Typing tool
|
|
|
|
|
|
Typing tool
|
Complete norovirus genomes
| PQ218785 | GII.4 Sydney | |
|
|---|---|---|---|
| GII.P16 |
ORF1: 1..5098
ORF2: 5079..6701
ORF3: 6701..7507
LOCUS PQ218785 7560 bp RNA linear VRL 01-JAN-2025
DEFINITION Norovirus GII isolate Hu/GII.4 Sydney[P16]/Bernalillo0012/2023/USA
nonstructural polyprotein (ORF1) gene, partial cds; and VP1 (ORF2)
and VP2 (ORF3) genes, complete cds.
ACCESSION PQ218785
VERSION PQ218785.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norovirus norwalkense.
REFERENCE 1 (bases 1 to 7560)
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JOURNAL Unpublished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 7560)
AUTHORS Nottke,S., Barclay,L., Montmayeur,A.M., Vinje,J. and Chhabra,P.
TITLE Direct Submission
JOURNAL Submitted (22-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. 11.0; SPAdes v. 3.5
Sequencing Technology :: Sanger dideoxy sequencing; Illumina
##Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..7560
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="Hu/GII.4 Sydney[P16]/Bernalillo0012/2023/USA"
/isolation_source="stool"
/host="Homo sapiens"
/db_xref="taxon:122929"
/geo_loc_name="USA"
/collection_date="08-Nov-2023"
/note="genotype: GII.4 Sydney[P16]"
gene <1..5098
/gene="ORF1"
CDS <1..5098
/gene="ORF1"
/codon_start=2
/product="nonstructural polyprotein"
/protein_id="XER81182.1"
/translation="KMASNDASAAVACNNNNDKEKSSGEGLFTNMSSTLKKALGARPK
QPAPRGEPQKPPRPPTPELVKRIPPPPPNGEEEDEPVIRYEVKSGISGLPELTTVPQP
DVANTAFSVPPLSMRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAAI
SMARVELAPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLND
SWLSRRMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLIG
KIKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPE
DLAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFF
PKKEEANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRLS
TKSASPDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLARE
VARKVASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELADT
CPLTLNCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVE
KAKRDFPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIAR
ASGLLHERMDEFELQGPTITTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVKT
MEELKQAIRNVTIKRCRIIYGGSTYDLESDGKGKVLVEKVKNTSIQTNNELTGALHHL
KHARIRYYVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEEA
PKSEDDEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGK
YSIEEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLVT
GSEIRRRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSPS
LFITSTHVIPAGITEAFGVPIKQIQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEGT
VATVLIKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDC
GCPYIYKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILGP
GGAPKLSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPR
GKPPRPSVLEAAKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFWN
GETFTGKLADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDLS
TMIRCARSFGGLMDEMKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWDS
TQQRAVLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKVAINEGLPSGVPCTS
QWNSIAHWLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLKE
YGLKPTRPDKTEGPLIISEDLDGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGPN
HEDPNETMIPHSQRPIQLMALLGEASLHGPSFYSRISKLVITELKEGGMDFYVPRQEP
MFRWMRFSDLSTWEGDRNLAPNFVNEDGVE"
mat_peptide <1..994
