Typing tool
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Typing tool
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Complete norovirus genomes
| MT362913 | GII.4 Sydney | |
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| GII.P4 New Orleans |
ORF1: 1..5093
ORF2: 5074..6696
ORF3: 6696..7499
LOCUS MT362913 7539 bp RNA linear VRL 01-JUN-2020
DEFINITION Norovirus GII isolate 432-3 nonstructural polyprotein (ORF1) gene,
partial cds; and VP1 (ORF2) and VP2 (ORF3) genes, complete cds.
ACCESSION MT362913
VERSION MT362913.1
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 7539)
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JOURNAL Unpublished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 7539)
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..7539
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="432-3"
/isolation_source="stool"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="USA"
/collection_date="10-Apr-2017"
/note="genotype: GII.4 New Orleans[P4 New Orleans]"
gene <1..5093
/gene="ORF1"
CDS <1..5093
/gene="ORF1"
/codon_start=3
/product="nonstructural polyprotein"
/protein_id="QJC69083.1"
/translation="ASNDATAAAVANSNNDTAKSSSDGVLSSMAVTFKRALGARPKQP
PPREKPQRPPRPPTPELVKNIPPPPPNGEDEIVVTYSVKDGVSGLPDLSTVRQPEESN
TAFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAISLAK
VELAPLSLYWRPVYTPQYLISPDTLKKLSGETFPYTAFDNNCYAFCCWVLDLNDSWLS
RRMIQRTTGFFRPYQDWNRKPLPTMDDSKIKKVANIFLCALSSLFTRPIKDIIGKIRP
LNILNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAV
ELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKE
EANELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLSTKSA
SPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREVAKR
IAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCPLT
LNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPDVEKAKR
DFPGQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGL
LHERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGKQLKDVKTMPEL
KQALKNVSIKKCQIVYNGCTYMLESDGKGNVKVDRIQSAAVQTNNELAGALHHLRCAR
IRYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQDLWSKPQVENTEETTSKDGCPKP
KDDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYS
IEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERVSLGLVTGS
EIRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSPSLF
ITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVV
TLLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCGC
PYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILGPGS
APTLSTKTKFWRSSTASLPPGTYEPAYLGGKDPRVKGGPSLQQVMREQLKPFTEPRGK
PPKPSVLEAAKKTIINVLEQTIDPPERWSFAQACASLDKTTSSGHPHHMRKNDCWNGE
SFTGKLADQASKANLMFEEGKNMTPVYTAALKDELVKTDKIYGKIKKRLLWGSDLATM
IRCARAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFERHSRYTYHYDADYSRWDSTQ
QRAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCTSQW
NSIAHWLLTLCALSEVTNLSPDTIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLKEYG
LKPTRPDKTEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHG
DPSETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQEPMF
RWMRFSDLSTWEGDRNLAPSFVNEDGVE"
mat_peptide <1..983
/gene="ORF1"
/product="p48"
mat_peptide 984..2081
/gene="ORF1"
/product="NTPase"
mat_peptide 2082..2618
/gene="ORF1"
/product="p22"
mat_peptide 2619..3017
/gene="ORF1"
/product="VPg"
