Typing tool
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Typing tool
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Complete norovirus genomes
| OR065090 | GII.4 Sydney | |
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| GII.P31 |
ORF1: 1..5100
ORF2: 5081..6703
ORF3: 6703..7509
LOCUS OR065090 7559 bp RNA linear VRL 06-OCT-2023
DEFINITION Norovirus GII isolate GII/Hu/US/2016/GII.4Sydney[P31]/NIH29.10
nonstructural polyprotein (ORF1), VP1 (ORF2), and VP2 (ORF3) genes,
complete cds.
ACCESSION OR065090
VERSION OR065090.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norovirus norwalkense.
REFERENCE 1 (bases 1 to 7559)
AUTHORS Chaimongkol,N., Dabilla,N., Tohma,K., Matsushima,Y., Behrle
Yardley,A., Levenson,E.A., Johnson,J.A., Ahorrio,C., Oler,A.J.,
Kim,D.Y., Souza,M., Sosnovtsev,S.V., Parra,G.I. and Green,K.Y.
TITLE Norovirus Evolves as One or More Distinct Clonal Populations in
Immunocompromised Hosts
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 7559)
AUTHORS Chaimongkol,N., Dabilla,N., Sosnovtsev,S.V. and Green,K.Y.
TITLE Direct Submission
JOURNAL Submitted (26-MAY-2023) LID, NIAID, 50 South Drive/R6318, Bethesda,
MD 20892, USA
COMMENT ##Assembly-Data-START##
Assembly Method :: HIVE Hexagon/Heptagon v. 2
Sequencing Technology :: Illumina
##Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..7559
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="GII/Hu/US/2016/GII.4Sydney[P31]/NIH29.10"
/isolation_source="feces"
/host="Homo sapiens"
/db_xref="taxon:122929"
/geo_loc_name="USA"
/collection_date="Jan-2016"
/note="genotype: GII.4"
gene 1..5100
/gene="ORF1"
CDS 1..5100
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="WIA95134.1"
/translation="MKMASNDASAAAVANSNNDIAKSSSDGVFSNMAVTFKRALGARP
KQPPPKEIPPRPPRPPTPELVKKIPPPPPNGEDELVVSYSAKDGVSGLPELTTVRQPE
ETNTAFSVPPLNLRESRDAKEPLTGTIIEMWDGEIYHYGLYVDRGLILGVHKPPAAIS
LAKVELAPLSLFWRPVYTPQYLISPDTLRRLHGESFPYTAFDNNCYAFCCWVLDLNDS
WLNRRMIQRTTGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCTLSSLFTRPIKDIIGK
LKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED
LAVELVPIVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
KKEEANELALVRSIEDAVLDLEAIENNHMTALLKDKDSLATYMRTLDLEEEKARKLST
KSASPDIVGTVNALLARIAAARSLVHRAKEEISSRPRPVVMMISGKPGIGKTHLAREL
AKKIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC
PLTLNCDRIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK
AKRDFPGQPDMWKNAFSSDFSHIKLTLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA
SGLLHERLDEYELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGKQLKDVKTM
SDLKQALKNIAIKKCQIVYNGGTYTLEADGKGSVKVDKVQSATVQTNNELAGALHHLR
CARIRYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQNLWSKPQVEDTEEMANKDGC
