tgggacgcat acaagggcga
1621 aagagttgtc ctatgggacg actatgggat gagcaacccc atccatgatg ccctcaggtt
1681 gcaggaactt gctgacactt gccccctcac gctaaattgt gacagaattg agaacaaagg
1741 gaaagtcttt gacagtgatg ccataattat caccaccaac ctggccaatc cagcaccact
1801 ggattatgtc aattttgaag catgctcgag acgtattgac ttcctcgtgt acgcagaagc
1861 ccctgaggtg gagaaggcaa agcgtgattt cccaggtcaa cctgacatgt ggaagaacgc
1921 tttcagccct gacttctcac acataaaact gtcattggct ccacagggtg gttttgacaa
1981 gaacggcaac accccgcatg gaaaaggggt catgaaaacc ctcaccactg gctccctcat
2041 cgcccgagca tcagggttac tccacgagag gctagatgaa tatgaactgc aaggcccggc
2101 cctcaccact ttcaactttg accgtaacaa gatacttgct tttagacagc ttgctgctga
2161 aaacaagtat gggctaatgg acacaatgag agttggaaaa cagctcaagg atgtcaagac
2221 catgtcagac ctcaaacaag cactcaagaa catcgcgatc aagaggtgcc agatagtgta
2281 caatggtggc acctacacac ttgaggccga tggcaagggt agtgtgaaag ttgacaaagt
2341 gcaaagtgcc actgtgcaga ccaacaatga actagccggc gccctacacc acctaaggtg
2401 cgctagaatc agatactatg ttaagtgcgt ccaggaggca ctgtattcca tcatccaaat
2461 cgctggggcc gcattcgtca ccacgcgcat cgctaagcgc atgaatatac agaatctctg
2521 gtccaagcca caggtggagg acacagaaga aatgaccaac aaagatggct gcctaaaacc
2581 caaagatgat gaagagtttg tcgtctcatc cgacgacatc aagactgagg gcaagaaagg
2641 gaagaacaag tccggccgtg gcaagaagca cacagccttt tcaagcaaag ggctcagtga
2701 tgaggagtac gatgagtaca agagaatcag agaagaaagg aatggtaagt actccataga
2761 agagtacctt caggacagag acaggtacta cgaggaggtg gccattgcca gggcaaccga
2821 agaggacttc tgtgaagaag aagaggccaa aatccggcag agaattttca gaccaacaag
2881 gaaacaacgt aaagaggaga gggcctctct cggcttggtc acaggctctg aaatcaggaa
2941 gagaaaccca gaagacttca aacccaaggg gaagctgtgg gctgatgatg acagaagtgt
3001 tgactacaat gagaaactca actttgaggc cccaccaagc atttggtcgc ggatagtcaa
3061 cttcggttca ggctggggct tctgggtctc ccccagtctg tttataacaa caacccatgt
3121 catacctcaa ggtgcaaaag agttcttcgg agtccctatc aagcaaatcc agatacacaa
3181 atcaggtgaa ttctgccggt tgagattccc aaagccaatc agaactgatg tgacgggcat
3241 gattctagaa gaaggtgcgc ccgagggcac cgtggtcaca ctgctcatca agagaccaac
3301 tggagagctc atgcctctgg cagccagaat ggggacccat gcaaccatga aaattcaggg
3361 gcgcacagtt ggagggcaaa tgggtatgct cctgacagga tccaacgcca agagtatgga
3421 cctaggcaca acaccaggcg actgtggctg cccctacatc tacaagaggg ggaatgacta
3481 cgtggtcata ggagtccaca cggccgctgc ccgtggagga aacaccgtca tatgcgccac
3541 ccaggggagt gagggagaag ccacacttga aggaggtgac agtaaaggga cgtactgtgg
3601 cgcaccaatc ttgggcccag ggagcgctcc gaagctcagc accaagacta agttttggag
3661 atcatccaca acaccactcc cacctggcac ctacgaacca gcctacctcg gtggcaaaga
3721 ccccagagtc aaaggtggcc cctcattgca acaagttatg agggaccagc taaaaccatt
3781 cacagaaccc agaggcaaac caccaagacc aaatgtgttg gaagctgcca agaaaaccat
3841 catcaatgtc cttgagcaaa caattgatcc accccaaaaa tggtcatttg cgcaagcttg
3901 cgcatccctt gacaaaacca cttccagcgg ccacccgcac catatgcgga aaaacgatgg
3961 ttggaatggg gagtccttta caggaaaatt ggctgatcaa gcctccaagg ccaacttaat
4021 gtttgaagag ggaaagaaca tgactccagt ctacacaggt gcacttaaag atgagttggt
4081 aaagaccgat aaagtttatg gtaagatcaa gaagaggctt ctgtggggtt cagatctggc
4141 gactatgata cggtgcgccc gagcttttgg aggccttatg gatgaactca aggcgcactg
4201 tgtcacactt cctgtcagag ttggcatgaa catgaatgag gatggcccca tcatctttga
4261 gaagcactcc agatatagat atcactatga tgctgattat tcccggtggg actcaacaca
4321 acaaagggat gtgctagcag cagcactaga aatcatggtt aagttctccc cagaaccaca
4381 cctggcccag gtagttgcag aagacctcct ttcccccagc gtaatggatg taggtgactt
4441 tcaaatatca ataagtgagg gtcttccctc tggggtgcct tgcacctccc agtggaattc
4501 catcgcccac tggctcctca ctctttgtgc actttctgaa gtcacggacc tgtcccctga
