Typing tool
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Typing tool
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Complete norovirus genomes
| MW559992 | GII.4 | |
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| GII.P31 |
ORF1: 1..5100
ORF2: 5081..6703
ORF3: 6703..7439
LOCUS MW559992 7439 bp RNA linear VRL 22-FEB-2021
DEFINITION Norovirus GII isolate Hu/GII.4/P31/005/2019/KEN nonstructural
polyprotein (ORF1) and VP1 (ORF2) genes, complete cds; and VP2
(ORF3) gene, partial cds.
ACCESSION MW559992
VERSION MW559992.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7439)
AUTHORS Lambisia,A.W., de Laurent,Z., Nokes,J.D. and Agoti,C.N.
TITLE Near complete genomes of five human norovirus GII.4 recovered from
diarrheal stool samples of hospitalized children in coastal Kenya
in 2019
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 7439)
AUTHORS Lambisia,A.W., de Laurent,Z., Nokes,J.D. and Agoti,C.N.
TITLE Direct Submission
JOURNAL Submitted (03-FEB-2021) Bioscience, KEMRI WELLCOME TRUST, KILIFI,
KILIFI, KILIFI 230-80108, Kenya
COMMENT ##Assembly-Data-START##
Assembly Method :: SPAdes v. v3.13.2
Sequencing Technology :: Illumina
##Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..7439
/organism="Norovirus GII"
/mol_type="genomic RNA"
/strain="KLF_NOV_005"
/isolate="Hu/GII.4/P31/005/2019/KEN"
/isolation_source="human stool"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="Kenya"
/collection_date="07-Aug-2019"
/note="genotype: GII.4"
gene 1..5100
/gene="ORF1"
CDS 1..5100
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="QRF49933.1"
/translation="MKMASNDASAAAAANGNNDIAKSSSDNVLSSMAITFKRALGARP
KQPPPKEIPPRPPRPPTPELVKKIPPPPPNGEDELVVSYSAKDGISGLPDLTTVSQPE
ENNTAFSVPPLNQRENRDAKEPLTGTIIEMWDGEIYHYGLYVERGLILGVHKPPAAIS
LAKVELTPLSLFWRPVYTPQYLISPDTLRRLHGESFPYTAFDNNCYAFCCWVLDLNDS
WLSRRMIQRTTGFFRPYQEWNRKPLPTMDDSKLKKVANIFLCTLSSLFTRPIKDIIGK
VKPLNILNILASCDWTFPGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED
LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
KKEEANELAMVRSIEDAVLDLEAIENNHMTALLKDKDSLATYMRTLDHEEEKARKLST
KSASPDIVGTINALLARIAAARSLVHRAKEELSSRSRPVVVMISGKPGIGKTHLAREL
AKKIAASLAGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC
PLTLNCDRIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK
AKRDFPGQPDMWKNAFSSDFSHIKLTLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA
TGLLHERLDEYELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMRIGKQLKDVKTM
PDLKQSLKNVAIKKCQIVYGGSTYTLEADGKGSVKVDKVQSATVQTNNELAGALHHLR
CARIRYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQNLWSKPQVEDTEETAGKDGC
PKPKDDEEFVVSSDDIKTEGKKGKNKSGRGKKHTAFSSKGLSDEEYDEYKRIRDERNG
KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV
TGTEIRKRNPEDFKPKGKLWADDDRSVDYNEKLNFEAPPSIWSRIVNFGSGWGFWVSP
SLFITSTHVIPQGAKEFFGVPIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG
TVATLLIKRPTGELMPLAARMGTHATMRIQGRTVGGQMGMLLTGSNAKNMDLGTTPGD
CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILG
PGSAPKLSTKTKFWRSSTTPLPPGTYEPAYLGGKDPRVRGGPSLQQVMRDQLKPFTEP
RGKPPRPNVLEAAKKTIINVLEQTIDPPQKWSFAQACASLDKTTSSGHPHHMRKNDCW
NGESFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDL
ATMIRCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFEKHSRYRYHYDADYSRWD
STQQRDVLAVALEIMVKFSPEPHLAQIVAEDLLSPSVMDVGDFQISISEGLPSGVPCT
SQWNSIAHWLLTLCALSEVTDLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLK
EYGLKPTRPDKTEGPLVISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP
NHEDPSETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQE
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="QRF49934.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPGLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKVIFAAVPPNFPTEGLSPSQVTMFPHIVVDVRQLDPVLIPLPD
VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKQFSVPILTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDLTHIANSHNYTMNLASQNWNDYDPTEEIPAPLGTPDFVGKIQGVL
TQTTRADGSTRGHKATVLTGSADFAPKLGRIQFQTDTDRDFEAHQNTKFTPVGVIQDG
GTTHQNEPQQWVLPSYSGRDTPNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMNLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYALAPMGNGTGRRRVV"
gene 6703..>7439
/gene="ORF3"
CDS 6703..>7439
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="QRF49935.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSVALPGRSNLRDTAPARGPSSKSS
NSSTVASVYSNQTASTRLGTTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAYNI
SFVTPPSSRSSSQGTVSTVPKEILDSWT"
ORIGIN
1 atgaagatgg cgtctaacga cgcttccgct gccgctgctg ccaatggcaa caacgacatc
61 gcaaaatctt caagtgacaa tgtgctttct agcatggcca tcacttttaa acgagccctc
121 ggggcgcggc ctaaacagcc gcccccgaag gaaataccac ccagaccccc acgaccaccc
181 acaccagaat tggtcaaaaa gatcccccct cccccgccca acggagagga tgaactagtg
241 gtttcgtaca gcgccaaaga tggcatttcc ggattgcctg atctaaccac tgtcagccaa
301 ccggaagaaa acaacacagc gttcagcgtt cccccgctca atcaaaggga gaatagggac
361 gccaaggaac cactaactgg aacaattatt gagatgtggg atggagaaat ctaccattac
421 ggtctgtacg tggaacgagg acttatactt ggtgtgcaca agccaccggc agccatcagc
481 cttgccaagg tcgagttaac accactctct ttgttctgga gacctgtgta tacccctcag
541 tacctcatct ctccagacac tcttaggaga ctacatggag agtcattccc ctatactgca
601 tttgacaaca attgctacgc cttctgctgc tgggtgttag acctaaacga ctcatggctg
661 agtaggagaa tgattcagag gactacggga ttcttcagac cataccagga atggaacaga
721 aaacccctcc ccactatgga tgattccaaa ctgaaaaagg tagccaacat attcttgtgc
781 accctatctt cattgttcac cagacccatt aaggacataa taggaaaagt gaaacctctt
841 aacatcctca atatcctggc ctcatgtgat tggacgttcc caggcatagt ggaatcccta
901 atactcttgg cagaactctt tggagttttc tggacacccc cagatgtgtc tgcgatgatc
961 gcccccctac taggtgatta tgaactgcaa ggacctgagg accttgcagt agaactggtc
1021 ccagtggtga tgggagggat aggtttggtg ctaggattta ccaaagagaa aattggaaag
1081 atgctgtcgt ccgccgcatc cactttgagg gcttgcaaag accttggtgc atacggacta
1141 gaaattttga aattggtcat gaaatggttc ttcccaaaga aagaggaagc aaatgagctg
1201 gccatggtga gatccatcga ggacgcagtg ctggacctcg aggcaattga aaacaaccac
1261 atgaccgccc tgctcaagga taaagacagc ttggcaacct acatgagaac ccttgaccat
1321 gaggaggaga aagccagaaa actctcaacc aaatctgctt cacccgacat tgtgggtaca
1381 atcaacgctc ttctggcacg aatcgccgct gcacgctccc tagtgcatcg ggcgaaagaa
1441 gagctttcca gtaggtcgag gcctgttgtt gtgatgatat cgggaaaacc agggatagga
1501 aaaactcacc ttgccaggga gttggccaag aagatcgcag cctccctcgc aggggaccag
1561 cgtgtgggcc tgatcccacg caatggcgtc gaccactggg acgcatacaa gggtgaaaga
1621 gttgttctat gggacgacta tgggatgagc aaccccatac acgatgccct caggttgcaa
1681 gaacttgctg acacttgccc cctcacgcta aattgtgaca ggattgagaa caaaggaaaa
1741 gtttttgata gtgacgccat aattattacc accaatctgg ccaacccagc accacttgat
1801 tatgtcaatt ttgaagcgtg ctcgaggcgc attgacttcc tcgtgtacgc ggaagctcct