LKPKDDEEFVVSSDDIKTEGKKGKNKSGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
KYSIEEYLQDRDRYYEEVAIARATEEDFCEEEEAKIRQRIFRPTKKQRKEERASLGLV
TGSEIRKRNPEDFKPKGKLWADDDRSVDYNEKLNFEAPPSIWSRIVNFGSGWGFWVSP
SLFITSTHVIPQGAKEFFGVPIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG
TVTTLLIKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDSKGTYCGAPILG
PGSAPNLSTKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP
RGKPPRPNVLEAAKKTIINVLEQTIDPPQKWSFAQACASLDKTTSSGHPYHMRKNDCW
NGESFTGNLADQASKANLMFEEGKNMTPIYTGALKDELVKTDKVYGKVKKRLLWGSDL
ATMIRCARAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFEKHSRYRYHYDADYSRWD
STQQRDVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVMDVGDFQISISEGLPSGVPCT
SQWNSIAHWLLTLCALSEVTDLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLK
EYGLKPTRPDKTEGPLVISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP
NHGDPFETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQE
PMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE"
mat_peptide 1..990
/gene="ORF1"
/product="p48"
mat_peptide 991..2088
/gene="ORF1"
/product="NTPase"
mat_peptide 2089..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="WIA95135.1"
/translation="MKMASSDASPSDGPAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTECLSPSQVTMFPHIITDVRQLEPVLIPLPD
VRNNFYHYNQSNEPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVGEMTNSRFPIPLEKLFTGPSGAFDVQPQNGRCTTDGVLLGTT
QLSPVNICAFRGDVTHTTGSHNYTMNLASQNWSVYDPAEEIPAPLGTPDFVGKIQGVL
TQTTRTNGSTRGHKATVLTGSAEFAPKLGRVQFATDTNHDFEDNQNTKFTPVGVIQDG
NTTPQNEPQQWVLPSYSGRSTPNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAQ"
gene 6703..7509
/gene="ORF3"
CDS 6703..7509
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="WIA95136.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSGTDAARGAIN
APMTKVLDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRDAVPARGSSSKSS
NSSTATSVYSNQTTSTRLGSTAGSGTSVSSFPPTARTRSWVEDQSRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTHRQPLFAHIRKRGESRV"
ORIGIN
1 atgaagatgg cgtctaacga cgcttccgct gccgctgttg ccaacagcaa caacgacatc
61 gcaaaatctt caagtgacgg tgtgttttct aacatggctg tcacttttaa gcgggccctc
121 ggggcgcggc ctaaacagcc gcccccgaag gaaataccac ccagaccccc gcgaccaccc
181 acaccagaat tggtcaaaaa gatccctcct cccccaccca acggggagga tgaactagtg
241 gtctcttaca gcgccaaaga tggcgtttcc ggactgcctg agctcaccac tgtcagacaa
301 ccggaagaaa ccaacacggc gttcagtgtc cccccactca atctaaggga gagcagggac
361 gccaaggagc cactaactgg aacaatcatt gaaatgtggg atggagaaat ctaccattac
421 ggcctgtatg tggatcgagg tcttatactt ggtgtgcaca agccaccggc agccattagc
481 cttgccaagg ttgagctagc accgctctct ttgttctgga gacctgtata caccccccag
541 tatctcatct ctccagacac tcttaggagg ttacatggag agtcattccc ctacactgca
601 tttgacaaca attgttacgc cttttgttgt tgggtattag acctaaacga ctcatggcta
