Typing tool
|
|
|
|
|
|
Typing tool
|
Complete norovirus genomes
| PQ209097 | GII.4 Sydney | |
|
|---|---|---|---|
| GII.P16 |
ORF1: 1..5094
ORF2: 5075..6697
ORF3: 6697..7503
LOCUS PQ209097 7528 bp RNA linear VRL 01-JAN-2025
DEFINITION Norovirus GII isolate Hu/GII.4 Sydney[P16]/Lincoln0054/2023/USA
nonstructural polyprotein (ORF1) gene, partial cds; and VP1 (ORF2)
and VP2 (ORF3) genes, complete cds.
ACCESSION PQ209097
VERSION PQ209097.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norovirus norwalkense.
REFERENCE 1 (bases 1 to 7528)
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JOURNAL Unpublished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 7528)
AUTHORS Tsaknaridis,L.J., Barclay,L., Montmayeur,A.M., Vinje,J. and
Chhabra,P.
TITLE Direct Submission
JOURNAL Submitted (20-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..7528
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="Hu/GII.4 Sydney[P16]/Lincoln0054/2023/USA"
/isolation_source="stool"
/host="Homo sapiens"
/db_xref="taxon:122929"
/geo_loc_name="USA"
/collection_date="08-May-2023"
/note="genotype: GII.4 Sydney[P16]"
gene <1..5094
/gene="ORF1"
CDS <1..5094
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="XEO40402.1"
/translation="MASNDASAAVACNNNNDKEKSSGEGLFTNMSSTLKKALGARPKQ
PAPRGEPQKPPRPPTPELVKRIPPPPPNGEEEDEPVIRYEVKSGISGLPELTTVPQPD
VANTAFSVPPLSMRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAAIS
MARVELAPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLNDS
WLSRRMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLIGK
IKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED
LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
KKEEANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRLST
KSASPDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAREV
ARKVASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELADTC
PLTLNCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK
AKRDFPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA
SGLLHERMDEFELQGPTITTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVKTM
EELKQAIRNVTIKRCRIIYGGSTYDLESDGKGKVLVEKVKNTSIQTNNELTGTLHHLK
HARIRYYVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEEAP
KSEDDEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKY
SIEEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLVTG
SEIRRRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSPSL
FITSTHVIPAGITEAFGVPIKQIQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEGTV
ATVLIKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDCG
CPYIYKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILGPG
GAPKLSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPRG
KPPRPSVLEAAKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFWNG
ETFTGKLADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDLST
MIRCARSFGGLMDEMKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWDST
QQRAVLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKIAINEGLPSGVPCTSQ
WNSIAHWLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLKEY
GLKPTRPDKTEGPLIISEDLDGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGPNH
EDPNETMIPHSQRPIQLMALLGEASLHGPSFYSRISKLVITELKEGGMDFYVPRQEPM
FRWMRFSDLSTWEGDRNLAPNFVNEDGVE"
mat_peptide <1..990
/gene="ORF1"
/product="p48"
mat_peptide 991..2088
/gene="ORF1"
/product="NTPase"
mat_peptide 2089..2619
/gene="ORF1"