mat_peptide 3018..3560
/gene="ORF1"
/product="Pro"
mat_peptide 3561..5090
/gene="ORF1"
/product="RdRp"
gene 5074..6696
/gene="ORF2"
CDS 5074..6696
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="QJC69084.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKVIFAAVPPNFPTEGLSPSQVTMFPHIVVDVRQLEPVLIPLPD
VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGAPDFVGKIQGML
TQTTRADGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG
STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRVV"
gene 6696..7499
/gene="ORF3"
CDS 6696..7499
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="QJC69085.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGVLPGRTNLRDAVPARGSSKSSN
SSTATSVYSNQTTSTRLGSTAGSGTSVSSLPSTARTRSWVEDQSRNLSPFMRGAHNIS
FVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRKRGESRA"
ORIGIN
1 tggcgtctaa cgacgctacc gctgccgctg ttgctaacag caacaacgac accgcaaaat
61 cttcaagtga cggagtgctt tctagcatgg ctgtcacttt taaacgagcc ctcggggcgc
121 ggcctaaaca gccccccccg agggaaaaac cacaaagacc cccacgacca cccacaccag
181 aactggttaa aaatattccc ccccccccac ccaacggaga ggatgaaata gtggttactt
241 atagtgtcaa agatggtgtt tccggcttgc ctgacctttc caccgtcaga cagccggaag
301 aatccaacac ggccttcagt gtccctccac tcaatcagag ggagaacaga gatgctaagg
361 aaccactcac tggaacaatt ctggaaatgt gggacgggga aatctaccat tatggcctgt
421 atgtggagcg aggtcttgta ctaggcgtac acaaaccgcc agctgccatc agcctcgcta
481 aggttgagtt ggcaccactc tccttatact ggaggcctgt gtacactcct cagtacctca
541 tctctccaga cactctcaag aaattgtctg gggaaacgtt cccctacaca gcatttgaca
601 acaactgcta tgccttttgt tgctgggttc tggacctaaa tgactcgtgg ctgagcagga
661 gaatgatcca gaggacaact ggtttcttca ggccctacca agactggaat aggaaacccc
721 ttcccactat ggatgactcc aaaataaaga aggtggccaa tatatttctg tgtgccctgt
781 cctcgctatt caccaggccc ataaaagata taatagggaa aataaggcct cttaacatcc
841 tcaacatctt ggcctcatgt gattggacct ttgcgggcat agtagagtcc ctgatactct
901 tagcagagct ctttggagtt ttctggacac ccccagatgt gtctgcaatg attgccccct
961 tacttggtga ctacgagcta caaggacctg aggaccttgc agtggagctc gtccccgtgg
1021 tgatgggggg aattggtttg gtgctaggat tcaccaaaga gaaaattggg aaaatgttgt
1081 catcagctgc gtccacctta agagcttgca aagaccttgg tgcatatggg ctagagatcc
1141 taaagctagt catgaagtgg ttcttcccga agaaggagga ggcaaatgag ctggctatgg
1201 tgaggtccat cgaggatgca gtcctggatc tcgaagcaat tgaaaacaat catatgacca
1261 ccttgcttaa agataaagac agtctggcaa cctacatgag aacactcgat cttgaagagg
1321 agaaagccag gaaactctca accaagtctg cctcacctga catcgtgggc acaatcaacg
1381 ccctcctggc gagaatcgct gccgcacgtt ctctggtgca tcgagcgaag gaggagcttt
1441 ccagcagacc aagacctgtg gtgttgatga tatcaggtag gccaggaata gggaagaccc
1501 acctcgctag ggaagtggct aagagaatcg cagcctccct tacaggagac cagcgtgttg
1561 gtctcatccc acgcaatggc gtcgaccact gggatgcgta taagggggag agggtcgtcc
1621 tatgggacga ttatggaatg agcaacccta ttcacgatgc cctcaggctg caagaactcg
1681 ctgacacttg ccccctcact ctgaactgtg acaggattga aaataaggga aaggtctttg
1741 acagcgatgt catcattatc accactaatc tggccaaccc agccccactg gactatgtca
1801 actttgaagc atgctcgagg cgcattgact tcctcgtata tgcagaagcc cctgatgtcg
1861 aaaaggcgaa gcgtgacttc ccaggccagc ctgacatgtg gaagaacgct ttcagttccg
1921 atttctcaca cataaaacta gcactggccc cacagggtgg tttcgacaag aacgggaaca
1981 ccccacacgg aaagggcgtc atgaagactc tcaccactgg ctcccttatt gcccgggcat
2041 cagggctact ccatgagagg ttagatgaat ttgaactgca gggcccagct ctcaccacct