661 aacaggagaa tgattcagag aacaacaggc ttcttcaggc cgtaccaaga ttggaacagg
721 aaacccctcc ccactatgga tgactccaaa ttaaagaagg tagccaatat attcttgtgc
781 actttgtctt cactattcac cagacccatt aaggacataa tagggaagtt gaaacctctc
841 aacatcctta acattctggc tacatgtgat tggaccttcg caggcatagt ggaatcctta
901 atactcttgg cagaactctt tggagttttc tggacgcccc cagatgtgtc tgcgatgatt
961 gcccccttgc taggtgatta tgaactgcaa ggacctgagg accttgcagt ggaactggtc
1021 ccaatagtga tgggggggat aggtttggtg ttaggattta ccaaagagaa aatcggaaag
1081 atgctatcat ccgctgcatc cactctaaga gcttgtaaag accttggtgc atacggactg
1141 gaaattttaa aattggtcat gaagtggttc ttcccaaaga aagaggaagc aaatgaactg
1201 gctttggtga gatccatcga ggatgcagta ctagacctcg aggcaattga aaacaatcac
1261 atgaccgccc tgctcaaaga caaagacagc ttggcaacct acatgagaac ccttgacctt
1321 gaggaggaga aagccagaaa actctcaacc aaatctgctt cacccgatat tgtgggcaca
1381 gtcaacgctc ttctggcaag aatcgctgct gcacgctccc tagtgcatcg ggcgaaagaa
1441 gagatctcca gcaggccgag acctgtcgtt atgatgatat cgggaaaacc agggataggg
1501 aaaactcacc ttgccaggga gctggccaag aagatcgcgg cctccctcac aggggaccag
1561 cgtgtaggtc ttatcccacg caatggtgtc gaccactggg acgcatacaa gggcgaaaga
1621 gttgtcctat gggacgacta tggaatgagc aaccccatcc atgatgccct caggttgcag
1681 gagcttgctg acacttgccc cctcacgcta aattgtgaca gaattgagaa taaagggaaa
1741 gtctttgaca gtgatgccat aattatcacc accaatctgg ccaacccagc accactggat
1801 tatgtcaact ttgaagcgtg ctcgagacgc attgatttcc tcgtgtacgc agaagcccct
1861 gaggtggaga aggcaaagcg cgacttccca ggtcaacctg acatgtggaa gaacgctttc
1921 agttctgact tctcacacat aaaactgaca ttggctccac aaggtggttt tgacaagaac
1981 ggcaacaccc cgcatggaaa aggggtcatg aagaccctca ccactggctc cctcatcgcc
2041 cgagcatcag ggttactcca tgagaggcta gatgaatatg aactgcaagg cccagccctc
2101 accactttca actttgaccg caacaaggta cttgccttta gacagcttgc tgctgaaaac
2161 aagtatgggc tgatggacac aatgagagtt ggaaaacagc tcaaggatgt caagaccatg
2221 tcagacctca aacaagcact caagaacatc gcgatcaaga agtgccagat agtgtacaat
2281 ggtggcacct acacacttga ggctgatggc aagggtagtg tgaaagttga caaagtgcaa
2341 agtgccactg tgcagaccaa caatgaacta gccggtgccc tacaccacct aaggtgcgct
2401 agaatcagat actatgttaa gtgcgtccag gaggcactgt attccatcat ccagatcgct
2461 ggggctgcat tcgtcaccac gcgcatcgct aagcgcatga atatacagaa tctctggtcc
2521 aagccacagg tggaagacac agaagagatg gccaacaaag atggttgcct aaaacccaaa
2581 gatgatgaag agtttgtcgt ctcatccgac gacatcaaaa ctgagggcaa gaaagggaag
2641 aacaagtccg gccgtggcaa gaagcacaca gccttttcaa gtaaagggct cagtgatgag
2701 gagtacgatg agtacaagag aatcagagaa gaaaggaatg gcaagtactc catagaagag
2761 taccttcagg acagagacag gtactacgag gaggtggcca ttgccagggc aaccgaagag
2821 gacttctgtg aagaagaaga ggccaaaatt cggcagagaa ttttcagacc aacaaagaaa
2881 caacgcaaag aagagagggc ctctctcggc ttagtcacag gctctgaaat caggaagaga
2941 aacccagaag acttcaagcc caaaggaaag ctgtgggctg atgatgacag aagtgttgac
