Typing tool
|
|
|
|
|
|
Typing tool
|
Complete norovirus genomes
| PQ196514 | GII.4 Sydney | |
|
|---|---|---|---|
| GII.P16 |
ORF1: 1..5100
ORF2: 5081..6703
ORF3: 6703..7509
LOCUS PQ196514 7524 bp RNA linear VRL 27-MAR-2025
DEFINITION Norovirus GII isolate Hu/GII.4 Sydney[P16]/SantaClara0200/2022/USA
nonstructural polyprotein (ORF1), VP1 (ORF2), and VP2 (ORF3) genes,
complete cds.
ACCESSION PQ196514
VERSION PQ196514.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norovirus norwalkense.
REFERENCE 1 (bases 1 to 7524)
AUTHORS Barclay,L., Montmayeur,A.M., Cannon,J.L., Mallory,M.L., Reyes,Y.I.,
Wall,H., Baric,R.S., Lindesmith,L.C., Vinje,J. and Chhabra,P.
TITLE Molecular Evolution and Epidemiology of Norovirus GII.4 Viruses in
the United States
JOURNAL J Infect Dis (2025) In press
PUBMED 40036172
REMARK Publication Status: Available-Online prior to print
REFERENCE 2 (bases 1 to 7524)
AUTHORS Pan,C.Y., Barclay,L., Montmayeur,A.M., Vinje,J. and Chhabra,P.
TITLE Direct Submission
JOURNAL Submitted (16-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 :: Sanger dideoxy sequencing; Illumina
##Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..7524
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="Hu/GII.4 Sydney[P16]/SantaClara0200/2022/USA"
/isolation_source="stool"
/host="Homo sapiens"
/db_xref="taxon:122929"
/geo_loc_name="USA"
/collection_date="17-May-2022"
/note="genotype: GII.4 Sydney[P16]"
gene 1..5100
/gene="ORF1"
CDS 1..5100
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="XEJ39570.1"
/translation="MKMASNDASAAVVCNNNNDKEKSSGEGLFTNMSSTLKKALGARP
KRPAPRDEPQKPPRPPTPELVKRIPPPPPNGEEEGEPVIRYEVKSGISGLPELTTVPQ
PDVANTAFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAA
ISMARVELAPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLN
DSWLSRRMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLI
GKIKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGP
EDLAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWF
FPKKEEANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRL
STKSASPDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAR
EVARKVASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELAD
TCPLTLNCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEV
EKAKRDFPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIA
RASGLLHERMDEFELQGPTTTTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVK
TMEELKQAIRNVTIKRCRIIYGGSTYDLESDGKGKVLVEKVKSASIQTNNELAGALHH
LKHARIRYYVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEE
APKSEDDEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
KYSIEEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLV
TGSEIRRRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSP
SLFITSTHVIPAGITEAFGVPIKQVQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEG
TVATVLIKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGD
CGCPYIYKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILG
PGGAPKLSTKTKFWRSSNMPLPPGTYEPAYLGGRDPRVRGGPSLQQVMRDQLKPFTEP
RGKPPRPSVLEAAKQTIINVLEQTLDPPQKWTYVQACASLDKTTSSGHPHHVRKNEFW
NGETFTGKLADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDL
STMIRCARSFGGLMDEMKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWD
STQQRAVLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCT
SQWNSIAHWLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLK
EYGLKPTRPDKTEGPLIIGEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGP
