Typing tool
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Typing tool
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Complete norovirus genomes
| MK616585 | GII.1 | |
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| GII.P33 |
ORF1: 1..5082
ORF2: 5063..6670
ORF3: 6670..7443
LOCUS MK616585 7456 bp RNA linear VRL 17-MAR-2019
DEFINITION Norovirus GII isolate CA-RGDS-1022 nonstructural polyprotein (ORF1)
gene, partial cds; and VP1 (ORF2) and VP2 (ORF3) genes, complete
cds.
ACCESSION MK616585
VERSION MK616585.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7456)
AUTHORS Pan,C.-Y., Huynh,T., Castro,C.J., Ng,T.F., Marine,R.L. and
Wadford,D.A.
TITLE Norovirus GII.Pg-GII.1 genomes from gastroenteritis outbreaks,
California, 2018
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 7456)
AUTHORS Pan,C.-Y., Huynh,T., Castro,C.J., Ng,T.F., Marine,R.L. and
Wadford,D.A.
TITLE Direct Submission
JOURNAL Submitted (11-MAR-2019) Viral and Rickettsial Disease Laboratory,
California Department of Public Health, 850 Marina Bay Parkway,
Richmond, CA 94804, USA
COMMENT ##Assembly-Data-START##
Assembly Method :: Geneious v. R10; SPAdes v. 3.6
Sequencing Technology :: Illumina
##Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..7456
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="CA-RGDS-1022"
/isolation_source="stool"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="USA: CA"
/collection_date="Feb-2018"
/note="genotype: GII.Pg-GII.1"
gene <1..5082
/gene="ORF1"
CDS <1..5082
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="QBL14412.1"
/translation="SAAAAATSNNDNAKSSSDGVLSSMAVTFKRALGARPKQPPPRET
EQKQKPPRPPTPELIKKIPPPPPNGEDDIVVSYSAKDGVSGLPELSTVRQPDGTNTAF
SVPPLNQRENKDAKEPLPGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAISLAKVEL
TPLSLYWRPVYTPQYLISPETLKKLHGETFPYTAFDNNCYAFCCWVLDLNDSWLSRRM
IQRTTGFFRPYQDWNRKPLPTMDDSKLKKVANIVLCALSSLFTRPIKDIIGKLRPLNI
LNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVELV
PVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKDEAN
ELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDLEEEKARKLSTKSASPD
IVGTINSLLARIAAARSLVHRAKEELSSRPRPVVVMISGKPGIGKTHLARDLAKKVAA
TLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCPLTLNC
DRIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYADAPDVEKAKRDFP
GQPDMWKDAFRPDFSHIKLMLAPQGGFDKNGNTPHGRGVMKTLTSGSLIARASGLLHE
RLDEYELQGPTPTTFNFDQNKVFAFRQLAAENKYGLVDTMRVGSQLKNVKTVSELKQA
LKNISIRRCQIVYGGLTYSLESDGKGNVRVEKVQSPAVQTNNELTGALHHLRCARIRY
YVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQNLWSRPQVDDEEETTSKDGCPKPKDE
EEFVISSEDIKAEGKKGKNKSGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEE
YLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERVSLGLVTGSEIR
KRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSPSLFITS
THVIPQGAQEFFGVSIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVATLL
IKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCGCPYI
YKRGNDYVVIGVHTAAARGGNTVICATQGSEGEAVLEGGDNKGTYCGAPILGPGNAPK
LSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRGKPPK
PSVLEAAKKTIINVLEQTIDPPQKWTFAQACASLDKTTSSGYPHHVRKNEHWNGESFT
GKLADQASKANLMFEEGKHMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDLATMIRC
ARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFGKHSRYTYHYDADYSRWDSTQQRA
VLASALEIMVKFSPEPHLAQIVAEDLLSPSVMDVGDFKISITEGLPSGVPCTSQWNSI
AHWLLTLCALSEVTDLSPDIIQANSLFSFYGDDEIVSTDIKLDPERLTAKLKEYGLKP
TRPDKTEGPLVISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHEDPS
ETMIPHSQRPIQLMSLLGEAALHGPSFYSKISKLVISELKEGGMDFYVPRQEPMFRWM
RFSDLSTWEGDRNLAPSFVNEDGVE"
mat_peptide <1..972
/gene="ORF1"
/product="p48"
mat_peptide 973..2070
/gene="ORF1"
/product="NTPase"
mat_peptide 2071..2607
/gene="ORF1"
/product="p22"
mat_peptide 2608..3006
/gene="ORF1"
/product="VPg"
mat_peptide 3007..3549
/gene="ORF1"
/product="Pro"
mat_peptide 3550..5079
/gene="ORF1"
/product="RdRp"
gene 5063..6670
/gene="ORF2"
CDS 5063..6670
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="QBL14410.1"
/translation="MKMASNDAAPSNDGAAGLVPEVNNETMALEPVAGASIAAPLTGQ
NNVIDPWIRMNFVQAPNGEFTVSPRNSPGEVLLNLELGPELNPFLAHLSRMYNGYAGG
VEVQVLLAGNAFTAGKLVFAAIPPHFPLENLSPGQITMFPHVIIDVRTLEPVLLPLPD
VRNNFFHYNQQPEPRMRLVAMLYTPLRSNGSGDDVFTVSCRVLTRPSPDFDFNYLVPP
TVESKTKPFTLPILTIGELSNSRFPVPIDELYTSPNEGVVVQPQNGRSTLDGELLGTT
QLVPSNICALRGRINAQVPDDHHQWNLQVTNANGTPFDPTEDVPAPLGMPDFLANIYG
VTSQRNPDNTCRAHDGVLATWSPKFTPKLGSVVLGTWEEQDLDLNQPTRFTPVGLYDT
NHFDQWILPNYSGRLTLNMNLAPSVAPLFPGEQILFFRSHIPLKGGTSNGAIDCLLPQ
EWIQHFYQESAPSPTDVALIRYTNPDTGRVLFEAKLHRQGFITVANSGSRPIVVPPNG
YFRFDSWVNQFYSLAPMGTGNGRRRVQ"
gene 6670..7443
/gene="ORF3"
CDS 6670..7443
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="QBL14411.1"
/translation="MAGAFVAGLAGDIVTNSIGSLVNAGANAINQKVDFENNKQLQQA
SFNHDKEMLQAQIQATKQLQADMIALRQGVLTAGGFSPTDAARGAVNVPMTQVLDWNG
TRYWAPGATKTTAFSGGFTSSPNTRTVDLPRKTSTTPAPTPISRPSSSASTVSTRSTI
ISGTSGLSSLTRSSFNSQPTSSSSRTSEWVRGQNRALEPYMRGALQTAYVTPPSSRAS
SNGTVSTVPKEVLDSWTSVFNTHRQPLFAHLRRRGESQV"
ORIGIN
1 tccgctgccg ctgctgctac cagcaacaac gacaacgcaa aatcttcaag tgacggagta
61 ctaagtagta tggctgtcac ttttaaacga gccctcgggg cccggcctaa acagccgccc
121 ccgagggaaa cagaacaaaa acaaaaacct ccacgaccgc ccaccccgga gttaatcaaa
181 aagattccac ctcccccgcc caacggggag gacgatatag tggtatccta tagtgccaaa
241 gatggtgtct ccggcctgcc tgagctatcc accgtcaggc agccagatgg gacaaacaca
301 gcatttagtg tccccccact caaccagagg gaaaacaaag atgctaaaga accgctgcct
361 ggcaccatct tggaaatgtg ggacggagag atttaccact acggcttgta cgtggagcgg
421 ggcttggtac ttggggtgca caaaccacca gcggctatta gccttgcaaa ggttgaacta
