Typing tool
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Typing tool
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Complete norovirus genomes
| PQ213802 | GII.4 Sydney | |
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| GII.P31 |
ORF1: 1..3406
ORF2: 3387..5009
ORF3: 5009..5717
LOCUS PQ213802 5717 bp RNA linear VRL 01-JAN-2025
DEFINITION Norovirus GII isolate Hu/GII.4 Sydney[P31]/Loudon0059/2013/USA
nonstructural polyprotein (ORF1) gene, partial cds; VP1 (ORF2)
gene, complete cds; and VP2 (ORF3) gene, partial cds.
ACCESSION PQ213802
VERSION PQ213802.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norovirus norwalkense.
REFERENCE 1 (bases 1 to 5717)
AUTHORS Barclay,L., Montmayeur,A.M., Cannon,J.L., Mallory,M.L., Reyes,Y.I.,
Lindesmith,L., Wall,H., Baric,R.S., Vinje,J. and Chhabra,P.
TITLE Norovirus GII.4 evolution in the United States since emergence of
GII.4 Sydney
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 5717)
AUTHORS Dill,J., Barclay,L., Montmayeur,A.M., Vinje,J. and Chhabra,P.
TITLE Direct Submission
JOURNAL Submitted (21-AUG-2024) Viral Gastroenteritis Branch, Centers for
Disease Control and Prevention, 1600 Clifton Road NE, Atlanta, GA
30329, USA
COMMENT ##Assembly-Data-START##
Assembly Method :: Geneious v. v. 11.1.2; SPAdes v. v. 3.6
Sequencing Technology :: 454; Illumina
##Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..5717
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="Hu/GII.4 Sydney[P31]/Loudon0059/2013/USA"
/isolation_source="stool"
/host="Homo sapiens"
/db_xref="taxon:122929"
/geo_loc_name="USA"
/collection_date="29-Jan-2013"
/note="genotype: GII.4 Sydney[P31]"
gene <1..3406
/gene="ORF1"
CDS <1..3406
/gene="ORF1"
/codon_start=2
/product="nonstructural polyprotein"
/protein_id="XEQ87056.1"
/translation="LPLTLNCDRIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSR
RIDFLVYAEAPEVEKAKRDFPGQPDMWKNAFSPDFSHIKLSLAPQGGFDKNGNTPHGK
GVMKTLTTGSLIARASGLLHERLDEYELQGPALTTFNFDRNKILAFRQLAAENKYGLM
DTMRVGKQLKDVKTMSDLKQALKNIAIKKCQIVYNGGTYTLEADGKGSVKVDKVQSAT
VQTNNELAGALHHLRCARIRYYVRCVQEALYSIIQIAGAAFVTTRIAKRMNIQNLWSK
PQVEDTEEMTNKDGCPKPKDDEEFVVSSDDIKTEGKKGKNKSGRGKKHTAFSSKGLSD
EEYDEYKRIREERNGKYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRP
TRKQRKEERASLGLVTGSEIRKRNPEDFKPKGKLWADDDRSVDYNEKLNFEAPPSIWS
RIVNFGSGWGFWVSPSLFITSTHVIPQGAKEFFGVPIKQIQIHKSGEFCRLRFPKPIR
TDVTGMILEEGAPEGTVATLLIKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLT
GSNAKSMDLGTTPGDCGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLE
GGDSKGTYCGAPILGPGSAPKLSTKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPS
LQQVMRDQLKPFTEPRGKPPRPNVLEAAKKTIINVLEQTIDPPQKWSFAQACASLDKT
TSSGHPHHMRKNDCWNGESFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDK
VYGKIKKRLLWGSDLATMIRCARAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFEKH
SRYRYHYDADYSRWDSTQQRDVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVMDVGDF
QISISEGLPSGVPCTSQWNSIAHWLLTLCALSEVTDLSPDIIQANSLFSFYGDDEIVS
TDIKLDPEKLTTKLKEYGLKPTRPDKTEGPLVISEDLDGLTFLRRTVTRDPAGWFGKL
EQSSILRQMYWTRGPNHEDPFETMIPHSQRPIQLMSLLGEAALHGPAFYSKVSKLVIA
ELKEGGMDFYVPRQEPMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE"
mat_peptide <1..394
/gene="ORF1"
/product="NTPase"
mat_peptide 395..931
/gene="ORF1"
/product="p22"
mat_peptide 932..1330
/gene="ORF1"
/product="VPg"
mat_peptide 1331..1873
/gene="ORF1"
/product="Pro"
mat_peptide 1874..3403
/gene="ORF1"
/product="RdRp"
gene 3387..5009
/gene="ORF2"
CDS 3387..5009
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="XEQ87057.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKVIFAAVPPNFPTEGLSPSQVTMFPHIVVDVRQLEPVLIPLPD
VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGVL
TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG
STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNTDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAV"
gene 5009..>5717
/gene="ORF3"
CDS 5009..>5717
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="XEQ87058.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPPGALPGRANLRDAVPARGSSSKSS
NSSTATSVYSNQTTSTRLGSTAGSGTSVSSLPSTARTGSWVEDQSRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVST"
ORIGIN
1 cttgcccctc acactaaatt gtgacagaat tgagaacaaa gggaaagtct ttgacagtga
61 tgccataatt atcaccacca atctggccaa cccagcacca ctggattatg tcaactttga
121 agcgtgctcg agacgtattg acttcctcgt gtacgcagaa gcccctgagg tggagaaggc
181 aaagcgcgac ttcccaggtc aacctgacat gtggaagaac gctttcagtc ctgacttctc
241 acacataaaa ctgtcactgg ctccacaggg tggttttgac aagaacggca acaccccgca
301 tggaaaaggg gtcatgaaga ccctcaccac tggctccctc atcgcccgag catcagggtt
361 actccatgag aggctagatg aatatgaact gcaaggccca gccctcacca ctttcaactt
421 tgaccgcaac aagatacttg cttttagaca gcttgctgct gaaaacaagt atgggctgat
481 ggacacaatg agagttggaa aacagctcaa ggatgtcaag accatgtcag acctcaaaca
541 agcactcaaa aacatcgcga tcaagaagtg ccagatagtg tacaatggtg gcacctacac
601 acttgaggcc gatggcaagg gtagtgtgaa agttgacaaa gtgcaaagtg ccactgtgca
661 gaccaacaat gaactagccg gtgccctaca ccacctaagg tgcgctagaa tcagatacta
721 tgttaggtgc gtccaggagg cactgtattc catcatccaa atcgctgggg ctgcattcgt
781 caccacgcgc atcgctaagc gcatgaatat acagaatctc tggtccaagc cacaggtgga
841 agacacagaa gagatgacta acaaagatgg ttgcccaaaa cccaaagatg atgaagagtt
901 tgtcgtctca tccgacgaca tcaaaactga gggcaagaaa gggaagaaca agtccggccg
961 tggcaagaag cacacagcct tttcaagcaa agggctcagt gatgaggagt acgatgagta
1021 caagagaatc agagaagaaa ggaatggtaa gtactccata gaagagtacc ttcaggacag
1081 agataagtac tacgaggagg tggccattgc cagggcaacc gaagaggact tctgtgaaga