2101 tcaatttcga tcgcaataaa gtgcttgcct ttagacagct tgctgctgaa aacaaatatg
2161 gactgatgga cacaatgagg gttgggaaac agctcaagga tgtcaaaacc atgccagaac
2221 tcaaacaagc actcaagaat gtctcaatca agaagtgtca aatagtgtat aatggttgca
2281 cctacatgct tgagtctgat ggcaagggca atgtgaaagt tgacaggatc cagagcgccg
2341 ccgtgcagac caacaatgag ctggctggtg ccctgcacca cttgaggtgc gccagaatca
2401 gatactatgt caagtgtgtc caggaagccc tgtattccat cattcaaatt gctggggctg
2461 catttgtcac cacgcgcatt gccaagcgca tgaacataca ggatctatgg tccaagccac
2521 aagtggaaaa tacagaggaa actaccagca aggacgggtg cccaaaaccc aaggatgatg
2581 aggagtttgt catttcatcc gacgacatca aaactgaggg caagaaaggg aagaacaaga
2641 ctggccgtgg caagaagcac acagcatttt caagcaaagg cctcagtgat gaagagtacg
2701 atgaatacaa gaggatcaga gaagaaagga atggcaagta ctctatagaa gagtacctcc
2761 aggacaggga caaatattat gaggaggtgg ccattgccag agcgactgag gaagacttct
2821 gtgaagagga ggaagccaag atccgacaaa ggatctttag gccaacaagg aaacaacgca
2881 aggaggaaag agtctctctc ggtttagtca cgggctctga aattaggaaa agaaacccag
2941 atgatttcaa acccaaaggg aaattgtggg ctgacgatga caggagtgtg gactacaatg
3001 agaaactcag ttttgaggcc ccgccaagca tttggtcaag aatagtcaac tttggttcag
3061 gctggggatt ctgggtctcc cccagcttgt tcataacatc aacccatgtt ataccccagg
3121 gcgcaaagga gttctttgga gtccccatca aacaaataca ggtacacaag tcaggcgagt
3181 tctgtcgctt gagattccct aaaccaatca ggactgatgt gacgggcatg atcttagaag
3241 aaggcgcacc tgagggcacc gtggttacac tactcatcaa aaggtccacc ggggaactta
3301 tgcccctagc agctaggatg gggacccatg cgaccatgaa gatccaaggg cgcactgttg
3361 ggggccagat gggcatgctt ctgacagggt ccaacgccaa gagtatggac ctgggtacta
3421 caccaggtga ttgtggctgc ccctacatct acaagagagg taatgactat gtggtcattg
3481 gagtccacac ggctgccgca cgtgggggga acactgtcat atgtgccacc caggggagtg
3541 aaggagaggc tacacttgag ggtggtgaca acaaggggac ttactgtggt gcaccaatcc
3601 taggcccagg gagtgcccca acacttagca ccaagaccaa attctggaga tcgtccacag
3661 catcactccc acctggcacc tatgaaccag cctatcttgg tggcaaggac cctagagtca
3721 agggtggccc ttcactacag caagtcatga gggaacagtt gaagccattc acagagccca
3781 gaggtaagcc accaaaacca agtgtgttag aagctgccaa gaaaaccatc atcaatgttc
3841 ttgagcaaac aattgatcca cctgagagat ggtcgttcgc acaagcttgc gcgtctcttg
3901 acaagaccac ttccagtggt catccgcatc acatgcggaa aaacgactgc tggaacgggg
3961 agtccttcac aggcaagctg gcagaccagg cttctaaggc caacctgatg tttgaagaag
4021 gaaagaacat gaccccagtc tacacagctg cgctcaagga tgagctagtt aaaactgaca
4081 aaatttatgg taagatcaag aagaggcttc tttggggctc ggacttggcg accatgatcc
4141 ggtgtgctcg ggcattcgga ggcctaatgg atgaactcaa agcacactgt gtcacacttc
4201 ccgttagagt tggcatgaat atgaatgagg atggccccat catcttcgag aggcattcca
4261 ggtacacgta ccactatgat gctgattact ctcgatggga ttcaacacaa cagagagccg
4321 tgttggcggc agctctagaa atcatggtaa agttctcccc agaaccacat ttggcccagg
4381 tagtcgctga agaccttctt tctcctagcg tggtggacgt gggcgacttc acaatatcaa
4441 tcaacgaggg tcttccctct ggggtgccct gcacctccca atggaactcc atcgcccact
4501 ggcttctcac tctctgcgcg ctctccgaag tcacaaacct gtctcctgac accatacagg
4561 ctaattctct cttttctttt tatggtgatg atgaaattgt tagcacagac ataaaattgg
4621 acccagagaa attgacagca aaactcaaag aatacgggtt aaaaccaacc cgccctgaca
4681 aaactgaagg accccttgtc atctctgaag acctgaatgg cctaactttc ctgcggagaa
4741 ctgtgacccg cgacccagct ggttggtttg gaaaactgga gcagagttca atactcaggc
