Typing tool
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Typing tool
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Complete norovirus genomes
| MT720841 | GII.13 | |
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| GII.P16 |
ORF1: 5..5101
ORF2: 5082..6710
ORF3: 6710..7441
LOCUS MT720841 7506 bp RNA linear VRL 12-JUL-2020
DEFINITION Norovirus GII isolate Hu/US/2015/GII.13[P16]/CA-RGDS-1088, complete
genome.
ACCESSION MT720841
VERSION MT720841.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7506)
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..7506
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="Hu/US/2015/GII.13[P16]/CA-RGDS-1088"
/isolation_source="stool"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="USA: California"
/collection_date="Dec-2015"
/note="genotype: GII.13[P16]"
gene 5..5101
/gene="ORF1"
CDS 5..5101
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="QLD96897.1"
/translation="MKMASNDASAAVACNNNNDKEKSSGEGLFTNMSSTLKKALGARP
KQPAPRDNSQKPPRPPTPELVKRIPPPPPNGEEEEPVIRYEVKSGISGLPELTTVPQP
DVANTAFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAAI
SMAKVELTPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLND
SWLNRRMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLIG
KIKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPE
DLAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFF
PKKEEANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRLS
TKSASPDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLARE
VARKVASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELADT
CPLTLNCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVE
KAKRDFPGQPDMWKDAFKSDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIAR
ASGLLHERMDEFELQGPTVTTFNFDRNRIAAFRQLAAENKYGLVDTMRVGNQLKGVKT
MEELKQAIKNVVIKRCRIIYGGSTYDLESDGKGRVLVEKVKNTSVQTNNELAGALHHL
KHARIRYYVKCVQEAVYSILQIAGAAFVTTRIARRMNIQELWSKPPLDQNESEAKEEA
PKSEDDEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGK
YSIEEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERVTLGLVT
GSEIRKRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVNFGSGWGFWVSPS
LFITSTHVIPAGITEAFGVPIKQIQVHKSGEFCRFRFPKPIRSDVTGMILEEGAPEGT
VATVLIKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDC
GCPYIYKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILGP
GGAPKLSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPR
GKPPRPSVLEAAKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFWN
GETFTGKLADQASKANLMFEEGKHMTPVYTAALKDELVKTDKVYGKIKKRLLWGSDLS
TMIRCARSFGGLMDEMKTHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWDS
TQQRAVLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKISINEGLPSGVPCTS
QWNSIAHWLLTLCALSEVTKLSPDIVQANSMFSFYGDDEIVSTDIKLDPEKLTTKLKE
YGLKPTRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGPN
HEDPNETMIPHSQRPIQLMALLGEASLHGPSFYSKISKLVITELKEGGMDFYVPRQEP
MFRWMRFSDLSTWEGDRNLAPNFVNEDGVE"
mat_peptide 5..997
/gene="ORF1"
/product="p48"
mat_peptide 998..2095
/gene="ORF1"
/product="NTPase"
mat_peptide 2096..2626
/gene="ORF1"
/product="p22"
mat_peptide 2627..3025
/gene="ORF1"
/product="VPg"
mat_peptide 3026..3568
/gene="ORF1"
/product="Pro"
mat_peptide 3569..5098
/gene="ORF1"
/product="RdRp"
gene 5082..6710
/gene="ORF2"
CDS 5082..6710
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="QLD96898.1"
/translation="MKMASNDAAPSNDGAASLVPEAINETMPLEPVAGASIAAPVAGQ
TNIIDPWIRTNFVQAPNGEFTVSPRNSPGEILLNLELGPDLNPYLAHLSRMYNGYAGG
VEVQVLLAGNAFTAGKILFAAIPPNFPVDMISPAQITMLPHLIVDVRTLEPIMIPLPD
VRNVFYHFNNQPQPRMRLVAMLYTPLRSNGSGDDVFTVSCRVLTRPTPDFEFIYLVPP
SVESKTKPFTLPILTISELTNSRFPIPIEQLYTAPNENNVIQCQNGRCTLDGELQGTT
QLLPSAVCSYRGRTVANSGDNWDQNLLQLTYPSGASYDPTDEVPAPLGTQDFSGILYG
VLTQDNMSEGTGEAKNAKGVYISTTSGRFTPKIGTIGLHSITENVHPNQQSRFTPVGV
AQNENTPFQQWVLPHYAGALALNTNLAPAVAPTFPGEQLLFFRSRVPCVQGLRGQDAF
IDCLLPQEWVNHFYQEAAPSQADVALIRYVNPDTGRTLFEAKLHRSGFITVSHTGTYP
LVVPPNGHFRFDSWVNQFYSLAPMGTGNGRRRVQ"
gene 6710..7441
/gene="ORF3"
CDS 6710..7441
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="QLD96899.1"
/translation="MAGAFIAGLAGDMLTSAVGSLTSAGANAINQKLNFDYNKQLQNA
SFQHDKEMLQAQIDATKKLQSEMIAIKHGVLTAGGFSPADAARGAVNAPMTRVLDWSG
TRYYAPNSVQTTSHSGQFTPSPVHRAQVKSPSNSSQRTAAPSSIRSLSTQSTSLGSTS
SGGSSTTSSSSRTADWVQQQRALSPYMQGALQTAYVTPPSSRASSMSSVSTVPKGVLD
SWTPVFNTRRQPLFAHLRKRGESQA"
ORIGIN
1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgtt gcttgcaaca acaacaacga
61 caaggaaaaa tcttcaggtg aaggcttatt cacaaacatg tcttccacct taaagaaagc
121 cctcggggcc cggcccaaac agcctgcccc gagggacaac tcacaaaaac ccccaagacc
181 accaactccc gagttggtta agaggatacc ccctccccca cctaatggag aagaagaaga
241 accagtcatt aggtatgagg ttaagagtgg aatctctggc ctgcccgagc tcacaacagt
301 ccctcaaccg gatgtggcca acacggcatt cagtgtccca ccgctgagct tgagagaaaa
361 cagggaggcc aaggaaccgc tgacaggggc aatattagag atgtgggatg gagagatata
421 ccactatggt ctgtacgtgg agaaaggctt agtgttgggt gtgcacaaac cacctgcagc
481 tataagcatg gcaaaagtgg agctgacgcc gttgtcattg tactggcgtg tggtctacac
541 cccccaatac ctcatctccc ctgaaactct caggaggctc aacggagagg cattccctta
601 cactgccttt gacaacaact gctatgcctt ttgctgttgg gtattagacc tcaatgactc
661 atggcttaac aggaggatgg tgcaaagaac aacaggcttc ttcagacctt atcaagagtg
721 gaacagaaaa cccctgccca ctatggatga ctccaaaatc aagaaggtgg caaacatatt
781 cctgtgttca ttgtccacgt tgttcaccag acctataaaa gacctcatag gaaaaattaa
841 gccattaaac atcttgaaca tcctggcaac gtgtgactgg acattcgccg gaatagtgga