4561 catcattcag gccaactccc ttttctcctt ctatggtgat gatgagattg tgagcacaga
4621 tataaagttg gacccagaga agctgacagc aaaactcaag gagtacgggc tgaaaccaac
4681 ccgccccgac aaaactgaag gaccccttgt tatctctgaa aacctggatg gcctaacatt
4741 cctccggaga actgtgaccc gtgacccagc tggctggttt ggaaaattgg aacagagttc
4801 aattcttaga caaatgtact ggactagggg tcccaaccat gaagatccat tcgaaacaat
4861 gataccacac tcccaaagac ccatacaatt gatgtccttg ctgggcgagg ctgcgctcca
4921 cggcccggca ttttatagca aaattagcaa attagtcatt gcagagttga aggaaggtgg
4981 catggatttt tacgtgccca gacaggagcc aatgttcaga tggatgagat tctcagatct
5041 gagcacgtgg gagggcgatc gcaatctggc tcccagtttt gtgaatgaag atggcgtcga
5101 gtgacgccaa cccatctgat gggtccgcag ccaacctcgt cccagaggtc aacaatgagg
5161 ttatggctct ggagcccgtt gttggtgccg ccattgcggc acctgtagcg ggccaacaga
5221 atgtaattga cccctggatc agaaacaatt ttgtacaagc ccctggtgga gagtttacag
5281 tatcccctag aaacgctcca ggtgaaatac tatggagcgc acccttgggc cctgatctaa
5341 atccctatct atcccatttg gccagaatgt acaatggtta tgcaggtggt tttgaagtgc
5401 aggtaattct cgcggggaac gcgttcaccg ctgggaaggt catatttgca gcagtcccac
5461 caaattttcc aactgaaggc ttgagcccta gccaggtcac tatgttcccc catatagtag
5521 tagatgttag gcaactagaa cctgtactga ttcccttacc cgatgttagg aataattttt
5581 atcattataa ccaatcaaat gatcccacca ttaagttgat agcaatgttg tatacaccac
5641 ttagggctaa taatgctggt gatgatgtct tcacagtttc ttgccgagtt ctcacgagac
5701 catcccccga ttttgatttc atatttttag tgccacccac agttgagtca agaactaaac
5761 cattctctgt cccagtttta actgttgagg aaatgaccaa ttcaagattc cccattcctt
5821 tggaaaagct gttcacgggc cccagcagtg cctttgttgt ccaaccacaa aacggcaggt
5881 gcacgactga tggcgtgctc ctaggtacca cccaactgtc ccctgtcaac atctgcacct
5941 tcagaggaga tgtcacccac atcacaggca gtcacaacta tacaatgaat ttggcttctc
6001 aaaattggaa taattatgac ccaacagaag aaatcccagc ccctctaggg actccagact
6061 ttgtggggaa gattcaaggt gtgctcaccc aaaccacaag gacagacggc tcaacacgcg
6121 gccacaaagc cacagtgtac actgggagcg ccgactttgc cccaaaactg ggtagagttc
6181 aatttgaaac cgacacaaac catgattttg aagctaacca aaacacaaag ttcaccccag
6241 tcggtgttat ccaagatggt ggtaccaccc accgaaatga accccaacag tgggtgctcc
6301 caagttactc aggcagaaat actcataatg tgcatctggc ccccgctgta gcccccactt
6361 ttccgggtga gcaacttctc ttcttcagat ccaccatgcc cggatgcagc gggtacccca
6421 acatggattt ggattgtctg ctcccccagg aatgggtgca gtacttctac caagaggcgg
6481 ccccagcaca atctgacgtg gctctgctaa gatttgtgaa tccagacaca ggtagggttt
6541 tgtttgagtg taagctccat aaatctggct atgttacagt ggctcacact ggtcaacatg
6601 atttggttat tccccccaat ggttatttta ggtttgattc ctgggtcaac cagttctaca
6661 cacttgcccc catgggaaat ggaacggggc gtagacgtgt agtataatgg ctggagcttt
6721 ctttgctgga ttggcatctg acgtccttgg ctctggactt ggttccctta tcaatgctgg
6781 ggctggggcc atcaaccaaa aagttgagtt tgaaaacaac agaaaattgc aacaagcatc
6841 cttccaattt agcagcaatc tacaacaggc ttcctttcaa catgacaaag agatgctcca
6901 agcacaaatt gaggccacca aaaagttaca acaggaaatg atgagagtca agcaggcaat
6961 gctcctagag ggtgggttct ctgagacgga tgcggcccgt ggggcaatca acgcccccat
7021 gacaaaagct ctggactgga gcgggacaag gtactgggct cccgatgctg ggatcacaac
7081 atacaatgca ggccgttttt ccacccctca accatcgggg gcactgccag gaagagctaa
7141 tcttagagat gctgtccctg ctcggggttc ctccagtaaa tctcctaact cttctgtcgc
7201 tacttctgtt tattcaaatc aaactacttc aacgagactt ggttctacag ctggttctgg
7261 cgccagtgtc tcgagcctcc cgtcaactgc aaggactagg agctgggttg aggatcaaaa
7321 taggagtttg tcacctttca tgaggggggc ccacaatata tcgtttgtca ccccaccatc
7381 tagcagatcc tctagccaag gcacagtctc aaccgtgccc aaagagattt tggactcctg
7441 gactggcgct ttcaacacgc gcaggcagcc actcttcgct cacattcgta ggcgagggga
7501 gtcacgggtg taatgtgaaa aggcaaaatt gattatcttt ctctttcttt agtgtctttt
7561 aaaaaaaa
//