/product="p22"
mat_peptide 2620..3018
/gene="ORF1"
/product="VPg"
mat_peptide 3019..3561
/gene="ORF1"
/product="Pro"
mat_peptide 3562..5091
/gene="ORF1"
/product="RdRp"
gene 5075..6697
/gene="ORF2"
CDS 5075..6697
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="XEO40403.1"
/translation="MKMASNDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPILTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHITGSHNFTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML
TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTNHDFEANQNTKFTPVGVIQDG
STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAV"
gene 6697..7503
/gene="ORF3"
CDS 6697..7503
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="XEO40404.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMRVKQAMLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARITTYNAGHFSTPQLSGALPGRANLRDAVPARGPSTKLS
NSPTATSVHSNQTVSTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMKGAYNI
SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRV"
ORIGIN
1 atggcgtcta acgacgcttc cgctgccgtt gcttgcaaca acaacaacga caaggaaaaa
61 tcttcaggtg aaggcttatt cacaaatatg tcttccacct taaagaaagc cctcggggct
121 aggcccaaac agcctgcccc gagaggtgaa ccacaaaagc ccccaagacc accaactccc
181 gagttggtca agaggatacc ccctcctcca cctaatggcg aagaagaaga tgaaccagtc
241 attaggtatg aggttaagag tgggatctct ggcctgcccg agctcacaac agtcccccaa
301 ccggacgtgg ccaacacagc atttagtgtt ccaccactga gcatgagaga aaacagggag
361 gccaaagaac cgctgacagg ggcaatacta gagatgtggg atggagagat ataccactat
421 ggcctgtacg tggagaaagg cttagtgttg ggtgtgcaca aaccacctgc agccataagc
481 atggcaagag tggagctggc gccgctgtca ttgtactggc gtgtggtgta cactccccaa
541 tacctcatct cccctgagac tctcaggagg ctcaacggtg aggcgttccc ttacaccgct
601 tttgacaaca actgctacgc tttttgctgc tgggtgttag acctcaatga ctcatggctt
661 agcaggagga tggtgcaacg aaccacgggc ttcttcaggc cttaccaaga gtggaacaga
721 aaacccttac ccaccatgga tgactccaaa ataaagaagg tagcaaatat attcctatgt
781 tcattgtcca cattattcac caggcccata aaagacctca taggaaagat taaaccatta
841 aacatattga acatcctggc aacgtgtgac tggacgtttg ccggaatagt ggagtctctg
901 atattgcttg ccgaactctt cggagttttc tggacacccc cagatgtgtc tgctatgatt
961 gctcccttac ttggggacta cgagttgcag gggccagaag acctcgccgt tgaactcgta
1021 cctgtggtaa tgggagggat tggtttggtg ttgggattca ccaaagagaa aattggcaaa
1081 atgttgtcct cagcagcatc aacactcaga gcttgtaaag atcttggtgc ctatggctta
1141 gagatactca aattggtcat gaagtggttt ttcccaaaga aagaagaggc caatgagcta
1201 gctatggtga gggccataga ggatgccgta ctagatcttg aggcaataga aaacaaccac
1261 atgacaaccc tgttgaaaga caaagacagc ttagcaacat acatgaaaac actggatatg
1321 gaggaggaga aagccaggag gttgtccaca aaatctgcat cccctgacat agttgggaca
1381 atcaacgccc tgctggctcg aatagcagca gccaggtcat tagtccacag ggccaaggaa
1441 gaactgtcta gcaggataag gccagtagtt gttatgatat ctggcaaacc aggaataggc
1501 aaaactcatc tagccagaga ggtggcaaga aaggtggcat ccactctcac aggggaccaa
1561 agagtcggac tcataccaag aaacggtgtg gaccactggg atgcatacaa aggcgagaga
1621 gtcgtgctgt gggacgacta tggcatgagt aaccccattc atgatgctct ccgcatacaa
1681 gaattggctg atacgtgtcc ccttacttta aattgcgaca gaattgaaaa taaggggaaa
1741 gtttttgaca gtgaagtcat aataattaca acaaacctcg ccaacccagc cccacttgac
1801 tatgtcaact ttgaggcctg ctccaggaga attgatttcc tggtgtacgc tgaggcacca
1861 gaagtagaaa aggcaaaacg ggattttcct ggtcagccag atatgtggaa ggacgccttc
1921 aagccggact tttcgcacat caagctacag cttgcacctc agggcggctt tgacaagaat