NHEDPNETMIPHSQRPIQLMALLGEASLHGPSFYSRISKLVITELKEGGMDFYVPRQE
PMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE"
mat_peptide 1..996
/gene="ORF1"
/product="p48"
mat_peptide 997..2094
/gene="ORF1"
/product="NTPase"
mat_peptide 2095..2625
/gene="ORF1"
/product="p22"
mat_peptide 2626..3024
/gene="ORF1"
/product="VPg"
mat_peptide 3025..3567
/gene="ORF1"
/product="Pro"
mat_peptide 3568..5097
/gene="ORF1"
/product="RdRp"
gene 5081..6703
/gene="ORF2"
CDS 5081..6703
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="XEJ39571.1"
/translation="MKMASSDANPSDGSAASLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHITGSHNFTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML
TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTNHDFEANQNTKFTPVGVIQDG
STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAV"
gene 6703..7509
/gene="ORF3"
CDS 6703..7509
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="XEJ39572.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMRVKQAMLLEGGFSETDAARGAVN
APMTKALDWSGTRYWAPDARITTYNAGHFSTPQPSGALPGRANLRDAVPARGSSTKPS
NSSTATSVYSNQTISTRLGSTAGSGTSVSSLPPTARTRSWVEDQNRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRV"
ORIGIN
1 atgaagatgg cgtctaacga cgcttccgct gccgttgttt gcaacaacaa caacgacaag
61 gaaaaatctt caggtgaagg cttattcaca aatatgtctt ccaccttaaa gaaagccctc
121 ggggctaggc ccaaacgacc tgccccgaga gacgaaccac aaaagccccc aagaccacca
181 actcccgagt tggtcaagag gatacccccc ccgccaccta atggcgaaga agaaggagaa
241 ccagtcatta ggtatgaggt taagagtggg atctctggcc tgcccgagct cacaacagtc
301 ccccaaccgg acgtggccaa cacagcattt agtgttccac cactgagctt gagagaaaac
361 agggaggcca aggaaccgct gacaggggca atactagaga tgtgggacgg agagatatac
421 cactatggcc tgtacgtgga gaaaggctta gtgttgggtg tacacaaacc acctgcagcc
481 ataagcatgg caagagtgga gctggcgccg ctgtcattgt actggcgtgt ggtgtacact
541 ccccaatacc tcatctcccc tgaaactctc aggaggctca atggagaggc gtttccttac
601 accgcttttg acaacaactg ctacgccttt tgctgctggg tgttagacct caatgactca
661 tggcttagca ggaggatggt gcaacgaaca acgggcttct tcaggcctta ccaagagtgg
721 aacagaaaac ccttacccac catggatgac tccaaaataa agaaggtagc aaatatattc
781 ctatgttcac tgtccacatt attcaccaga cccataaagg acctcatagg aaaaattaaa
841 ccattaaaca tattgaacat cctggcaacg tgtgattgga cgttcgccgg aatagtggag
901 tctctgatat tgcttgccga actcttcgga gttttctgga cacccccaga tgtgtctgct
961 atgatcgctc ccttactcgg ggactacgag ttgcaagggc cagaagacct cgccgttgaa
1021 ctcgtacctg tggtaatggg agggattggt ttggtgttgg gattcaccaa agagaaaatt
1081 ggcaaaatgt tgtcctcagc agcatcaaca ctcagggctt gtaaagatct tggtgcctat
1141 ggcttagaga tactcaaatt ggtcatgaag tggtttttcc caaagaaaga agaggccaat
1201 gagctagcca tggtgagggc catagaggat gccgtattag atcttgaggc aatagagaac
1261 aaccacatga caaccctgtt gaaagataaa gacagcttag caacatacat gaaaacactg
1321 gatatggagg aggagaaagc cagaaggttg tccacaaaat ctgcatcccc tgacatagtt
1381 gggacaatca acgccctgct ggctcgaata gcagcagcca ggtcattagt ccacagggcc
1441 aaggaagaac tgtctagcag gataaggcca gtagttgtta tgatatctgg caagccagga
1501 ataggcaaaa ctcatctggc cagagaggtg gcaagaaagg tggcatccac tctcacaggg
1561 gatcaaagag tcggactcat accaagaaac ggtgtggacc attgggatgc atacaaaggt
1621 gagagagtcg tgctgtggga cgactatggc atgagtaacc ccattcatga tgctctccgc
1681 atacaagaat tggctgatac gtgccccctt accctaaatt gtgacagaat tgaaaataag
1741 gggaaagttt ttgacagtga agtcataata attacaacaa acctcgccaa cccagcccca
1801 cttgattatg tcaactttga ggcctgctcc aggagaattg atttcctggt gtacgctgag