/gene="ORF1"
/product="p48"
mat_peptide 995..2092
/gene="ORF1"
/product="NTPase"
mat_peptide 2093..2623
/gene="ORF1"
/product="p22"
mat_peptide 2624..3022
/gene="ORF1"
/product="VPg"
mat_peptide 3023..3565
/gene="ORF1"
/product="Pro"
mat_peptide 3566..5095
/gene="ORF1"
/product="RdRp"
gene 5079..6701
/gene="ORF2"
CDS 5079..6701
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="XER81183.1"
/translation="MKMASNDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPILTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHITGSHNFTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML
TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTNHDFEANQNTKFTPVGVIQDG
STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAV"
gene 6701..7507
/gene="ORF3"
CDS 6701..7507
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="XER81184.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMRVKQAMLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARITTYNAGHFSTPQPSGALPGRANLRDAVPARGPSTKPS
NSPTATSVHSNQTVSTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMKGAHNI
SFVTPPPSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRV"
ORIGIN
1 gaagatggcg tctaacgacg cttccgctgc cgttgcttgc aacaacaaca acgacaagga
61 aaaatcttca ggtgaaggct tattcacaaa tatgtcttcc accttaaaga aagccctcgg
121 ggctaggccc aaacagcctg ccccgagagg tgaaccacaa aagcccccaa gaccaccaac
181 tcccgagttg gttaagagga taccccctcc tccacctaat ggcgaagaag aagacgaacc
241 agtcattagg tatgaggtta agagtgggat ctctggcctg cccgagctca caacagtccc
301 ccaaccggac gtggccaaca cagcatttag tgttccacca ctgagcatga gagaaaacag
361 ggaggccaaa gaaccgctga caggggcaat attagagatg tgggatggag agatatacca
421 ctatggcctg tacgtggaga aaggcttagt gttgggtgtg cacaaaccac ctgcagccat
481 aagcatggca agagtggagc tggcgccgct gtcattgtac tggcgtgtgg tgtacactcc
541 ccaatacctc atctcccctg agactctcag gaggctcaac ggtgaggcgt ttccttacac
601 cgcttttgac aacaactgct acgctttttg ctgctgggtg ttagacctca atgactcatg
661 gcttagcagg aggatggtgc aacgaaccac gggcttcttc aggccttacc aagagtggaa
721 cagaaaaccc ttacccacca tggatgactc caaaataaag aaggtagcaa atatatttct
781 gtgctcattg tccacattat tcaccaggcc cataaaagac ctcataggaa aaattaaacc
841 attaaacata ttgaacatcc tggcaacgtg tgactggacg tttgccggaa tagtggagtc
901 tctgatattg cttgccgaac tcttcggagt tttctggaca cccccagatg tgtctgctat
961 gattgctccc ttacttgggg actacgagtt gcaggggcca gaagacctcg ccgttgaact
1021 cgtacctgtg gtaatgggag ggattggttt ggtgttggga ttcaccaaag agaaaattgg
1081 caaaatgttg tcctcagcag catcaacact cagagcttgt aaagatcttg gtgcctatgg
1141 cttagagata ctcaaattgg tcatgaagtg gtttttccca aagaaagaag aggccaatga
1201 gctagctatg gtgagggcca tagaggatgc cgtactggat cttgaggcaa tagaaaacaa
1261 ccacatgaca accctgttga aagacaaaga cagcttagca acatacatga aaacactgga
1321 catggaggag gagaaagcca gaaggttgtc cacaaaatct gcatcccctg acatagttgg
1381 gacaatcaac gccctgctgg ctcgaatagc agcagccagg tcattagtcc acagggccaa
1441 ggaagaactg tctagcagga taaggccagt agttgttatg atatctggca aaccaggaat
1501 aggcaaaact catctagcca gagaggtggc aagaaaggtg gcatccactc tcacagggga
1561 ccaaagagtc ggactcatac caagaaacgg tgtggaccac tgggatgcat acaaaggtga
1621 gagagtcgtg ctgtgggacg actatggcat gagtaacccc attcatgatg ctctccgcat
1681 acaagaattg gctgatacgt gtcccctcac cttaaattgc gacagaattg aaaataaggg
1741 gaaagttttt gacagtgaag tcataataat tacaacaaac ctcgccaacc cagccccact
1801 tgattatgtc aactttgagg cctgctccag gagaattgat ttcctggtgt acgctgaggc