901 gtctctgata ttacttgctg aactctttgg agttttctgg acacccccag atgtgtctgc
961 tatgatcgct cctttacttg gagactacga gttgcaaggg ccagaagacc ttgccgttga
1021 gctcgtacct gtagtaatgg gggggattgg tttggtgttg ggattcacca aggagaaaat
1081 tggaaaaatg ttgtcctcag cagcatcaac gctcagggct tgtaaagatc ttggtgccta
1141 tggcttagag atactcaaat tggtcatgaa gtggttcttc ccgaagaaag aagaggccaa
1201 tgagctagcc atggtgagag ctatagaaga tgctgtactg gatcttgagg caatagaaaa
1261 taatcacatg acaactctgt tgaaagacaa agacagccta gcaacctaca tgaaaacact
1321 agacatggag gaggaaaaag ccagaagatt gtccacaaaa tctgcatccc ctgacatagt
1381 tgggacgatc aacgccctgc tggctcgaat agcagcggct aggtcactag tccacagggc
1441 caaggaggag ttatctagca ggataagacc agtggttgtt atgatatctg gtaaaccagg
1501 gataggcaaa actcatctgg ccagggaggt ggcaagaaag gtggcatcca ctctcacagg
1561 ggatcaaaga gtcgggctca taccgagaaa cggtgtggac cattgggatg catacaaagg
1621 tgagagggtc gtgctgtggg acgactatgg catgagcaac cccattcatg atgccctgcg
1681 catacaagaa ttggctgata cgtgtcccct taccttaaat tgtgacagaa tcgaaaataa
1741 gggaaaagtt tttgacagtg aagtcataat aatcacaaca aaccttgcca atccagctcc
1801 acttgattat gtcaactttg aggcctgttc caggagaatt gacttcctgg tgtacgccga
1861 ggcaccagaa gtagaaaagg cgaaacgaga ctttcctggt caaccagata tgtggaagga
1921 cgccttcaag tcggactttt cacatatcaa gttgcaactt gcaccccagg gcggctttga
1981 caagaatggc aacaccccac atgggaaagg agtgatgaag accctcacca ccggttccct
2041 gatcgcccgt gcatcaggct tactgcatga gaggatggat gaatttgaac tccaaggccc
2101 cacagtcacc accttcaatt ttgaccggaa cagaatcgct gcattcagac aattggctgc
2161 agaaaacaag tatggattgg tggacaccat gagagttggc aatcaattaa aaggggtgaa
2221 aaccatggaa gaactcaaac aagcaatcaa gaatgtggtc atcaagaggt gccggatcat
2281 ctacggcggc tccacgtatg accttgaatc tgatggcaag ggcagagttc tggtggaaaa
2341 ggtcaagaac acctctgtac agaccaacaa cgagttggcc ggagccctgc atcacctcaa
2401 acatgcccga atcaggtact atgtcaaatg tgtgcaagaa gcagtctact ctattttaca
2461 aatcgccggc gctgcgtttg tcaccacacg catagcacgc cgcatgaaca tacaagagct
2521 ttggtcgaag ccaccattag accaaaatga atcagaggct aaggaagagg cccccaagtc
2581 agaagatgac gagttcatca tatcttctaa ggacatcaag gaggaaggaa agaagggcaa
2641 aaacaaaact ggccgtggca agaaacacac tgcattctct agcaagggct tgagcgatga
2701 ggagtatgac gagtacaaga ggataagaga agagagaaat gggaagtact ctatagagga
2761 gtatcttcaa gacagagaca ggtactatga ggagctcgcc atcgccaagg ccacggaaga
2821 agacttctgt gaggaggagg agatcaaaat ccgtcagagg atcttccgtc ccaccaggaa
2881 gcaaaggaag gaagagaggg tcacactagg gctagtaact ggttcagaaa tcagaaaaag
2941 aaaccctgat gacttcaaac ctaaagggaa actgtgggct gatgacaaca gaagtgttga
3001 ctacaatgag aaactggact ttgaggcccc cccaagcata tggtctagga ttgtgaattt
3061 tggttctggt tggggcttct gggtgtcacc aagcctgttc ataacatcaa ctcacgtaat