1861 gcaccagaag tagaaaaggc aaaacgggat tttcctggtc agccagatat gtggaaggac
1921 gccttcaagc cggacttttc gcacatcaag ctacagcttg cacctcaggg cggttttgac
1981 aagaatggca acaccccgca tgggaaagga gtgatgaaga ccctcactac cggttctctg
2041 attgcccgtg catcaggcct attgcatgag aggatggatg aatttgaact ccaaggtccc
2101 acaaccacca ctttcaattt cgaccggaac agaatcacag cattcagaca actggctgca
2161 gaaaacaagt atggactggt ggacaccatg aaagttggta atcaactaaa aggagtgaaa
2221 accatggaag aactcaaaca agcaatcagg aatgtgacca tcaagaggtg ccggatcatc
2281 tacggtggct ccacgtatga ccttgaatct gatggcaagg gcaaagtttt ggtggaaaag
2341 gtcaagagcg cctctataca gaccaacaac gagttggccg gggccctgca tcatcttaaa
2401 catgcccgaa tcaggtacta tgtcaaatgt gtgcaagaag cagtctattc catcatacaa
2461 attgccggcg ctgcgtttgt caccacgcgc attgcacgcc gcatgaacat acaagagctc
2521 tggtcgaagc cacaattaga tcaaaatgaa tcagagacta aggaagaggc ccccaagtca
2581 gaagatgacg agttcatcat atcttctaag gatatcaagg aggaaggaaa gaagggcaaa
2641 aacaaaactg gccgcggcaa gaaacacacc gcattctcca gcaagggctt gagcgatgag
2701 gagtatgacg agtacaagag gataagagaa gagagaaatg ggaagtactc catagaggag
2761 tatcttcaag acagagacag gtattatgag gagctcgcca ttgccaaggc cacggaagaa
2821 gatttctgtg aagaggagga gatcaaaatc cgtcagagga ttttccgtcc caccaggaaa
2881 caaagaaagg aagagagggc cacactagga ctggtaacag gttcagaaat cagaagaaga
2941 aaccctgatg atttcaaacc caaagggaag ctatgggccg atgacaacag aagtgttgac
3001 tacaatgaga aactggattt tgaggccccc ccaagtatat ggtctaggat tgtgagcttt
3061 ggttctggct ggggcttctg ggtgtcacca agcctgttca taacgtcaac tcatgtgatc
3121 cctgcaggca taacagaagc atttggagtc cccatcaaac aagttcagat ccacaaatca
3181 ggcgaatttt gccgattcag attcccaaaa ccaattagac cagatgtgac aggaatgatc
3241 ttggaagaag gtgcgcctga aggcaccgtg gcaactgtgc tcatcaaacg ccccaccgga
3301 gagctcatgc ctcttgcagc cagaatggga acacacgcaa ccatgaagat tcaaggccgc
3361 atggttggtg gacagatggg tatgttactc actgggtcaa atgctaaagg aatggatttg
3421 ggaacaactc ctggtgactg tggctgccct tacatctata aaaggggcaa tgactatata
3481 gtcattgggg tgcacactgc agcagcccgt ggtggaaaca ccgtcatctg tgccacacag
3541 ggaagtgagg gtgaggcaac tcttgagggt ggagatgaca aaggaacata ctgtggggca
3601 cccattctag gccctggggg tgcaccaaaa ttgagcacta aaaccaaatt ttggaggtca
3661 tcgaacatgc cccttccacc agggacgtat gagcctgcct acctcggtgg ccgtgacccg
3721 cgtgttaggg gtgggccctc cttacaacag gtaatgagag accagttgaa gccattcact
3781 gaacccaggg gcaaacctcc aagaccaagt gttttggaag cagccaaaca aaccattatc
3841 aatgtccttg aacaaaccct ggatcctcca caaaaatgga catacgtaca ggcgtgtgcc
3901 tcacttgaca aaaccacctc cagcgggcat ccccaccacg tccgaaagaa tgaattctgg
3961 aatggtgaga ccttcactgg taaattggca gaccaagcat caaaagcaaa cctaatgttt
4021 gaggaaggga aacacatgac accagtgtac acagcagcac tcaaggacga gctagtcaag
4081 actgagaaaa tctatggaaa gatcaagaag agactgctct ggggctctga cttgtccacc
4141 atgatccggt gcgctaggtc atttggtggg ctcatggacg agatgaaggc acactgcata
4201 tcactcccag tacgagttgg catgaatatg aatgaagatg gcccaataat attcgagaaa
4261 cattccagat acaaatatca ctatgatgca gactactctc gttgggattc aacacagcag
4321 agggcagtat tagcagcagc cttggaaatt atggtcagat tctctgcaga accacaattg
4381 gcacaaatag tcgctgagga tctactggcc cctagtgtag tagatgtagg agactttaaa
4441 attacaataa atgaagggct cccatctggc gtgccatgca cttctcaatg gaactccatt
4501 gcacactggc tgctaactct ctgtgctctg tctgaagtca ccaaactgtc ccccgacatt
4561 atacaagcaa actccatgtt ctcattttac ggtgatgacg agattgtcag caccgacata
4621 aaattggacc ctgaacagtt gaccgccaag ttgaaggagt acggcctgaa accaacccgc