1141 agaagaggcc aaaatccggc agagaatttt cagaccaaca aggaaacaac gcaaagaaga
1201 gagggcctct ctcggcttgg tcacaggctc tgaaatcagg aagagaaacc cagaagactt
1261 caaacccaag ggaaagctat gggctgatga tgacagaagt gttgactaca atgagaaact
1321 caactttgag gccccaccaa gcatctggtc gcggatagtc aactttggtt caggctgggg
1381 cttctgggtc tcccccagtc tgtttataac atcaacccat gtcatacccc aaggtgcaaa
1441 agagttcttc ggagtcccta tcaagcaaat ccagatacac aaatcaggtg aattctgccg
1501 gttgagattc ccaaagccaa tcagaactga tgtgacgggc atgattctag aagaaggtgc
1561 gcccgagggg accgtggcca cactgctcat caagagacca actggagagc tcatgcctct
1621 ggcagccaga atggggaccc atgcaaccat gaaaattcag gggcgcacag ttggagggca
1681 aatgggtatg ctcctgacag gatccaacgc caagagtatg gacctaggca caacaccagg
1741 cgactgcggc tgcccctaca tctacaagag ggggaatgac tacgtagtca taggagtcca
1801 tacggccgct gcccgtggag gaaacactgt catatgtgcc acccagggga gtgagggaga
1861 agccacactt gaaggaggcg acagtaaagg gacatactgt ggcgcaccaa tcttgggccc
1921 agggagcgct ccgaagctca gtaccaagac taagttttgg agatcatcca caacaccact
1981 cccacctggc acctacgaac cagcctacct cggtggcaaa gaccccagag tcaaaggtgg
2041 cccttcattg caacaagtta tgagggacca gctaaagcca ttcacagaac ccagaggcaa
2101 accaccaaga ccaaatgtgt tggaagctgc caagaaaacc atcatcaatg tccttgagca
2161 aacaattgat ccaccccaaa aatggtcatt tgcgcaagct tgcgcatccc ttgacaaaac
2221 cacctccagc ggccacccgc accacatgcg gaaaaacgat tgttggaatg gggagtcctt
2281 cacaggaaaa ttggctgatc aagcctccaa ggccaaccta atgtttgaag agggaaagaa
2341 catgactcca gtctacacag gtgcacttaa agatgagttg gtaaagaccg ataaagttta
2401 tggtaagatt aagaagaggc ttctgtgggg ttcagatctg gcgaccatga tacggtgcgc
2461 ccgagctttt ggaggcctta tggatgaact caaggcgcac tgtgtcacac ttcctgtcag
2521 agttggtatg aacatgaatg aggatggccc catcatattt gagaagcact ccagatatag
2581 atatcactat gatgctgatt attcccggtg ggactcaaca caacaaaggg atgtgctagc
2641 agcagcacta gaaatcatgg ttaagttctc tccagaacca cacctggccc aggtagttgc
2701 agaagacctc ctttctccta gcgtaatgga tgtaggtgac tttcaaatat caataagtga
2761 gggtcttccc tctggggtac cttgcacctc ccagtggaat tccatcgccc actggctcct
2821 cactctttgt gcactctctg aagtcacgga cctgtcccct gacatcattc aggccaactc
2881 ccttttctcc ttctatggtg atgatgagat tgtaagcaca gacataaagt tggacccaga
2941 gaagctaaca acaaaactca aggagtacgg gttgaaacca acccgccccg acaaaactga
3001 aggacccctt gttatctctg aagacctgga tggcctgaca ttcctccgga gaactgtgac
3061 ccgtgatcca gctggctggt ttggaaaatt ggaacaaagt tcaattctca gacaaatgta
3121 ctggaccagg ggtcccaacc atgaagatcc atttgaaaca atgataccac actcccaaag
3181 acccatacaa ttgatgtcct tgctgggcga ggctgcactc cacggcccgg cattttatag
3241 caaagttagc aaattagtca ttgcagagtt gaaggaaggt ggcatggatt tttacgtgcc
3301 cagacaagag ccaatgttca gatggatgag attctcagat ctgagcacgt gggagggcga
3361 tcgcaatctg gctcccagtt ttgtgaatga agatggcgtc gagtgacgcc aacccatctg