1981 ggcaacaccc ctcatgggaa aggagtgatg aagaccctca ctaccggttc tctgattgcc
2041 cgtgcatcag gcctactgca tgagaggatg gatgaatttg aactccaagg tcccacaatc
2101 accactttca atttcgaccg gaacagaatc acagcattca gacaattggc tgcagaaaac
2161 aagtatggac tggtggacac catgaaagtt ggcaatcaac taaaaggagt gaaaaccatg
2221 gaagaactca aacaagcaat caggaacgtg accatcaaga ggtgccggat catctacggt
2281 ggctccacgt atgaccttga gtctgatggc aagggcaaag ttttggtgga aaaggtcaag
2341 aacacctcta tacagaccaa caacgagttg accgggaccc tgcatcatct caagcatgcc
2401 cgaatcaggt actatgtcaa atgtgtgcaa gaggcagtct attccatcat acaaattgcc
2461 ggcgctgcgt ttgtcaccac gcgcattgca cgccgcatga acatacaaga gctctggtcg
2521 aagccacaat tagatcaaaa tgaatcagag actaaggaag aggcccccaa gtcagaagat
2581 gacgagttca tcatatcttc taaggatatc aaggaggaag gaaagaaggg caaaaacaaa
2641 actggccgtg gcaagaaaca caccgcattc tccagcaagg gcttaagcga tgaggagtat
2701 gacgagtaca agaggataag agaagagaga aatgggaagt actccataga agagtatctt
2761 caagacagag acaggtatta tgaggagctc gccattgcca aggccacgga agaagacttc
2821 tgtgaagagg aggagattaa aatccgtcag agaatttttc gtcccaccag gaaacaaaga
2881 aaggaagaaa gggccacact agggctggta actggctcag aaatcagaag aagaaaccct
2941 gatgacttca aacccaaagg gaagctgtgg gccgatgaca acagaagtgt tgactacaat
3001 gagaaactgg attttgaggc tcccccaagc atatggtcta ggattgtgag ctttggttct
3061 ggctggggct tctgggtatc accaagcctg ttcataacgt caactcatgt gatccctgca
3121 ggcataacag aagcatttgg agtccccatc aaacaaatcc agatccacaa atcaggtgaa
3181 ttttgccgat tcagattccc aaaaccaatc agaccagatg tgacaggaat gatcttggaa
3241 gaaggtgcgc ctgaaggcac cgtggcaact gtgctcatca aacgccccac cggagagctc
3301 atgcctcttg cagccagaat gggaacacac gcaaccatga agattcaagg ccgcatggtt
3361 ggtggacaga tgggtatgct gctcactgga tcaaatgcta aagggatgga tttgggaaca
3421 actcctggtg actgtggctg cccttacatc tataaaaggg gcaatgacta tatagtcatt
3481 ggggtgcaca ccgcagcagc ccgtggtgga aacaccgtca tctgtgccac acagggaagt
3541 gagggtgagg caactcttga gggtggagat gacaaaggaa catactgtgg ggcacccatt
3601 ctaggccctg gaggtgcacc aaaattgagc actaaaacca aattttggag gtcatcgaac
3661 acgccccttc caccggggac gtacgaacct gcctacctcg gtggccgtga cccgcgtgtt
3721 aagggtgggc cctccttaca acaggtaatg agagatcagt tgaagccatt cactgaaccc
3781 aggggcaaac ctccaagacc aagtgttttg gaagcagcca aacaaaccat tatcaatgtc
3841 cttgaacaaa ccctggatcc tccacaaaag tggacatacg cacaggcgtg tgcctcactt
3901 gacaaaacca cctccagcgg gcatccccac catgtccgaa agaatgaatt ctggaatggt
3961 gagaccttca ctggtaaatt ggcagaccaa gcatcaaaag caaacctaat gtttgaggaa
4021 gggaaacaca tgacaccagt gtacacagca gcactcaagg acgagctagt caagactgag
4081 aaaatctatg gaaagatcaa gaagagactg ctctggggct ctgacttgtc caccatgatc
4141 cggtgcgcta ggtcatttgg tgggctcatg gacgagatga aggcgcactg tatatcactc
4201 ccagtgcgag ttggcatgaa tatgaatgaa gatggcccaa taatatttga gaaacattct
4261 aggtacaaat atcactatga tgcagactat tctcgttggg attcaacaca gcaaagggca
4321 gtattagcag cagccttgga aattatggtc agattctctg cagaaccaca attggcacaa
4381 atagtcgctg aggatctact ggcccctagt gtagtagatg taggagactt taagattgca
4441 ataaatgaag ggctcccatc tggcgtgcca tgcacttctc aatggaactc cattgcacac
4501 tggctgctaa ctctctgtgc cttgtctgaa gtcaccaaac tgtcccctga cattatacaa
4561 gcaaattcca tgttctcatt ttacggtgat gacgagattg tcagcaccga cataaaatta
4621 gaccctgaac agttgaccgc caagttgaag gagtatggcc tgaaaccaac ccgcccagac
4681 aagactgagg ggcctctgat catcagtgaa gatttggacg gactcacttt cctccgaagg