4681 ccagacaaga ccgagggacc tctgatcatc ggtgaagatt tgaacggact cactttcctc
4741 cgaagaacgg tgactcgtga cccagctggc tggtttggaa aactggacca aagctcaatt
4801 ttgaggcaga tgtactggac tagaggacca aatcatgaag accccaatga gacaatgata
4861 ccccattccc agagacccat acagctcatg gcactgcttg gtgaagcctc tcttcacgga
4921 ccctctttct acagtagaat cagtaaattg gtcataactg aacttaaaga aggtgggatg
4981 gacttttacg tgccaaggca ggaacccatg ttcaggtgga tgaggttctc tgacttgagc
5041 acgtgggagg gcgatcgcaa tctggctccc agctttgtga atgaagatgg cgtcgagtga
5101 cgccaaccca tctgatgggt ccgcagccag ccttgtacca gaggtcaaca atgaggttat
5161 ggctttggag cccgttgttg gtgccgctat tgcggcacct gtagcgggcc aacaaaatgt
5221 aattgacccc tggattagaa ataattttgt acaagcccct ggtggggagt ttacagtgtc
5281 ccctagaaat gctccaggtg aaatactatg gagcgcaccc ctaggccctg acctaaatcc
5341 ctacctatcc cacttggcca gaatgtacaa tggttatgca ggtggttttg aagtgcaggt
5401 aattctcgcg gggaacgcgt tcaccgccgg gaagattata tttgcagcag tcccaccaaa
5461 ttttccaact gaaggcttaa gccctagcca ggtcactatg ttcccccaca taatagtaga
5521 tgttagacaa ttggaacctg tgctgatccc cttacccgat gttaggaata atttctatca
5581 ttataatcag tcaaatgact ccactattaa gttgatagca atgttgtaca caccacttag
5641 ggctaataat gctggggatg atgttttcac agtttcgtgc cgagttctca cgagaccatc
5701 ccccgatttt gatttcatat tcttagtacc acccacagtt gagtcaagaa ctaaaccatt
5761 ctctgtccca gttttaactg ttgaggagat gaccaactca agattcccca tccctttgga
5821 aaagttgttc acaggcccca gtagtgcatt tgttgttcaa ccacaaaacg gcagatgcac
5881 aactgatggc gtgctcctag gcaccaccca actttctcct gtcaacatct gcaccttcag
5941 aggggatgtc acccacatca caggtagtca caacttcact atgaatttgg cttctcaaaa
6001 ttggaacaac tatgacccaa cagaagaaat cccagccccc ctaggaactc cagattttgt
6061 ggggaagatc caaggcatgc tcacccaaac cacaaggaca gatggttcaa cacgcggcca
6121 caaagctaca gtgtacactg ggagcgccga ctttgctcca aaactgggta gggttcaatt
6181 tgaaactgac acaaaccatg actttgaagc taatcaaaac acaaagttca ccccagtcgg
6241 cgtcatccaa gatggtagca ccacccaccg aaacgaaccc caacagtggg tgctcccaag
6301 ttactcaggc agaaatactc acaatgtaca tttggccccc gctgtagccc ccacctttcc
6361 gggtgagcaa ctcctcttct tcaggtccac catgcccgga tgcagcgggt accccaatat
6421 ggatttggac tgtctgctcc cccaggaatg ggtgcagtac ttctaccaag aggcagcccc
6481 agcacaatct gatgtagctc tgctaagatt tgtgaatcca gatacaggta gggttttgtt
6541 tgagtgcaag cttcacaaat caggctatgt cacagtggct cacactggcc aacatgattt
6601 ggttatcccc cccaatggtt actttaggtt tgattcctgg gtcaaccagt tctacacgct
6661 tgcccccatg ggaaatggaa cggggcgtag acgtgcagta taatggctgg agctttcttt
6721 gctggattgg catctgatgt ccttggctct ggacttggtt cccttatcaa tgctggagct
6781 ggggccatca accaaaaagt tgagtttgaa aataatagaa aattgcaaca agcatccttc
6841 caatttagca gcaatttgca acaggcttcc tttcagcatg acaaagagat gctccaagca
6901 caaattgagg ccaccaaaaa gctacagcag gaaatgatga gagttaagca ggcaatgctc
6961 ctagagggtg ggttctctga gacagatgcg gcccgcgggg cagttaacgc ccccatgaca
7021 aaggctttgg actggagcgg gacaaggtac tgggctccag atgctagaat tacaacatac
7081 aatgcaggcc acttttccac ccctcaacca tcgggggcac tgccaggaag agctaatctt
7141 agagatgctg tccctgctcg tggatcatct accaaacctt ctaactcttc tactgccacc
7201 tctgtgtact caaatcaaac tatttcaacg agacttggtt ctacagctgg ttctggaacc
7261 agtgtctcga gcctcccgcc aactgcaagg actaggagct gggttgagga tcagaatagg
7321 aatttgtcac ctttcatgag gggggcccac aacatatcat ttgtcacccc accatctagc
7381 agatcctcta gccaaggcac agtctcaacc gtgcctaaag aaattttgga ctcctggact
7441 ggcgctttca acacgcgcag gcagcctctc ttcgctcaca ttcgtaagcg aggggagtca
7501 cgggtgtaat gtgaaaagac caaa
//