Typing tool
|
|
|
|
|
|
Typing tool
|
Complete norovirus genomes
| MT362917 | GII.4 New Orleans | |
|
|---|---|---|---|
| GII.P4 New Orleans |
ORF1: 1..5088
ORF2: 5069..6691
ORF3: 6691..7497
LOCUS MT362917 7515 bp RNA linear VRL 01-JUN-2020
DEFINITION Norovirus GII isolate 963-1 nonstructural polyprotein (ORF1) gene,
partial cds; and VP1 (ORF2) and VP2 (ORF3) genes, complete cds.
ACCESSION MT362917
VERSION MT362917.1
DBLINK BioProject: PRJNA604000
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7515)
AUTHORS Silva,A., Wolfe,J., Yang,Z., Hirneisen,K. and Ruelle,S.
TITLE Application of whole-genome sequencing for Norovirus outbreak
tracking and surveillance efforts in Orange County, CA
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 7515)
AUTHORS Silva,A., Wolfe,J., Yang,Z., Hirneisen,K. and Ruelle,S.
TITLE Direct Submission
JOURNAL Submitted (21-APR-2020) Schmid College of Science and Technology,
Chapman University, 1 University Drive, Orange, CA 94526, USA
COMMENT ##Assembly-Data-START##
Assembly Method :: CLC Genomics Workbench v. 11
Sequencing Technology :: Illumina
##Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..7515
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="963-1"
/isolation_source="stool"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="USA"
/collection_date="11-Apr-2012"
/note="genotype: GII.4 New Orleans[P4 New Orleans]"
gene <1..5088
/gene="ORF1"
CDS <1..5088
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="QJC69095.1"
/translation="SNDASAAAVANSNNDTAKSSSDGVLSSMAVTFKRALGARPKQPP
PREKPQRPPRPPTPELVKNIPPPPPNGEDEIVVSYSVKDGVSGLPDLSTVRQPEESNT
AFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAISLAKV
ELAPLSLYWRPVYTPQYLISPDTLKKLSGETFPYTAFDNNCYAFCCWVLDLNDSWLSR
RMIQRTTGFFRPYQDWNRKPLPTMDDSKIKKVANIFLCALSSLFTRPIKDIIGKIRPL
NILNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVE
LVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEE
ANELAIVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLSTKSAS
PDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREVAKRI
AASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALKLQELADTCPLTL
NCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRD
FPGQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLL
HERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMKVGKQLKDVRTMPELK
QALKNVSIKKCQIVYSGCTYMLESDGKGNVKVDRIQSAAVQTNNELAGALHHLRCARI
RYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQDLWSKPQVENTEETTSKDGCPKPK
DDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSI
EEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERVSLGLVTGSE
IRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSPSLFI
TSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVVT
LLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCGCP
YIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILGPGSA
PTLSTKTKFWRASTASLPPGTYEPAYLGGKDPRVKGGPSLQQVMREQLKPFTEPRGKP
PKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCWNGES
FTGKLADQASKANLMFEEGKNMTPVYTAALKDELVKTDKIYGKIKKRLLWGSDLATMI
RCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFERHSRYTYHYDADYSRWDSTQQ
RAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCTSQWN
SIAHWLLTLCALSEVTNLSPDTIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLREYGL
KPTRPDKTEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHGD
PSETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQEPMFR
WMRFSDLSTWEGDRNLAPSFVNEDGVE"
mat_peptide <1..978
/gene="ORF1"
/product="p48"
mat_peptide 979..2076
/gene="ORF1"
/product="NTPase"
mat_peptide 2077..2613
/gene="ORF1"
/product="p22"
mat_peptide 2614..3012
/gene="ORF1"
/product="VPg"
mat_peptide 3013..3555
/gene="ORF1"
/product="Pro"
mat_peptide 3556..5085
/gene="ORF1"
/product="RdRp"
gene 5069..6691
/gene="ORF2"
CDS 5069..6691
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="QJC69096.1"
/translation="MKMASSDANPSDGSTANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHIAGSRNYTMNLASQNWNSYDPTEEIPAPLGTPDFVGKIQGVL
TQTTRTDGSTRGHKATVYTGSADFSPKLGRVQFATDTDNDFVTNQNTKFTPVGVIQDG
STTPRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL"
gene 6691..7497
/gene="ORF3"
CDS 6691..7497
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="QJC69097.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEYENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMRVKQAMLLEGGFSETDAARGAIN
APMTKTLDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRAAVPARGSSSTSS
NSSVATSVYSNQTTSTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRKRGESRV"
ORIGIN
1 tctaacgacg cttccgctgc cgctgttgct aacagcaaca acgacaccgc aaaatcttca
61 agtgacggag tgctttctag catggctgtt actttcaaac gagccctcgg ggcgcggcct
121 aaacagcccc ccccgaggga aaaaccacaa agacccccac gaccacctac tccagaactg
181 gttaaaaata ttccccctcc cccacccaac ggagaggatg aaatagtggt ttcttatagt
241 gtcaaagatg gtgtttccgg cttgcctgac ctttccaccg tcaggcaacc ggaagaatcc
301 aacacggcct tcagtgtccc tccactcaat cagagggaga atagagatgc taaggagcca
361 ctcactggaa caattctgga aatgtgggac ggggaaatct accattatgg cctgtatgtg
421 gagcgaggtc ttgtactagg tgtgcacaaa ccgccagctg ccatcagcct tgctaaggtt
481 gagctggcac cactctcctt gtactggaga cctgtgtaca ctcctcagta cctcatctct
541 ccggacactc tcaagaaatt gtccggagaa acgttcccct acacagcttt tgacaacaac
601 tgttatgctt tttgttgctg ggtcctggac ctaaatgact cgtggctgag caggagaatg
661 atccagagaa caactggttt cttcaggccc taccaagact ggaataggaa gccccttccc
721 actatggatg actccaaaat aaagaaggta gctaacatat ttctgtgtgc tttgtcctcg
781 ctattcacta gacccataaa agatataata gggaagataa ggcctcttaa catcctcaac
841 atcttggcct catgtgattg gacctttgcg ggcatagtgg agtccctgat actcttggca
901 gaactctttg gagttttctg gacaccccca gatgtgtctg cgatgattgc ccccttactt
961 ggtgactacg agctacaagg acctgaggac cttgcagtgg agctcgtccc cgtggtgatg
1021 gggggaattg gtttggtgct aggattcacc aaagagaaga ttgggaaaat gttgtcatct
1081 gctgcgtcca ctttgagagc ttgcaaagac cttggtgcat atgggctaga gatcctaaag
1141 ttagtcatga agtggttctt cccgaagaag gaggaggcaa atgagctggc tatagtgagg
1201 tccatcgagg atgcagtcct ggatctcgag gcaattgaaa acaatcatat gaccaccttg
1261 cttaaagaca aagacagtct ggcaacctac atgagaacac ttgaccttga agaggagaaa
1321 gccaggaaac tctcaaccaa gtctgcctca cccgacatcg tgggcacaat caacgccctc
1381 ctggcgagaa tcgctgccgc acgttctctg gtgcatcgag cgaaggagga gctttccagc
1441 agaccaagac ctgtggtgtt gatgatatca ggcaggccag gaatagggaa gacccacctc
1501 gctagggaag tggctaagag aatcgcagcc tcccttacag gagaccagcg tgtgggcctc
1561 atcccacgca atggcgtcga ccattgggat gcgtacaagg gagagagggt cgttctatgg
1621 gacgattatg gaatgagcaa ccctattcac gatgccctca agctgcaaga actcgctgac
1681 acttgccccc tcactctgaa ctgtgacagg attgaaaata aaggaaaggt ctttgacagc
1741 gatgtcatca ttatcaccac taatctggcc aacccagcac cactggacta tgtcaacttt
1801 gaagcatgct cgaggcgcat tgacttcctc gtgtatgcag aagcccctga agtcgaaaag
