Typing tool
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Typing tool
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Complete norovirus genomes
| MW559993 | GII.4 | |
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| GII.P31 |
ORF1: 1..5100
ORF2: 5081..6703
ORF3: 6703..7443
LOCUS MW559993 7443 bp RNA linear VRL 22-FEB-2021
DEFINITION Norovirus GII isolate Hu/GII.4/P31/002/2019/KEN nonstructural
polyprotein (ORF1) and VP1 (ORF2) genes, complete cds; and VP2
(ORF3) gene, partial cds.
ACCESSION MW559993
VERSION MW559993.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7443)
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JOURNAL Unpublished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 7443)
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..7443
/organism="Norovirus GII"
/mol_type="genomic RNA"
/strain="KLF_NOV_002"
/isolate="Hu/GII.4/P31/002/2019/KEN"
/isolation_source="human stool"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="Kenya"
/collection_date="06-Mar-2019"
/note="genotype: GII.4"
gene 1..5100
/gene="ORF1"
CDS 1..5100
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="QRF49936.1"
/translation="MKMASNDASAAVAANSNNDIAKSSSDGMFSNMAVTFKRALGARP
KQPPPKEIPPKPPRPPTPELVKKIPPPPPNGEDELVVSYSAKDGISGLPELTTVSQPE
EINTAFSVPPLNQRENRDAKEPLTGTIIEMWDGEIYHYGLYEERGLILGVHKPPAAIS
LAKVELTPLSLFWRPVYTPQYLISPDTLRRLHGESFPYTAFDNNCYAFCCWVLDLNDS
WLSRRMIQRTTGFFRPYQEWNRKPLPTMDDSKLKKVANIFLCTLSSLFTRPIKDIIGK
LKPLNILNILATCDWTFPGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED
LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
KKEEANELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST
KSASPDIVGTINSLLARIAAARSLVHRAKEELSSRPRPVVVMISGRPGIGKTHLAREL
AKKIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC
PLTLNCDRIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK
AKRDFPGQPDMWKNAFSPDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA
SGLLHERLDEYELQGPALTTFNFDRNKILAFRQLAAENKYGLMDTMRVGKQLKDVRTM
PDLKQALKNVAIKKCQIVYNGGTYTLEADGKGSVKVDKVQNATVQTNNELAGALHHLR
CARIRYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQNLWSKPQVEDTEETASKDGC
PKPKDDEEFVVSSDDIKAEGKKGKNKSGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV
TGSEIRKRNPEDFKPKGKLWADDDRSVDYNEKLNFEAPPSIWSRIVNFGSGWGFWVSP
SLFITSTHVIPQGTKEFFGVPIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG
TVATLLIKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILG
PGSAPKLSTKTRFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP
RGKPPRPNVLEAAKKTIINVLEQTIDPPQKWSFAQACASLDKTTSSGHPHHMRKNDCW
NGDSFTGRLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDL
ATMIRCARAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWD
STQQRDVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVMDVGDFQISISEGLPSGVPCT
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="QRF49937.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKVIFAAVPPNFPTEGLSPSQVTMFPHIVVDVRQLEPVLIPLPD
VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSIPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHITGSHNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML
TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTNNDFEANQNTKFTPVGVIQDG
STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGAGRRRVV"
gene 6703..>7443
/gene="ORF3"
CDS 6703..>7443
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="QRF49938.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKDMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARTTTYNTGRFSTPQLSGAPPGRANLRDAVPARGSPNKTS
NSSTATSVYSNQTTSTRLGSTAGSGTSVSSLPSTARTRSWVEDQSRNLSPFMRGAHNI