1861 gaggtggaga aggcaaaacg cgacttccca ggccaacccg acatgtggaa gaacgctttc
1921 agttctgact tctcacacat aaaactgaca ctggctccgc agggtggctt tgacaagaac
1981 ggcaacaccc cacatggaaa aggtgtcatg aagaccctca ccactggctc cctcatcgcc
2041 cgagcaacag gattactcca tgagaggcta gatgaatatg aattgcaagg tccagccctc
2101 actaccttca actttgatcg caacaaggta cttgccttta ggcagcttgc tgctgaaaac
2161 aagtatgggc tgatggacac aatgagaatt ggaaaacagc ttaaggatgt caagaccatg
2221 ccagacctca aacaatcact caagaatgtt gcgattaaga agtgccagat agtgtatggt
2281 ggtagcacct acacgcttga ggccgatggc aagggtagtg tgaaagttga caaagtgcaa
2341 agtgccaccg tgcaaactaa caatgaacta gccggcgccc tgcaccacct gaggtgcgcc
2401 agaatcaggt actatgtcaa gtgtgtccag gaggcattgt attccatcat ccaaatcgcc
2461 ggggccgcgt ttgtcaccac gcgcatcgcc aagcgcatga acatacaaaa cctctggtcc
2521 aagccacagg tggaagacac agaagagacg gccggcaaag atggttgccc aaaacccaaa
2581 gatgatgaag agttcgtcgt ctcatccgat gacatcaaga ctgagggcaa gaaagggaaa
2641 aacaagtccg gccgtggcaa gaagcacaca gccttctcaa gcaaagggct cagtgatgag
2701 gagtacgatg agtacaagag aatcagagat gaaaggaatg gtaagtactc catagaagag
2761 tacctccagg acagagacaa gtactatgag gaggtggcca ttgccagggc aactgaagag
2821 gacttctgtg aagaagaaga agccaaaatc cggcagagaa ttttcagacc aacaagaaaa
2881 caacgtaaag aagagagggc ctctttaggc ttggtcacag gcacagagat caggaagaga
2941 aacccagaag acttcaaacc caagggaaag ctgtgggctg atgatgacag aagtgttgac
3001 tacaacgaga aactcaactt tgaggcccca ccaagcatct ggtcgcggat agtcaacttt
3061 ggttcaggtt ggggcttctg ggtctccccc agcttgttta taacatcaac ccatgtcata
3121 ccccaaggtg caaaagagtt cttcggagtc cccatcaaac agatccaaat acacaaatca
3181 ggtgaattct gccgattgag attcccaaaa ccaatcagaa ctgatgtgac gggcatgatt
3241 ctggaagaag gtgcgccaga aggaaccgtg gccacactgc tcatcaagag accaactgga
3301 gagctcatgc ctttggcagc cagaatggga acccatgcga ccatgaggat tcaggggcgc
3361 acagttggag gacagatggg tatgctcttg acaggatcca acgccaagaa tatggacttg
3421 ggcacaacac caggcgactg cggttgcccc tacatttaca aaagagggaa cgactatgtg
3481 gtcatagggg tccatacagc cgctgcccgt ggaggaaaca ctgtcatctg tgccacccag
3541 ggtagtgagg gagaagccac acttgaagga ggtgacaaca aaggaacgta ctgtggtgca
3601 ccaattttgg gcccagggag tgctccgaaa ctcagcacca agactaagtt ttggagatca
3661 tccacaacgc cactcccgcc aggcacctac gaaccagcct acctcggtgg caaggacccc
3721 agagtcagag gtggcccttc actgcaacaa gttatgaggg accagctaaa accattcaca
3781 gaacctagag gcaaaccacc aagaccgaat gtgttggaag ctgccaagaa aaccatcatt
3841 aatgttcttg agcaaacaat tgacccaccc caaaaatggt cattcgcgca agcttgcgca
3901 tcccttgaca aaaccacctc cagcggccat ccacaccaca tgcggaaaaa cgactgttgg
3961 aatggggagt cctttacagg taaattggca gatcaggcct ccaaggccaa cctaatgttt
4021 gaagagggaa agaacatgac tccagtctac acaggtgcac ttaaggatga attggtgaag
4081 actgacaaaa tttatggcaa gatcaagaag aggctcctgt ggggctcgga cctggcgacc
4141 atgatacggt gcgcccgggc ttttgggggc ctcatggatg aactcaaggc acactgtgtt
4201 acccttccta tcagagttgg tatgaacatg aatgaggatg gccccataat ctttgagaag
4261 cactccaggt ataggtatca ctatgatgct gactactcca ggtgggactc aacacaacaa
4321 agggatgtgc tagcagtagc actagaaatc atggttaagt tttctccaga accacacttg
4381 gcccagatag ttgcagaaga cctcctctct cctagtgtaa tggatgtggg tgacttccaa
4441 atatcaataa gtgagggact cccctccggg gtgccttgca cctcccagtg gaactccatc
4501 gcccactggc tcctcaccct ctgtgcactt tcagaagtca cagacctgtc ccctgacatc
4561 atccaggcca actctctctt ctccttctat ggtgatgatg agattgtgag tacagacata
4621 aaattggacc cagagaaact gacagcaaaa ctcaaagagt acgggctgaa gccaacccgc