1861 gcgaagcgtg acttcccagg ccagcctgac atgtggaaga acgctttcag ttctgatttc
1921 tcacacataa aactagcact ggccccacag ggtggtttcg acaagaacgg gaacacccca
1981 cacggaaagg gcgtcatgaa gactctcacc actggctccc ttattgcccg ggcatcaggg
2041 ctactccatg agaggttaga tgaatttgaa ctgcagggcc cagctctcac caccttcaat
2101 ttcgatcgca ataaagtgct tgcctttaga cagcttgctg ctgaaaataa atatggattg
2161 atggacacaa tgaaggttgg gaaacagctc aaggatgtca gaaccatgcc agaactcaaa
2221 caagcactca agaatgtctc aatcaagaag tgtcaaatag tgtatagtgg ttgcacctac
2281 atgcttgagt ctgatggcaa gggcaatgtg aaagttgaca gaatccaaag cgccgccgtg
2341 cagaccaaca atgagctggc tggtgccctg caccacttga ggtgcgccag aatcaggtac
2401 tatgtcaagt gtgtccagga agccctgtat tccatcatcc aaatcgctgg ggctgcattt
2461 gtcaccacgc gcatcgccaa gcgcatgaac atacaagacc tatggtccaa gccacaagtg
2521 gaaaacacag aggagactac cagcaaggac gggtgcccaa aacctaagga tgatgaggag
2581 tttgtcattt catccgacga catcaaaact gagggcaaga aagggaagaa caagactggc
2641 cgtggcaaga agcacacagc attttcaagc aaaggcctca gtgatgaaga gtacgatgaa
2701 tacaagagga tcagagaaga aaggaatggc aagtactcta tagaagagta ccttcaggac
2761 agggacaaat actatgagga ggtggccatt gccagggcga ctgaggagga cttctgtgaa
2821 gaagaggagg ccaagatccg gcaaaggatc tttagaccaa caaggaaaca acgcaaggag
2881 gaaagagtct ctctcggtct ggtcacaggc tctgaaatta ggaaaagaaa cccagatgac
2941 ttcaaaccca aggggaaatt gtgggctgac gatgacagga gtgtggacta caatgagaaa
3001 ctcagttttg aggccccacc aagcatttgg tcgagaatag tcaactttgg ttcaggctgg
3061 ggattttggg tctcccccag tctgttcata acatcaaccc atgttatacc ccagggcgca
3121 aaggagttct ttggagtccc catcaaacaa atacaggtac acaagtcagg cgagttctgt
3181 cgcttgagat tccctaaacc aatcaggact gatgtgacgg gcatgatcct agaagaaggc
3241 gcacctgagg gcaccgtggt cacactactc atcaaaaggt ccactgggga actcatgccc
3301 ctagcagcta ggatggggac ccatgcgacc atgaagatcc aagggcgcac tgtcgggggc
3361 cagatgggca tgcttttgac aggatccaac gccaagagca tggacctggg tactacacca
3421 ggtgattgtg gctgccccta catctacaag agaggtaatg actatgtggt cattggagtc
3481 cacacggctg ccgcacgtgg gggaaacact gtcatatgtg ccacccaggg gagtgaagga
3541 gaggctacac ttgagggtgg tgacaacaag gggacatact gtggtgcacc aatcctaggc
3601 ccagggagtg ccccaacact tagcaccaag accaaattct ggagggcgtc cacagcatca
3661 ctcccacctg gcacctatga accagcctat cttggtggca aggaccctag agtcaagggt
3721 ggcccttcac tgcagcaagt catgagggaa cagttgaagc cattcacaga gcccaggggc
3781 aagccaccaa aaccaagtgt attagaagct gccaagaaga ccatcattaa tgtccttgag
3841 caaacaattg atccacctga gaaatggtcg ttcgcacaag cttgcgcgtc ccttgacaag
3901 accacttcca gtggtcatcc gcaccacatg cggaaaaacg actgctggaa cggggagtcc
3961 ttcacaggca agctggcaga ccaggcttcc aaggccaacc tgatgtttga agaagggaag
4021 aacatgaccc cagtctacac agctgcgctc aaggatgagt tagttaaaac tgacaaaatt
4081 tatggtaaga tcaagaagag gcttctctgg ggctcggact tggcgaccat gatccggtgt
4141 gctcgagcat tcggaggcct aatggatgaa ctcaaagcgc actgtgtcac acttcccatt
4201 agagttggca tgaatatgaa tgaggatggc cccatcatct tcgagaggca ttccaggtac
4261 acgtaccact atgatgctga ttactctcga tgggattcaa cacaacagag agccgtgttg
4321 gcagcagctc tagaaatcat ggttaaattc tccccagaac cacatttggc tcaggtagtc
4381 gcggaagacc ttctttctcc tagcgtggtg gacgtgggcg acttcacaat atcaatcaac
4441 gagggtcttc cctctggggt gccctgcacc tcccaatgga actccatcgc ccactggctt
4501 ctcactctct gtgcgctctc tgaagtcaca aacctgtctc ctgataccat acaggctaat
4561 tccctcttct ctttttatgg tgatgatgaa attgttagca cggatataaa attggaccca
4621 gagaaattga cagcaaagct cagagaatat gggttaaaac caacccgccc tgacaaaact