3001 tacaatgaga aactcaactt tgaggcccca ccaagcatct ggtcgcggat agtcaacttt
3061 ggttcaggct ggggcttctg ggtctccccc agtctgttta taacatcaac ccatgtcata
3121 ccccaaggtg caaaagagtt cttcggagtc cctatcaagc aaatccagat acacaagtca
3181 ggtgaattct gccggttgag attcccaaag ccaatcagaa ctgatgtgac gggcatgatt
3241 ctagaagaag gtgcgcccga ggggaccgtg accacactgc tcatcaagag accaactgga
3301 gaactcatgc ctctggcagc cagaatgggg acccatgcaa ccatgaaaat tcaggggcgc
3361 acagttggag ggcaaatggg tatgctcctg acagggtcca atgccaagag tatggaccta
3421 ggcacaacac caggcgactg cggctgcccc tacatctaca agagggggaa tgactacgtg
3481 gtcataggag tccatacggc cgctgcccgt ggaggaaaca ctgtcatatg tgccacccag
3541 gggagtgagg gagaagccac acttgaagga ggtgacagta aagggacgta ctgtggcgca
3601 ccaatcttgg gcccagggag cgctccgaat ctcagtacca agactaagtt ttggagatca
3661 tccacaacac cactcccacc cggcacctac gaaccagcct acctcggtgg caaagaccct
3721 agagtcaaag gtggcccttc attgcaacaa gttatgaggg accagctgaa gccattcaca
3781 gaacccagag gcaaaccacc aagaccaaat gtgttggaag ctgccaagaa aaccatcatc
3841 aatgtccttg agcaaacaat tgatccaccc caaaaatggt catttgcgca agcttgcgca
3901 tcccttgaca aaaccacctc cagcggccac ccgtaccaca tgcggaaaaa cgactgttgg
3961 aatggggagt ccttcacagg aaatttagct gatcaagcct ccaaggccaa cctaatgttt
4021 gaagagggaa agaacatgac tccaatctac acaggtgcac ttaaagatga gttggtaaag
4081 accgataaag tttatggtaa ggtcaagaag aggcttctgt ggggttcaga tctggcgacc
4141 atgatacggt gcgcccgagc ttttggaggc cttatggatg aactcaaggc acactgtgtc
4201 acacttcctg tcagagttgg tatgaacatg aatgaggatg gcccgatcat ctttgagaag
4261 cactccagat atagatatca ctatgatgct gattattccc ggtgggactc aacacaacaa
4321 agggatgtgc tagcagcagc actagaaatc atggttaagt tctctccaga accacacctg
4381 gcccaggtag ttgcagaaga cctcctctcc cctagcgtga tggacgtagg tgactttcaa
4441 atatcaataa gtgagggtct cccctctggg gtaccttgta cctcccagtg gaattccatc
4501 gcccactggc tcctcactct gtgtgcactc tctgaagtca cggacctgtc ccctgatatc
4561 attcaggcca actccctttt ctccttctat ggtgatgatg agattgtaag cacagacata
4621 aagttggacc cagagaagct gacagcaaaa ctcaaggagt acgggctgaa accaacccgc
4681 cccgacaaaa ctgaaggacc ccttgttatc tctgaagatc tggatggcct aacattcctc
4741 cggagaactg tgacccgtga tccagctggt tggtttggaa aattggaaca aagctcaatc
4801 ctcaggcaaa tgtactggac caggggtccc aaccatggag acccatttga aacaatgata
4861 ccacactccc aaagacccat acaattgatg tccttgctgg gcgaggctgc actccacggc
4921 ccggcattct atagcaaaat tagcaaatta gtcattgcag agttgaagga aggtggcatg
4981 gatttttacg tacccagaca agagccaatg ttcagatgga tgagattctc agacctgagc
5041 acgtgggagg gcgatcgcaa tctggctccc agttttgtga atgaagatgg cgtcgagtga
5101 cgccagccca tctgatgggc ccgcagccaa cctcgtccca gaggtcaaca atgaggttat
5161 ggctctggag cccgttgttg gtgccgccat tgcggcacct gtagcgggcc aacaaaatgt
5221 aattgacccc tggattagaa ataattttgt acaagcccct ggtggagagt ttacagtgtc