3121 ccctgcaggc ataacagagg catttggagt ccccatcaaa caaatccagg tccacaagtc
3181 aggtgaattt tgtcggttca gattcccaaa accaattaga tcagatgtga caggaatgat
3241 cttggaggaa ggtgcgcctg agggcaccgt ggcaaccgtg ctcattaaac gccctaccgg
3301 agagctcatg ccccttgcag ccagaatggg aacacacgca accatgaaaa ttcagggccg
3361 catggttggc gggcagatgg gtatgttgct cactggttca aatgctaaag gaatggattt
3421 gggaacaact cctggtgatt gtggctgtcc ctacatctac aaaaggggca atgactatat
3481 agtcattggg gtgcacacag cagcagcccg tggtggaaac accgtcatct gtgccacaca
3541 gggaagcgag ggtgaggcaa ctcttgaggg tggagatgac aaaggaacat actgtggggc
3601 acccattcta ggccctgggg gggcaccaaa attgagcacc aaaaccaaat tttggaggtc
3661 atcgaacacg cctcttccac cagggacgta tgagcctgcc tacctcggtg gccgcgaccc
3721 gcgtgttaag ggtgggccct ccttgcagca ggtaatgaga gaccagttga agccatttac
3781 cgagcccagg ggtaaacctc caagaccaag tgtgttggaa gcagctaaac aaaccatcat
3841 caatgtcctc gaacaaaccc tggaccctcc acaaaaatgg acatacgcac aggcgtgtgc
3901 ttcacttgac aaaaccacct ccagcgggca tccccaccac gtccgaaaga atgaattctg
3961 gaatggtgag accttcactg gtaaattggc agaccaagca tcaaaagcaa atttaatgtt
4021 tgaggaaggg aaacacatga caccagtgta tacagcagcc ctcaaggatg agctggtcaa
4081 gactgacaaa gtctatggaa agatcaagaa gagactgctc tggggctctg acttgtccac
4141 catgatccgg tgcgccaggt cttttggtgg gctcatggat gagatgaaaa cacactgcat
4201 atcactccca gtccgagttg gcatgaacat gaatgaagat ggtccaataa tatttgagaa
4261 gcactccaga tacaagtatc actatgatgc agattactcc cgctgggatt caacacaaca
4321 gagggcagta ctagcagcag ccttggagat catggtcagg ttctctgcag agccacaatt
4381 ggcacaaata gtcgctgagg atctcctagc ccccagtgtg gtagatgtag gagactttaa
4441 aatttcaata aatgaagggc tcccctctgg tgtaccatgc acttctcaat ggaattccat
4501 cgcacactgg ctgctaaccc tctgcgcctt gtctgaagtc accaaactgt cccctgacat
4561 tgtacaggca aattccatgt tctcatttta cggtgatgac gagattgtca gcaccgatat
4621 aaaattggac cctgaaaagc taaccaccaa attgaaggag tacggcctga aaccaactcg
4681 cccagacaaa accgaaggac ccctgatcat cagtgaggat ctgaacggac tcactttcct
4741 ccggaggacg gtgactcgtg acccagctgg ctggtttgga aagttggacc aaagctcaat
4801 attgaggcag atgtactgga ctagaggacc aaatcatgaa gaccccaatg agacaatgat
4861 accccactct caaagaccca tacagctcat ggcactgctt ggtgaggcct cccttcacgg
4921 accctctttc tacagcaaaa ttagtaagtt ggtcataact gaactcaaag aaggtgggat
4981 ggacttttac gtgccaaggc aggaacccat gttcaggtgg atgaggtttt ctgacttgag
5041 cacgtgggag ggcgatcgca atctggctcc caattttgtg aatgaagatg gcgtcgaatg
5101 acgccgctcc atcgaatgat ggtgcagcta gtctcgtacc agaggccatt aatgagacta
5161 tgccattgga acccgttgct ggcgcatcta ttgctgcccc agtggcggga caaactaaca
5221 taattgaccc ctggataaga acaaattttg tgcaagcccc taatggagag tttacagtgt