4681 gaaggacccc ttgtcatctc tgaagacctg aatggcctaa ctttcctgcg gagaactgtg
4741 acccgcgacc cagctggttg gtttggaaaa ctggagcaga gttcaatact caggcaaatg
4801 tactggacta ggggtcccaa ccatggagac ccatctgaaa caatgattcc acactcccaa
4861 agacccatac aattgatgtc cctactgggg gaggccgctc tccacggccc agcattttac
4921 agcaaaatca gcaaattggt cattgcagag ctaaaagaag gtggtatgga tttttacgtg
4981 cccagacaag agccaatgtt cagatggatg agattctcag atctgagcac gtgggagggc
5041 gatcgcaatc tggctcccag ttttgtgaat gaagatggcg tcgagtgacg ccaacccatc
5101 tgatgggtcc acagccaacc tcgtcccaga ggtcaacaat gaggttatgg ctttggagcc
5161 cgtagttggt gccgctattg cggcacctgt agcgggccag caaaatgtaa ttgacccctg
5221 gattagaaac aattttgtac aagcccctgg tggagagttt acagtatccc ctagaaacgc
5281 tccaggtgaa atactatgga gcgcgccctt aggccctgat ttgaatccct acctttccca
5341 tttggccaga atgtacaatg gttatgcagg tggttttgaa gtgcaggtaa tcctcgcggg
5401 gaatgcgttc accgccggga aaatcatatt tgcagcagtc ccaccaaact tcccaactga
5461 aggtttgagc cccagccaag tcactatgtt cccccacata atagtagatg ttaggcaatt
5521 ggaacctgtg ttgatcccct tacccgatgt taggaataat ttctaccatt ataatcagtc
5581 aaatgactcc accatcaaat tgatagcaat gttgtacaca ccacttaggg ctaacaatgc
5641 cggggacgat gtcttcacag tttcctgtcg agttctcacg agaccatccc ccgattttga
5701 tttcatattt ttggtgccac ccacagttga atcaagaact aaaccattct ctgtcccagt
5761 tttaactgtt gaagagatga ccaattcaag gttccccatt cctttggaaa agttgttcac
5821 gggccccagt agtgcctttg ttgttcaacc acaaaacggc aggtgcacga ctgatggcgt
5881 gctcctaggt actacccaac tgtctcctgt caacatctgc accttcaggg gggatgtcac
5941 ccacattgca ggcagtcgta actacacaat gaatttggcc tcccaaaatt ggaacagtta
6001 cgatccaaca gaagaaatcc cagcccccct aggaactcca gatttcgtgg ggaagattca
6061 aggtgtgctc acccaaacca caaggacaga tggctcgacc cgcggtcaca aagctacagt
6121 gtacactggg agcgccgact tttctccaaa actgggtagg gttcaatttg ctactgacac
6181 agacaatgat tttgtaacta atcagaatac aaagttcacc ccagtcggtg ttatccagga
6241 tggtagtact accccccgaa atgaacccca acaatgggtg ctcccaagtt actcaggcag
6301 aaacactcat aatgtgcacc tggcccccgc tgtggccccc actttcccgg gcgagcagct
6361 cctcttcttc agatctacca tgcccggatg cagcgggtac cccaacatgg atttggactg
6421 tctgctcccc caggaatggg tgcagtattt ctaccaggag gcagccccag cacaatctga
6481 tgtggcactg ttaagatttg tgaatccaga tacaggtagg gttttgtttg agtgtaagct
6541 tcataaatca ggctatgtta cagtggctca cactggccaa catgatttag ttatcccccc
6601 aaatggttat tttagatttg attcctgggt caaccagttc tacacacttg cccccatggg
6661 aaatgggacg gggcgtagac gtgcattata atggctggag ccttctttgc tggattggca
6721 tctgacgtcc ttggctctgg acttggttcc ctaatcaatg ctggggctgg ggccatcaac
6781 caaaaagttg aatatgaaaa caacagaaaa ttgcaacaag cttccttcca atttagtagc
6841 aatctacaac aggcttcctt tcaacatgac aaagagatgc tccaagcaca aattgaggcc
6901 accaaaaagt tgcaacagga aatgatgaga gttaaacaag caatgctcct agagggtgga
6961 ttctctgaga cagatgcagc ccgtggggca atcaacgccc ccatgacaaa aactttggac
7021 tggagcggaa caaggtactg ggctcccgat gccaggacta caacatacaa tgcaggccgc
7081 ttttccaccc ctcaaccctc gggggcacta ccaggaagag ctaatcttag ggctgctgtc
7141 cccgcccggg gttcctccag cacgtcttct aactcttctg ttgctacttc tgtgtattca
7201 aatcaaacca cctcaacgag acttggttct acagctggtt ctggtaccag tgtctcgagc
7261 ctcccgtcaa ctgcaaggac caggagctgg gttgaggatc aaaataggaa tttgtcacct
7321 ttcatgaggg gggcccacaa catctcgttt gtcaccccac catctagcag atcctctagc
7381 caaggcacag tctcaaccgt gcccaaagaa gttttggact cctggactgg cgctttcaac
7441 acgcgcaggc agcctctctt cgctcacatt cgcaagcgag gggagtcacg ggtgtaatgt
7501 gaaaagacaa aattg
//