1861 accagaagta gaaaaggcaa aacgggattt tcctggtcag ccagatatgt ggaaggacgc
1921 cttcaagccg gacttttcgc acatcaagct acagcttgca cctcagggcg gctttgacaa
1981 gaatggcaac acccctcatg ggaaaggagt gatgaagacc ctcactaccg gttccctgat
2041 tgcccgtgca tcaggcctac tgcatgagag gatggatgaa tttgaactcc aaggtcccac
2101 gatcaccact ttcaatttcg accggaacag aatcacagca ttcagacaat tggctgcaga
2161 aaacaagtat gggctggtgg acaccatgaa agttggcaat caactaaaag gagtgaaaac
2221 catggaagaa ctcaaacaag caatcaggaa tgtgaccatc aagaggtgcc ggataatcta
2281 cggtggctcc acgtatgacc ttgagtctga tggcaagggc aaagttttgg tggaaaaggt
2341 caagaacacc tctatacaga ccaacaacga gttgaccggg gccctgcatc atctcaagca
2401 tgcccgaatc aggtactatg tcaaatgtgt gcaagaggca gtctattcca tcatacaaat
2461 tgccggcgct gcgtttgtca ccacgcgcat tgcacgccgc atgaacatac aagagctctg
2521 gtcgaagcca caattagacc aaaatgaatc agagactaag gaagaggccc ccaagtcaga
2581 agatgacgag ttcatcatat cttctaagga tatcaaggag gaaggaaaga agggcaaaaa
2641 caagactggc cgtggcaaga aacacaccgc attctccagc aagggcttaa gcgatgagga
2701 gtatgacgag tacaagagga taagagaaga gagaaatggg aagtactcca tagaagagta
2761 tcttcaagac agagacaggt attatgagga gctcgccatt gccaaggcca cggaagaaga
2821 cttctgtgaa gaggaggaga tcaaaatccg tcagaggatt tttcgtccca ccaggaaaca
2881 aagaaaggaa gagagggcca cactagggct ggtaactggc tcagaaatca gaagaagaaa
2941 ccctgatgat ttcaaaccca aagggaagct gtgggccgat gacaacagaa gcgttgatta
3001 caatgagaaa ctggattttg aggctccccc aagcatatgg tctaggattg tgagctttgg
3061 ttctggttgg ggcttctggg tatcaccaag cctgttcata acgtcaactc atgtgatccc
3121 tgcaggcata acagaagcat ttggagtccc catcaaacaa atccagatcc acaaatcagg
3181 tgaattttgc cgattcagat tcccaaaacc aatcagacca gatgtgacag gaatgatctt
3241 ggaagaaggt gcgcctgaag gcaccgtggc aactgtgctc atcaaacgcc ccaccggaga
3301 gctcatgcct cttgcagcca gaatgggaac acacgcaacc atgaagattc aaggccgcat
3361 ggttggtgga cagatgggta tgctgctcac tgggtcaaat gctaaaggga tggatttggg
3421 aacaactcct ggtgactgtg gctgccctta catctataaa aggggcaatg actatatagt
3481 cattggggtg cacaccgcag cagcccgtgg tggaaacacc gtcatctgtg ccacacaggg
3541 aagtgagggt gaggcaactc ttgagggtgg agatgacaaa ggaacatact gtggggcacc
3601 cattctaggc cctggaggtg caccaaaatt gagcactaaa accaaatttt ggaggtcatc
3661 gaacacgccc cttccaccgg ggacgtacga acctgcctac ctcggtggcc gtgacccgcg
3721 tgttaagggt gggccctcct tacaacaggt gatgagagat cagttgaagc cattcactga
3781 acccaggggc aaacctccaa gaccaagtgt tttggaagca gccaaacaaa ccattatcaa
3841 tgtccttgaa caaaccctgg atcctccaca aaagtggaca tacgcacagg cgtgtgcctc
3901 acttgacaaa accacctcca gcgggcaccc ccaccatgtc cgaaagaatg aattctggaa
3961 tggtgagacc ttcactggta aattggcaga ccaagcatca aaagcaaacc taatgtttga
4021 ggaagggaaa cacatgacac cagtgtacac agcagcactc aaggacgagc tagtcaagac
4081 tgagaaaatc tatggaaaga tcaagaagag actgctctgg ggctctgact tgtccaccat
4141 gatccggtgc gctaggtcat ttggtgggct catggacgag atgaaggcac actgtatatc
4201 actcccagtg cgagttggca tgaatatgaa tgaagatggc ccaataatat ttgagaaaca
4261 ttctaggtac aaatatcact atgatgcaga ctactctcgt tgggattcaa cacagcaaag
4321 ggcagtatta gcagcagcct tggaaattat ggtcagattc tctgcagaac cacaattggc
4381 acaaatagtc gctgaggatc tactggcccc tagtgtagta gatgtaggag actttaaagt
4441 tgcaataaat gaagggctcc catctggcgt gccatgcact tctcaatgga actccattgc
4501 acactggctg ctaactctct gtgccttgtc tgaagtcacc aaactgtccc ctgatattat
4561 acaagcaaat tccatgtttt cattttacgg tgatgacgag attgtcagca ccgacataaa
4621 attagaccct gaacagttga ccgccaagtt gaaggagtac ggtctgaaac caacccgccc
4681 agacaagact gagggacctc tgatcatcag tgaagatttg gacggactca ctttcctccg