481 acaccactgt ctctgtactg gaggccagtg tacacccctc agtacctcat atccccagaa
541 actctcaaaa agttacatgg agagacattc ccttacacgg cctttgacaa caactgttac
601 gccttttgtt gttgggtctt ggatctaaat gactcttggc tcagcaggag gatgatacag
661 agaacaactg gcttcttcag accctaccag gactggaaca ggaaacctct ccccaccatg
721 gatgattcca aattgaaaaa ggtggctaat atagtcctgt gtgcattgtc atcattattc
781 accaggccca ttaaggacat aataggaaaa ctaaggcccc taaacatact caatatacta
841 gcttcctgcg actggacttt cgcgggaata gtagaatccc taattctcct tgcagaactc
901 ttcggagttt tctggacacc cccagatgtg tctgcgatga tcgccccctt actaggcgac
961 tacgaactac agggacctga agatctcgct gtggaactcg tgccagtagt gatggggggg
1021 ataggtttgg ttctaggttt caccaaggag aagattggca agatgctatc atctgccgcg
1081 tccaccctca gagcttgtaa agatctcgga gcatatggat tggaaattct aaagttggtc
1141 atgaagtggt tcttcccgaa gaaggatgag gcgaatgaac ttgcaatggt gagatccatt
1201 gaggatgcag tgctagacct tgaagcaatt gagaacaatc acatgacaac cctactcaaa
1261 gacaaagaca gcttagcaac ctacatgaag actctggacc ttgaggagga gaaagccagg
1321 aaactctcca ccaaatctgc ttctcctgat attgtgggca ctatcaattc acttctggca
1381 cggattgcag ctgcccgttc cctggtacat cgggcaaaag aagagctttc cagtaggcca
1441 agacccgttg ttgtcatgat atcaggaaag ccagggatag ggaaaaccca ccttgccaga
1501 gatttggcaa agaaagttgc agccaccctc acaggggacc agagggtagg cctcatccca
1561 cggaatggtg tcgatcactg ggacgcgtac aaaggtgaga gagtcgtcct ttgggatgac
1621 tatggaatga gtaaccccat ccacgacgcc cttaggctac aagaacttgc tgacacttgc
1681 cccctaacat taaattgtga tagaattgag aacaaaggaa aggtctttga cagtgatgcc
1741 ataattatca caactaatct ggctaacccg gcaccactgg actatgttaa ttttgaagca
1801 tgttcgaggc gcatcgactt cctagtgtat gctgatgccc ccgatgttga aaaagcaaaa
1861 cgcgacttcc cagggcagcc tgacatgtgg aaggatgctt ttagacctga cttctcacac
1921 ataaaattga tgttggctcc tcagggtggt tttgataaga atggtaacac cccacatgga
1981 agaggtgtca tgaaaaccct cacatctggc tccctcattg cccgtgcttc aggactcctc
2041 cacgaaagac tggatgagta cgagttacaa gggccaacac ccacaacctt caatttcgac
2101 caaaacaagg tgttcgcctt tagacagctt gccgctgaaa acaagtacgg gctggtggac
2161 accatgagag taggaagcca gctcaagaat gtcaagaccg tgtcagagct taaacaggca
2221 cttaagaaca tttcaattag aaggtgccag atagtctatg gtggtctcac ctattcactt
2281 gaatctgatg gcaaaggtaa tgtgagggtt gagaaggtgc aaagtccagc tgtgcagacc
2341 aacaatgagc taactggcgc actacaccac ttgaggtgcg ctaggattag atattatgtt
2401 aagtgtgtcc aggaagcttt gtattccatc atccaaattg ctggagccgc gtttgtcacc
2461 acgcgcattg caaagcgcat gaacatacaa aacctctggt ccagaccaca ggtagatgat
2521 gaggaagaga ccaccagcaa agacgggtgc ccaaaaccaa aggatgagga ggagtttgtc
2581 atctcgtctg aagacatcaa agctgaaggt aagaagggaa agaacaagtc tggccgcggc
2641 aagaaacaca cagccttctc gagtaagggt cttagtgatg aggagtacga tgagtacaag
2701 agaatcagag aagaaagaaa tggcaagtac tccatagagg aatacctcca agatagagac
2761 aagtactatg aggaggttgc catagccagg gccactgaag aggacttttg tgaggaagaa