4801 aaatgtactg gactaggggt cccaaccatg gagacccatc tgaaacaatg attccacatt
4861 cccaaagacc catacaattg atgtccctac tgggggaggc cgctctccac ggcccagcat
4921 tttacagtaa gattagcaaa ttggtcattg cagagctaaa agaaggtggt atggattttt
4981 acgtgcccag acaagagcca atgttcagat ggatgagatt ctcagatctg agcacgtggg
5041 agggcgatcg caatctggct cccagttttg tgaatgaaga tggcgtcgag tgacgccaac
5101 ccatctgatg ggtccgcagc caacctcgtc ccagaggtca acaatgaggt tatggctctg
5161 gagcccgttg ttggtgccgc tattgcggca cctgtagcgg gccaacaaaa tgtaattgac
5221 ccctggatta gaaacaattt tgtacaagcc cctggtggag agtttacagt gtcccccaga
5281 aacgctccag gtgaaatact atggagcgcg cccttaggcc ctgatttaaa tccctaccta
5341 tcccacttgg ccagaatgta taatggttat gcaggtggtt ttgaagtgca ggtgattctc
5401 gcggggaacg cgttcaccgc cgggaaggtc atatttgcag cagtcccacc aaattttcca
5461 actgaaggct tgagccccag ccaggtcact atgttccccc atatagtagt ggatgttagg
5521 caactagaac ctgtgttgat tcccttaccc gatgttagga ataatttcta ccattacaat
5581 caatcaaatg accccaccat taagttgata gcaatgttat atacaccact tagggctaat
5641 aatgctgggg atgatgtctt cacagtttct tgccgagttc tcacgaggcc atcccccgat
5701 tttgatttca tatttctagt gccacccaca gttgagtcta gaaccaaacc attttccgtc
5761 ccagttttga ctgttgagga gatgaccaat tcaagattcc ccattccttt ggaaaagttg
5821 ttcacgggcc ccagtagtgc ctttgttgtt caaccacaaa acggtaggtg cacgactgat
5881 ggcgtgctcc taggcaccac ccaattgtct cctgtcaaca tctgcacctt cagaggggat
5941 gtcacccaca ttacaggtag tcgtaactac acaatgaatt tggcttctca aaattggaac
6001 aattatgacc caacagaaga aatcccagcc cctctaggag ctccagattt tgtggggaag
6061 attcaaggca tgctcaccca aaccacaagg gcagatggct caacacgcgg ccacaaggct
6121 acggtgtaca ctgggagcgc cgacttcgct ccaaaactgg gcagagttca atttgaaact
6181 gacacagacc atgattttga agctaaccaa aacacaaagt tcactccagt cggtgtcatc
6241 caagatggca gcaccaccca ccgaaatgaa ccccaacagt gggtgctccc aagttactca
6301 ggcagaaata ctcataatgt tcatctggcc cccgctgtgg cccccacttt tccgggtgaa
6361 caacttctct tctttagatc caccatgccc ggatgtagcg ggtatcccaa catggatttg
6421 gactgtttgc tcccccagga atgggtgcag tacttctacc aagaggcagc cccagcacaa
6481 tctgatgtgg ccctgctaag atttgtgaat ccagacacag gtagggtttt gtttgaatgc
6541 aaacttcata aatcaggcta tgttacagtg gctcacactg gccaacatga tttggtcatc
6601 ccccccaatg gttattttag gtttgattcc tgggtcaacc agttctacac gcttgccccc
6661 atgggaaatg gaacggggcg tagacgcgta gtataatggc tggagctttc tttgctgggt
6721 tagcatctga tgtcctcggc tctggacttg gttcccttat caatgctggg gctggggcca
6781 tcaaccaaaa agttgagttt gaaaataaca gaaaattgca acaagcatcc ttccaattta
6841 gcagcaattt acaacaggct tcctttcaac atgacaaaga aatgcttcaa gcacaaattg
6901 aggccactaa aaagctacaa caggaaatga tgaaagttaa gcaggcaatg ctcctagagg
6961 gtgggttctc tgaaacagat gcagcccgcg gggcaatcaa cgcccccatg acaaaagctt
7021 tggactggag cgggacaagg tactgggctc ctgatgctag gactacaact tataatgcag
7081 gccgcttttc cacccctcaa ccatcggggg tactaccagg aaggactaat cttagggatg
7141 ctgtccctgc tcggggttcc tctaaatctt ctaactcttc tactgctact tctgtgtact
7201 caaatcaaac cacttcaacg agacttggtt ctacagctgg ttctggcacc agtgtctcga
7261 gtctcccgtc aactgcaagg accaggagct gggttgagga tcaaagtagg aatttgtctc
7321 ctttcatgag gggggcccac aacatatcgt ttgtcacccc accatctagc agatcctcta
7381 gccaaggcac agtctcaacc gtgcctaaag aggttttgga ctcctggact ggcgccttca
7441 acacgcgcag gcagcctctc ttcgctcaca ttcgtaaacg aggggagtca cgggcgtaat
7501 gtgaaaagac aaaattgatt atctttcttt ttctttagt
//