4741 aaggacggtg actcgtgacc cagctggctg gtttggaaaa ctggaccaaa gttcaatttt
4801 gaggcagatg tattggacta gaggaccaaa tcatgaagac cccaatgaga caatgatacc
4861 ccattcccag aggcccatac agctcatggc actgcttggt gaagcttctc ttcacggacc
4921 ctctttctac agtagaatca gtaaattggt tataactgaa ctcaaagaag gtgggatgga
4981 cttttacgtg ccaaggcagg aacccatgtt caggtggatg aggttctctg acttgagcac
5041 gtgggagggc gatcgcaatc tggctcccaa ctttgtgaat gaagatggcg tcgaatgacg
5101 ccaacccatc tgatgggtcc gcagccaacc tcgtaccaga ggtcaacaat gaggttatgg
5161 ctttggagcc cgttgttggt gccgctattg cggcacccgt agcgggccaa caaaatgtaa
5221 ttgacccctg gattagaaat aattttgtac aagcccctgg tggggagttc acagtatccc
5281 ctagaaatgc tccaggtgaa atactgtgga gcgcaccctt aggccctgac ctaaatccct
5341 acctatccca tttggccaga atgtacaatg gttatgcagg tggtttcgaa gtgcaggtaa
5401 ttctcgcggg gaacgcgttc accgcaggga agattatatt tgcagcagtc ccaccaaatt
5461 ttccaactga aggcttaagc cctagccagg ttaccatgtt tccccatata atagtagatg
5521 ttagacaatt ggaacctgtg ctgatcccct tacccgatgt taggaataac ttctatcatt
5581 acaatcagtc aaatgactcc actatcaagt tgatagcaat gttgtacaca ccacttaggg
5641 ctaataatgc tggggatgat gttttcacag tttcgtgccg agttctcacg agaccatccc
5701 ccgattttga ttttatattc ttagtaccac ccacagttga gtcaagaact aaaccattct
5761 ctgtcccaat tttaactgtt gaggagatga ccaattcaag attccccatc cctttggaaa
5821 agttgttcac aggccccagc agtgcatttg ttgttcaacc acaaaacggc agatgcacaa
5881 ctgatggcgt gctcctaggt accacccaac tttctcctgt caatatctgc accttcagag
5941 gggacgtcac ccatatcaca ggtagtcaca acttcactat gaatttggct tctcaaaatt
6001 ggaacaacta tgacccaaca gaagaaatcc cagcccccct aggaactcca gattttgtgg
6061 ggaagatcca aggcatgctc acccaaacca caaggacaga tggttcaaca cgcggccaca
6121 aagctacagt gtacactggg agcgccgact ttgctccaaa actgggtaga gttcaatttg
6181 aaactgacac aaaccatgac tttgaagcca atcagaacac aaagttcacc ccagtcggtg
6241 tcattcaaga tggtagcacc acccaccgaa acgaacccca acagtgggtg ctcccaagtt
6301 actcaggcag aaatactcac aatgtacatt tggcccccgc tgtagccccc acctttccgg
6361 gtgagcaact cctcttcttt agatccacca tgcccggatg cagcgggtac cccaacatgg
6421 acttggactg tctgctcccc caggaatggg tgcagtactt ctatcaagag gcagccccag
6481 cacaatctga tgtggctctg ctaagatttg taaacccaga cacaggtagg gttctgtttg
6541 agtgcaagct tcacaaatca ggctatgtta cagtggctca cactggtcaa catgatttag
6601 ttatcccccc caatggttac tttaggtttg attcctgggt caaccagttc tacacgcttg
6661 cccccatggg aaatggaacg gggcgtagac gtgcagtata atggctggag ctttctttgc
6721 tggattggca tctgatgtcc ttggctccgg acttggttct cttatcaatg ctggggctgg
6781 ggccatcaac caaaaagttg agtttgaaaa taacagaaaa ttgcaacaag catccttcca
6841 atttagcagc aatttgcaac aggcttcctt tcaacatgat aaagagatgc tccaagcaca
6901 aattgaggcc accaaaaagc tacagcagga aatgatgaga gttaagcagg caatgctctt
6961 agagggtggg ttctctgaga cagatgcagc ccgcggggca attaacgccc ccatgacaaa
7021 ggctttggac tggagcggga caaggtactg ggctccagat gctagaatta caacatacaa
7081 tgcaggccac ttttccaccc ctcaaccatc gggggcactg ccaggaagag ctaatctcag
7141 ggatgctgtc cctgctcgtg ggccctccac caaaccttct aactctccta ctgccacctc
7201 tgtgcactca aaccaaactg tttcaacgag acttggttct acagctggtt ctggaaccag
7261 tgtctcgagc ctcccgtcaa ctgcaagaac taggagctgg gttgaggatc agaataggaa
7321 tttgtcacct tttatgaagg gggcccacaa catatcattt gtcaccccac cacctagcag
7381 atcctctagc cagggcacag tctcaaccgt gcccaaagaa attttggact cctggactgg
7441 cgctttcaac acgcgcaggc agcctctctt cgctcacatt cgtaagcgag gggagtcacg
7501 ggtgtaatgt gaaaagacaa aattgattat ctttttcttt tctttagtgt cttttaaaaa
//