5281 caccgagaaa ttcccctgga gagattttat taaatttaga gttaggacca gatttgaatc
5341 cttatttggc ccacctatca aggatgtaca atggatatgc tggaggtgtt gaggtgcaag
5401 tgcttcttgc tgggaacgcg ttcacagcag gaaagatatt atttgcagca atcccaccca
5461 actttcctgt agatatgatc agcccagctc aaattactat gcttccccat ttgattgtag
5521 atgttaggac attggaacct attatgatac ccttacctga tgttaggaat gtgttctatc
5581 attttaataa tcaaccccaa cctaggatga gattagtggc tatgctctat accccattga
5641 gatctaatgg ttcaggagat gatgtcttta ctgtgtcttg tagagtgttg actaggccaa
5701 cccctgactt tgaattcatt tacctagtgc ctccctctgt agagtccaaa actaaaccat
5761 tcacacttcc aatattgacc atttctgaac taaccaactc ccggtttccc atcccaattg
5821 agcaactgta cacggcccca aatgagaata atgttataca gtgtcaaaat ggaaggtgca
5881 ccttggatgg agagcttcag ggcaccaccc agctactacc aagtgcagtc tgctcgtaca
5941 ggggcaggac tgtggctaac agtggggaca attgggacca gaatttgctc cagctgacct
6001 acccaagcgg tgcaagctat gaccccactg atgaagtacc agcacccttg ggcacccagg
6061 atttcagtgg gatattgtat ggggtgttaa cccaagataa tatgagtgag ggtacagggg
6121 aggccaaaaa tgctaaggga gtatacatat ccaccaccag tggaagattc accccaaaaa
6181 ttgggacaat tggattgcat tcaataactg aaaatgtgca ccccaatcag caatcacggt
6241 tcacccccgt tggagtcgct cagaatgaaa acaccccctt ccagcaatgg gttctaccac
6301 actacgcagg tgctctcgct ctaaatacca atttggcacc cgctgttgcc ccgactttcc
6361 ctggcgagca attactgttc ttcaggtccc gtgttccatg tgttcaaggt ctgcgggggc
6421 aggatgcttt catagattgt ctcctacctc aagagtgggt gaaccatttt tatcaagagg
6481 ctgctccctc ccaagcagac gttgccctca tcaggtatgt caaccctgat actggtcgca
6541 cgttgtttga ggccaaattg cacaggtcag gtttcattac tgtatcacac actggtacct
6601 accctcttgt ggtcccccca aatggtcatt tcaggtttga ttcttgggtt aaccaattct
6661 actcactcgc ccccatggga actggcaatg ggcgtagaag agttcaataa tggcaggagc
6721 attcatagct ggtctagccg gtgacatgct gacttctgct gttggttcac tgacctctgc
6781 aggagccaat gccatcaatc agaaattgaa ttttgattac aacaaacaac tccaaaatgc
6841 atcctttcaa catgataagg aaatgttgca ggcccaaatt gatgctacaa agaagctcca
6901 atcagagatg attgcaatta agcatggggt tctgaccgcg ggcggctttt ccccagctga
6961 tgcagccaga ggggcagtca acgccccaat gactcgagtg ttggattggt cagggacacg
7021 ctactacgct ccaaattctg tgcaaaccac cagtcattct gggcaattca ccccctcgcc
7081 tgtccatcgg gcgcaggtga agtccccttc caattcgtct cagcggactg cagctccaag
7141 cagtatccgc agcctgtcaa cccaatcaac ttctttaggc tctacctcct caggggggtc
7201 ctctacaacc tcctccagtt cgaggacagc agactgggtg caacaacaaa gggctcttag
7261 cccgtacatg cagggagccc tgcagacggc atacgtcaca ccgccgtcta gtagggcttc
7321 cagtatgagc tctgtctcaa cagtgcccaa aggggttttg gactcctgga cacctgtgtt
7381 taacacacgc aggcagccgc tgtttgcaca cctcaggaag aggggggagt cacaggctta
7441 gtgaaaagga taatcaactt ttaaatgtga ttttattttc cttttaaaaa aaaaaaaaaa
7501 aaaaaa
//