4741 acggtgactc gtgacccagc tggctggttt ggaaaactgg accaaagttc gattttgagg
4801 cagatgtatt ggactagagg accaaatcat gaagacccca atgagacaat gataccccat
4861 tcccagaggc ccatacagct catggcactg cttggtgaag cctctcttca cggaccctct
4921 ttctacagta gaatcagtaa attggttata actgaactca aagaaggtgg gatggacttt
4981 tacgtgccaa ggcaggaacc catgttcagg tggatgaggt tctctgactt gagcacgtgg
5041 gagggcgatc gcaatctggc tcccaacttt gtgaatgaag atggcgtcga atgacgccaa
5101 cccatctgat gggtccgcag ccaacctcgt accagaggtc aacaatgagg ttatggcttt
5161 ggagcccgtt gttggtgccg ctattgcggc acccgtagcg ggccaacaaa atgtaattga
5221 cccctggatt agaaataact ttgtacaagc ccctggtggg gagtttacag tatcccctag
5281 aaatgctcca ggtgaaatac tgtggagcgc acccttaggc cctgatctaa atccctacct
5341 atcccatttg gccagaatgt acaatggtta tgcaggtggt ttcgaagtgc aggtaattct
5401 cgcggggaac gcgttcaccg cagggaagat tatatttgca gcagtcccac caaattttcc
5461 aactgaaggc ttaagcccta gccaggttac catgtttccc catataatag tagatgttag
5521 acaattggaa cctgtgctga tccccttacc cgatgttagg aataacttct atcattacaa
5581 tcagtcaaat gactccacta tcaagttgat agcaatgttg tacacaccac ttagggctaa
5641 taatgctggg gatgatgttt tcacagtttc gtgccgagtt ctcacgagac catcccccga
5701 ttttgatttt atattcttag taccacccac agttgagtca agaactaaac cattctctgt
5761 cccaatttta actgttgagg agatgaccaa ttcaagattc cccatccctt tggaaaagtt
5821 gttcacaggc cccagcagtg catttgttgt tcaaccacaa aacggcagat gcacaactga
5881 tggcgtgctc ctaggtacca cccaactctc tcctgtcaac atctgcacct tcagggggga
5941 cgtcacccat atcacaggta gtcacaactt cactatgaat ttggcttctc aaaattggaa
6001 caactatgac ccaacagaag aaatcccagc ccccctagga actccagatt ttgtggggaa
6061 gatccaaggc atgctcaccc aaaccacaag gacagatggt tcaacacgcg gccacaaagc
6121 tacagtgtac actgggagcg ccgactttgc tccaaaactg ggtagagttc aatttgaaac
6181 tgacacaaac catgactttg aagccaatca gaacacaaag ttcaccccag taggtgtcat
6241 tcaagatggt agcaccaccc accgaaacga accccaacag tgggtgctcc caagttactc
6301 aggcagaaat actcacaatg tacatttggc ccccgctgta gcccccacct ttccgggtga
6361 acaactcctc ttctttagat ccaccatgcc cggatgcagc gggtacccca acatggattt
6421 ggactgtctg ctcccccagg aatgggtgca gtacttctac caagaggcag ccccagcaca
6481 atctgatgtg gctctgctaa gatttgtaaa tccagacaca ggtagggttc tgtttgagtg
6541 caagcttcac aaatcaggct atgtcacagt ggctcacact ggtcaacatg atttggttat
6601 cccccccaat ggttacttca ggtttgattc ctgggtcaac cagttctaca cgcttgcccc
6661 catgggaaat ggaacggggc gtagacgtgc agtataatgg ctggagcctt ctttgctgga
6721 ttggcatctg atgtccttgg ctccggactt ggttctctta tcaatgctgg ggctggggcc
6781 atcaaccaaa aagttgagtt tgaaaataac agaaaattgc aacaagcatc cttccaattt
6841 agcagcaatt tgcaacaggc ttcctttcaa catgataaag agatgctcca agcacaaatt
6901 gaggccacca aaaagctaca gcaggaaatg atgagagtta agcaggcaat gctcttagag
6961 ggtgggttct ctgagacaga tgcagcccgc ggggcaatta acgcccccat gacaaaggct
7021 ttggactgga gcgggacaag gtactgggct ccagatgcta gaattacaac atacaatgca
7081 ggccactttt ccacccctca actatcgggg gcactgccag gaagagctaa tctcagggat
7141 gctgtccctg ctcgtgggcc ctccaccaaa ctttctaact ctcctactgc cacctctgtg
7201 cactcaaacc aaactgtttc aacgagactt ggttctacag ctggttctgg aaccagcgtc
7261 tcgagcctcc cgtcaactgc aagaactagg agctgggttg aggatcagaa taggaatttg
7321 tcacctttca tgaagggggc ctacaacata tcatttgtca ccccaccatc tagcagatcc
7381 tctagccagg gcacagtctc aaccgtgccc aaagaaattt tggactcctg gactggcgct
7441 ttcaacacgc gcaggcagcc tctcttcgct cacattcgta agcgagggga gtcacgggtg
7501 taatgtgaaa agacaaaatt gattatct
//