2821 gaggccaaga tccggcagag gattttcaga ccaacaagga aacaacgcaa ggaggagagg
2881 gtttcactcg gactggtcac aggctcggaa atcaggaaaa ggaacccgga tgacttcaaa
2941 cctaaaggaa agttgtgggc tgatgacgac aggagtgtcg attacaatga aaaactcagt
3001 tttgaagctc ccccaagcat ctggtcgaga atagtcaact ttggatcagg ttggggcttc
3061 tgggtctcac caagcctttt tataacatcc actcatgtca tacctcaagg ggcacaagag
3121 ttcttcggtg tatccatcaa acagatccaa attcacaagt caggtgagtt ctgccgacta
3181 agattcccaa agccaatcag aactgatgtg acaggcatga tcctagagga aggggcccct
3241 gaaggcaccg tggccacact gctcataaag aggccaactg gagagctgat gccactagcg
3301 gctagaatgg gcacccatgc aactatgaag atccaaggcc gaactgtcgg gggacagatg
3361 gggatgctcc tgacaggatc caacgccaag agcatggatt tgggtactac accaggtgat
3421 tgtggatgcc catatatcta caaaagagga aatgactacg tagtcatcgg ggtccacaca
3481 gctgccgccc gcggagggaa cactgttatc tgtgcaaccc aaggaagtga gggcgaggcc
3541 gttcttgaag gtggtgacaa caaaggcacc tattgtggcg ccccaatcct aggtccagga
3601 aatgccccca aactcagtac taaaactaaa ttctggaggt cctcaacagc accactcccg
3661 cctggcacat atgaaccagc ttacctcgga ggtaaagacc ccagggtgaa gggtggtccc
3721 tcattacaac aagttatgag agaccaattg aaaccgttca cagaacccag aggtaagcca
3781 ccaaagccta gtgtattgga agcagccaaa aagacaatta ttaacgtcct tgagcaaact
3841 atagatccac cccagaaatg gacgttcgca caggcgtgcg cctcccttga taaaacaacc
3901 tctagtggct atccgcacca cgtgcggaag aatgaacatt ggaatgggga atctttcaca
3961 gggaagttgg ctgatcaggc ttcaaaggct aatttgatgt ttgaggaagg aaaacacatg
4021 acaccagtct atacaggagc tctcaaggat gagttagtca aaactgacaa aatatatggt
4081 aagatcaaga aaaggttatt atggggctca gatctggcaa ccatgattcg ttgtgctcga
4141 gcgttcggag ggttgatgga tgagctcaag gcccattgtg tcacactccc catcagggtg
4201 gggatgaaca tgaatgaaga tggtcccatc atttttggga aacactctag gtacacctac
4261 cattatgatg cagactactc tcgatgggac tcaacacagc agagagctgt tttagcttca
4321 gccctagaga tcatggtaaa gttttcccca gaaccacacc tggctcaaat tgtcgcagaa
4381 gatctcctat ctcccagcgt gatggacgtg ggcgatttta aaatatcaat cactgaagga
4441 ctcccctctg gggtgccttg cacctcacaa tggaactcca ttgctcattg gcttctcacg
4501 ctctgtgcgc tctctgaggt gacagatcta tctcctgaca tcatccaagc aaactcactt
4561 ttctctttct atggtgatga tgaaattgtg agcactgata ttaaattaga tccagaaagg
4621 ctaacagcca aactaaaaga gtatggcctc aagccaaccc gcccggacaa gactgaaggg
4681 cctttggtca tttctgagga cttagatggt ctgacctttt tgcggagaac tgtgacccgt
4741 gatccagcag gttggtttgg aaaattggaa caaagctcaa tactaagaca gatgtattgg
4801 accaggggcc ccaaccatga agacccctct gagacaatga taccacattc tcaacgaccc
4861 atacagttga tgtccctatt gggtgaagct gcattgcatg gcccatcgtt ctacagcaaa
4921 atcagcaaat tggtcatctc agagttgaaa gaaggtggca tggactttta cgtgccaaga
4981 caagagccaa tgttccggtg gatgaggttc tcagacttga gcacgtggga gggcgatcgc
5041 aatctggctc ccagttttgt gaatgaagat ggcgtcgaat gacgccgctc catctaatga
5101 tggtgcagcc ggtctcgtac cagaggtcaa caacgagacg atggcacttg agccggtggc