3421 atgggtccgc agccaacctc gtcccagagg tcaacaatga ggttatggct ctggagcccg
3481 ttgttggtgc cgccattgcg gcacctgtag cgggccaaca aaatgtaatt gacccctgga
3541 ttagaaacaa ttttgtacaa gcccctggtg gagagtttac agtatcccct agaaacgctc
3601 caggtgaaat actatggagc gcgcccttgg gccctgatct aaatccctac ctatcccatt
3661 tggccagaat gtacaatggt tatgcaggtg gttttgaagt gcaggtaatt ctcgcgggga
3721 acgcgttcac cgccgggaag gtcatatttg cagcagtccc accaaatttt ccaactgaag
3781 gcttgagccc cagccaggtc actatgttcc cccatatagt agtagatgtt aggcaactag
3841 aacctgtgtt gattccctta cccgatgtta ggaataattt ctatcattat aatcaatcaa
3901 atgaccccac catcaagttg atagcaatgt tgtatacacc acttagggct aataatgctg
3961 gggatgatgt cttcacagtt tcttgccgag ttctcacgag accatccccc gattttgatt
4021 tcatatttct agtgccaccc acagttgagt caagaactaa accattctct gtcccagttt
4081 taactgttga ggagatgacc aattcaagat tccccattcc tttggaaaag ttgttcacgg
4141 gtcccagcag tgcctttgtt gtccaaccac aaaacggcag gtgcacgact gatggcgtgc
4201 tcctaggcac cacccaactg tctcctgtca acatctgcac cttcagagga gatgtcaccc
4261 atatcacagg tagtcgtaac tacacaatga atttggcttc tcaaaattgg aacaattatg
4321 acccaacaga agaaatccca gcccctctag gaactccaga ctttgtgggg aagattcaag
4381 gcgtgctcac ccaaaccaca aggacagatg gctcaacacg cggccacaaa gccacagtgt
4441 acactgggag cgccgacttt gctccaaaac tgggtagagt tcaatttgaa actgacacag
4501 accatgattt cgaagctaac caaaacacaa agttcacccc agtcggtgtc atccaagatg
4561 gtagcaccac ccaccgaaat gaaccccaac agtgggtgct cccaagttac tcaggcagaa
4621 atactcataa tgtgcatctg gcccccgctg tagcccccac ttttccgggt gagcaacttc
4681 tcttcttcag atccaccatg cccggatgca gcgggtaccc caacacggat ttggactgtc
4741 tgcttcccca ggaatgggtg cagtacttct accaagaggc agccccagca caatctgatg
4801 tggctctgct aagatttgtg aatccagaca ctggtagggt tttatttgag tgcaagcttc
4861 ataaatcagg ctatgttaca gtggctcaca ctggccaaca tgatttggtt attcccccca
4921 atggttattt tagatttgat tcctgggtca accagttcta cacgcttgcc cccatgggaa
4981 atggaacggg gcgtagacgt gcagtataat ggctggagct ttctttgctg gattggcatc
5041 tgatgtcctt ggctctggac ttggttccct catcaatgct ggggctgggg ccatcaacca
5101 aaaagttgag tttgaaaata atagaaaatt gcaacaagca tccttccaat ttagcagcaa
5161 tctacaacag gcttcctttc aacacgacaa agagatgctc caagcacaaa ttgaggccac
5221 caaaaagcta caacaggaaa tgatgaaagt taagcaggca atgctcctag agggtgggtt
5281 ctctgagaca gatgcagccc gcggggcaat caacgccccc atgacaaaag ctttggactg
5341 gagcgggaca aggtactggg ctcccgatgc taggactaca acatacaatg caggccgctt
5401 ttccacccct caaccaccgg gggcactgcc aggaagagct aatcttaggg atgctgtccc
5461 tgctcggggt tcctccagta aatcttctaa ctcttctact gccacttctg tgtactcaaa
5521 tcaaactact tcaacgagac ttggttctac agctggttct ggtaccagtg tctcgagcct
5581 cccgtcaact gcaaggactg ggagctgggt tgaggatcaa agtaggaatt tgtcaccttt
5641 catgaggggg gcccacaaca tatcgtttgt caccccacca tctagcagat cctctagcca
5701 aggcacagtc tcaaccg
//