5281 ccctagaaac gctccaggtg aaatactatg gagcgcgccc ttgggccccg atctaaatcc
5341 ctacctatcc catttggcca gaatgtacaa tggttatgca ggtggttttg aagtgcaggt
5401 aattctcgcg gggaacgcgt tcaccgccgg gaagatcata tttgcagcag tcccaccaaa
5461 ttttccaact gaatgcttga gccccagcca ggtcactatg ttcccccata taataacaga
5521 tgttaggcaa ctagaacctg tgttgattcc cttacccgat gttaggaata atttctatca
5581 ttacaatcaa tcaaatgaac ccaccattaa gttgatagca atgttgtata caccacttag
5641 ggctaataat gctggggatg atgtcttcac agtttcttgc cgagttctca cgagaccatc
5701 ccctgatttt gatttcatat ttctagtgcc acccacagtt gagtcaagaa ctaaaccgtt
5761 ctctgtccca gttttaactg ttggggagat gaccaattca agattcccca ttcctttgga
5821 aaagctgttc acgggtccca gcggtgcctt tgatgtccaa ccacaaaacg gtaggtgcac
5881 gactgatggc gtgctcctag gcaccaccca actgtctcct gtcaacatct gcgccttcag
5941 aggagatgtc acccatacca caggtagtca taactacaca atgaatttgg cctctcaaaa
6001 ttggagcgtt tatgacccag cagaagaaat cccagcccct ctaggaactc cagattttgt
6061 ggggaagatt cagggcgtgc tcacccaaac cacaaggaca aatggctcaa cacgcggcca
6121 caaagccaca gtgctcactg ggagcgccga atttgctcca aaactgggta gagttcaatt
6181 tgcaactgac acaaatcatg attttgaaga taaccaaaac acaaagttca ccccagtcgg
6241 tgtcatccaa gatggtaaca ccacccccca aaatgaaccc caacagtggg tgcttccaag
6301 ttactcaggc agaagtactc ctaatgtgca tctggccccc gctgtggccc ccacttttcc
6361 gggtgagcaa cttctcttct tcagatccac catgcccgga tgcagcgggt accccaacat
6421 ggacttggac tgtctgctcc cccaggaatg ggtgcagcac ttctaccaag aggcagcccc
6481 agcacaatct gatgtggctc tgctaagatt tgtgaatcca gacacaggta gggttttgtt
6541 tgagtgcaag cttcacaaat caggctatgt tacagtggct catactggcc aacatgattt
6601 ggttatcccc cccaatggtt attttaggtt tgattcctgg gtcaaccagt tttacacgct
6661 tgcccccatg ggaaatggaa cggggcgtag acgtgcacaa taatggctgg agctttcttt
6721 gctgggttgg catctgatgt ccttggctct ggacttggtt ccctcatcaa tgctggggct
6781 ggggccatca accaaaaagt tgagtttgaa aacaacagaa aactgcaaca agcatccttc
6841 caatttagca gcaatctaca acaggcttcc tttcaacatg acaaagagat gctccaagca
6901 caaattgagg ccaccaaaaa gctacaacag gaaatgatga aagttaagca ggcaatgctc
6961 ctagagggtg ggttctctgg aacagatgcg gcccgcgggg caatcaacgc ccccatgaca
7021 aaagttttgg actggagcgg gacaaggtac tgggctcccg atgctaggac tacaacatac
7081 aatgcaggcc gcttttctac ccctcaacca tcgggggcac tgccaggaag agctaatctt
7141 agggatgctg tccctgctcg aggttcctct agtaagtctt ctaattcttc tactgctact
7201 tctgtgtatt caaatcaaac tacttcaacg agacttggtt ctacagctgg ttctggcacc
7261 agtgtctcga gcttcccgcc aactgcaagg actaggagct gggttgagga tcaaagtagg
7321 aatttgtcac ctttcatgag gggggcccac aacatatcgt ttgtcacccc accatctagc
7381 agatcctcta gccaaggcac agtctcaacc gtgcctaaag agattttgga ctcctggact
7441 ggcgctttca acacgcacag gcagccactc ttcgctcaca ttcgtaagcg aggggagtca
7501 cgggtgtaat gtgaaaagac aaaattgatt atctttcttt tctttcttta gtgtctttt
//