5161 tggggcctct atagctgccc ctttgaccgg ccaaaataat gtgatagacc cctggattag
5221 aatgaatttt gtccaagctc caaatggtga atttacagtg tccccccgta attccccagg
5281 tgaagttttg ttgaatttgg aattaggccc tgaactaaat ccattcttgg cacatctttc
5341 aagaatgtat aatggttatg ctggtggggt tgaagtgcag gtgctacttg ctgggaatgc
5401 gttcacagca ggaaaactag tgttcgcggc aatccccccg cacttccctc ttgagaatct
5461 aagtcctggt caaattacaa tgttccctca cgtgattatt gatgttagaa ctttagaacc
5521 tgttcttttg cctttaccag atgttaggaa taatttcttt cattacaatc agcagcctga
5581 gccccgtatg agacttgtgg ctatgttgta tactcctctt agatctaatg gctctggtga
5641 cgatgtgttc acagtctctt gtagggtcct cacccgcccc tctccagatt ttgattttaa
5701 ttatttggtt cccccaactg tggaatctaa aactaaacca ttcaccctgc caatattgac
5761 cattggagaa ttgtcaaatt ctaggttccc agtgccaata gatgaattgt acaccagccc
5821 caatgaagga gtggttgtgc aacctcaaaa tggcagatca acacttgatg gtgaactgct
5881 tggcacaaca caacttgtac catcaaacat ctgtgccttg cgagggcgca tcaacgccca
5941 agtgccagac gaccaccatc aatggaactt gcaggttaca aacgcaaatg ggactccctt
6001 cgaccccact gaagatgtcc ctgcaccatt gggcatgcca gacttcctgg caaacatcta
6061 cggagttact agccagagga accctgacaa cacttgccgt gcccatgatg gggtcttggc
6121 aacctggagc cctaaattta cacctaagtt aggatctgtg gttttgggca cttgggaaga
6181 acaagatctt gatctcaacc aacctaccag attcacacct gtcggtttgt atgatacaaa
6241 ccactttgat cagtggattc tacccaacta ttctggaaga ttaaccttaa acatgaattt
6301 ggcgccctcc gttgctcccc ttttcccagg tgaacaaata ctcttcttta ggtcccacat
6361 accacttaaa ggaggcactt ccaatggtgc cattgactgt ctactccctc aggagtggat
6421 ccagcatttc tatcaggaat cagccccgtc acccacagat gttgctctga ttaggtacac
6481 caaccctgac acgggccgtg tcctttttga ggccaaacta cataggcagg ggttcattac
6541 agtagcaaat tctggttcta gacctattgt tgtcccccct aatggttatt ttaggtttga
6601 ttcttgggtt aatcagtttt attctctcgc ccccatggga actgggaatg ggcgcagaag
6661 ggtgcagtaa tggctggagc ttttgtagca ggtcttgccg gtgacatagt caccaatagc
6721 attggttcac ttgtgaacgc tggagccaat gcaataaacc aaaaagtaga ctttgaaaac
6781 aacaaacaac tacagcaggc ctctttcaac catgataagg aaatgttgca agctcaaatt
6841 caggccacaa aacaattaca ggctgacatg attgcgctca gacaaggggt gttgaccgca
6901 ggcggcttct cccctactga tgcagcaaga ggggcggtta atgtgcccat gacgcaagtc
6961 ttggactgga atgggactag gtactgggcc cccggagcca ccaaaacaac tgctttctcc
7021 ggtgggttca caagctctcc caataccagg actgttgatt tgcctaggaa aacatcaacc
7081 acaccagccc ccacacctat atccagacct agttcttctg cttctactgt ttctacccgc
7141 tcaacaatta ttagcgggac ttctggcctt tcttctttga ctaggagctc ttttaattcc
7201 cagcccacct cctcttcttc tcggactagc gaatgggtgc gtggtcaaaa cagggcgctg
7261 gagccctaca tgaggggagc gctgcaaact gcttacgtga cgcctccctc tagtagagcg
7321 tctagcaatg gcacagtctc aaccgtgcca aaagaagttt tggactcctg gacatctgtg
7381 ttcaacaccc acagacaacc gcttttcgct catctccgtc ggagagggga gtcacaggtt
7441 tagtgaaaag atgatt
//