4681 cccgacaaaa ctgaaggacc ccttgtcatc tctgaagatc tggatggcct gaccttcctc
4741 cgaaggactg tgacccgtga cccagctggt tggtttggaa aattggaaca gagctcaatt
4801 ctcaggcaaa tgtattggac caggggcccc aaccatgaag acccatctga aacaatgata
4861 ccacactccc aaagacccat acaattgatg tccttgctgg gcgaggctgc actccacggc
4921 ccagcatttt acagcaaaat tagcaaattg gtcattgcag aattgaaaga aggtggcatg
4981 gatttttacg tgcccaggca agagccaatg ttcagatgga tgagattctc agatctgagc
5041 acgtgggagg gcgatcgcaa tctggctccc agttttgtga atgaagatgg cgtcgagtga
5101 cgccaaccca tctgatgggt ccgcagccaa cctcgtccca gaggtcaaca atgaggttat
5161 ggctctggag cccgttgttg gtgccgctat cgcggcacct gtagcgggcc aacaaaatgt
5221 aattgacccc tggattagaa ataattttgt gcaagcccct ggtggagagt ttacagtatc
5281 ccctagaaac gctccaggtg aaatactatg gagcgcgccc ttaggccccg gtctaaatcc
5341 ctacctatcc catttggcca gaatgtacaa tggttatgca ggtggttttg aagtgcaggt
5401 aatcctcgcg gggaacgcgt ttaccgctgg gaaggtcata tttgcagcag tcccaccaaa
5461 ttttccaact gaaggcttga gccccagcca ggtcactatg ttcccccata tagtagtgga
5521 tgttaggcaa ttagaccctg tgttgattcc cttacccgat gttaggaata atttctatca
5581 ctacaatcaa tcaaatgacc ctactattaa gttgatagca atgctttata caccacttag
5641 ggctaataat gctggggacg acgtcttcac agtctcttgc cgggtcctca cgagaccgtc
5701 ccctgatttt gattttatat tcctagtgcc acccacagtt gagtcaagaa ctaagcaatt
5761 ctctgtccca atcttaactg ttgaggagat gaccaattca agattcccca ttcctttaga
5821 aaagttgttc acgggtccca gcagtgcctt tgttgttcaa ccacaaaacg gcaggtgcac
5881 gactgatggc gtgctcctag gcaccaccca actgtctcct gtcaacatct gcaccttcag
5941 aggagatctc actcacattg caaatagtca taactataca atgaatttgg cttctcaaaa
6001 ttggaacgat tatgacccaa cagaagaaat cccggcccct ctaggaactc cagattttgt
6061 agggaagata caaggagtgc tcacccaaac cacaagggca gatggctcaa cacgcggcca
6121 caaagccaca gtgctcactg ggagcgctga ttttgctcca aaattgggta gaattcaatt
6181 tcaaactgac acagaccgtg attttgaagc tcaccaaaac acaaagttca ccccagtcgg
6241 tgtcatccaa gatggtggca ccacccatca aaatgaaccc caacagtggg tgctcccaag
6301 ttactcaggc agggacaccc ccaatgtgca tttggccccc gctgtagccc ccacttttcc
6361 gggtgaacaa cttctcttct tcagatccac catgcccgga tgcagcgggt accccaatat
6421 gaatctggac tgcctgctcc cccaggaatg ggtgcagtac ttctaccaag aggcagcccc
6481 agcacaatct gatgtagctc tgctgagatt tgtgaatcca gatacaggca gggttttgtt
6541 tgaatgtaag cttcataagt cgggctatgt tacagtggcc cacactggcc aacatgattt
6601 ggttatcccc cccaatggtt attttaggtt tgattcctgg gtcaaccagt tctacgcgct
6661 tgcccccatg ggaaatggaa cggggcgtag acgtgtggta taatggctgg agctttcttt
6721 gctggattgg catctgatgt ccttggctct ggacttggtt cccttatcaa tgctggggct
6781 ggggccatca accaaaaagt tgaatttgaa aataacagaa aattgcaaca agcatccttc
6841 caatttagta gtaacctaca acaggcttcc tttcaacatg ataaagagat gctccaggca
6901 caaattgagg ccaccaaaaa gctacaacag gaaatgatga aagttaaaca ggcaatgctc
6961 ctagagggtg ggttctctga gacagatgca gcccgcgggg caatcaacgc ccccatgaca
7021 aaagctttgg actggagcgg gacaaggtac tgggctcccg atgctaggac tacaacatac
7081 aatgcaggcc gcttttccac ccctcaacca tcggtggcac tgccaggaag atctaatctt
7141 agggatactg cccctgctcg gggtccctct agcaaatctt ctaattcttc tactgttgct
7201 tctgtgtatt caaatcaaac tgcttcaacg agacttggta ctacagctgg ttctggcacc
7261 agtgtctcga gcctcccgtc aactgcaagg actaggagct gggttgagga tcaaaacagg
7321 aatttgtcac ctttcatgag gggggcctac aacatatcgt ttgtcacccc accatctagc
7381 agatcctcta gccaaggcac agtctcaacc gtgcctaaag agattttgga ctcctggac
//