SYVTPPSSRSSSQGTVSTVPKEVLDSWTG"
ORIGIN
1 atgaagatgg cgtctaacga cgcttccgct gccgttgctg ccaacagcaa caacgacatc
61 gcaaaatctt caagtgacgg tatgttttcc aacatggctg tcacttttaa acgggccctc
121 ggggcgcggc ctaaacagcc gcccccgaag gagataccac ccaaaccccc acgaccaccc
181 acaccagaat tggtcaaaaa gatccctcct cccccaccca acggggagga tgaactagtg
241 gtttcttaca gtgccaaaga tggcatttcc ggattgcctg agctcaccac tgtcagccaa
301 ccggaagaaa tcaacacggc gttcagtgtc cccccgctca atcaaaggga gaatagggac
361 gccaaggaac cactgactgg aacaattatt gaaatgtggg atggagaaat ctaccattac
421 ggcctgtatg aggaacgggg tcttatactt ggtgtgcata agccaccggc agccatcagc
481 cttgccaagg tcgagctaac accgctctct ttgttctgga gacctgtgta tacccctcag
541 taccttatct ctccagacac tcttaggaga ctacatggag aatcattccc ctacaccgca
601 tttgacaaca attgttacgc cttctgctgt tgggtattag acctaaacga ctcatggcta
661 agtagaagaa tgattcagag aacaacgggt ttcttcagac cataccagga atggaacagg
721 aaacccctcc ccactatgga tgattccaag ttaaagaagg tagccaacat attcttgtgc
781 accttgtctt cactattcac cagacccatt aaggacataa tagggaaatt gaaacctctt
841 aacatcctca atattctggc tacatgtgac tggaccttcc caggcatagt ggaatcccta
901 atactcttgg cagaactctt tggagttttc tggacacccc cagatgtgtc tgcgatgatc
961 gcccccttac taggtgatta tgaactgcaa ggacctgagg accttgcagt agaactagtc
1021 ccagtggtga tgggggggat aggcttggtg ctaggattca ccaaagagaa aattggaaag
1081 atgttgtcgt ccgctgcatc cactttgaga gcttgcaaag acctgggtgc atacggactg
1141 gaaatcttga agttagttat gaaatggttc ttcccgaaga aagaggaagc aaatgaactg
1201 gctatggtga ggtccatcga agatgctgta ctagacctcg aggcaattga aaacaaccac
1261 atgaccaccc tgctcaagga caaggatagc ttggcaacct acatgagaac cctcgacctt
1321 gaggaggaaa aagccagaaa actctcaacc aaatctgctt cgcctgatat cgtgggcaca
1381 atcaactctc ttctggcacg aatcgccgct gcgcgctccc tagtgcaccg agcgaaagag
1441 gagctctcca gcaggccgag acctgttgtt gtgatgatat cgggaagacc aggaataggg
1501 aaaactcatc ttgctaggga gttggccaag aagatcgcag cctctctcac aggggaccag
1561 cgtgtaggtc taatcccacg caatggcgtc gaccactggg acgcatacaa gggtgaaaga
1621 gttgtcctat gggacgacta tgggatgagc aaccccatac acgatgccct caggctacag
1681 gaacttgctg acacttgccc cctcacgcta aactgtgaca ggattgagaa caaaggaaaa
1741 gtctttgaca gtgacgccat aattatcacc accaatctgg ccaacccagc accactggat
1801 tatgtcaatt ttgaggcgtg ctcaaggcgc attgacttcc tcgtgtacgc ggaagctcct
1861 gaggtggaaa aggcaaaacg tgacttccca ggccaacctg acatgtggaa gaacgctttc
1921 agtcctgact tctcacacat aaaactggca ttggctccac agggtggttt tgacaagaac
1981 ggcaacaccc cgcatggaaa aggtgtcatg aagaccctca caactggctc cctcatcgcc
2041 cgagcatcag gactactcca tgagaggcta gatgaatatg aattacaagg cccagccctc
2101 accactttca attttgaccg caacaagata cttgctttta gacagcttgc tgctgaaaac
2161 aagtatgggc tgatggacac aatgagagtt ggaaaacagc tcaaggatgt caggaccatg
2221 ccagacctca aacaagcact caagaatgtc gcaattaaga agtgccagat agtgtacaat
2281 ggtggcacct atacgcttga ggccgatggc aagggtagtg tgaaagttga caaagtgcaa
2341 aatgccaccg tgcagaccaa caatgaactg gccggcgccc tgcaccacct aaggtgcgcc
2401 agaatcaggt actatgttaa gtgtgtccag gaggcactgt attccatcat tcaaatcgct
2461 ggggctgcgt tcgtcaccac gcgcatcgcc aagcgcatga acatacaaaa tctctggtcc
2521 aagccacagg tggaagacac agaagagacg gccagcaaag atggttgccc taagcccaaa
2581 gatgatgaag agttcgtcgt ttcatccgac gacatcaaag ctgagggcaa gaaagggaag
2641 aacaagtccg gccgtggcaa aaagcacaca gccttctcaa gcaaaggact cagtgatgag
2701 gagtacgatg agtacaagag aatcagggag gaaaggaatg gcaagtactc catagaagag
2761 tacctccagg acagagacaa gtactatgag gaggtggcca ttgccagggc aactgaagag
2821 gacttctgtg aagaagaaga ggccaaaatc cggcagagaa ttttcagacc aacaagaaaa
2881 caacgtaagg aagaaagggc ctctctaggc ttggtcacag gttcagaaat caggaagaga
2941 aaccctgagg acttcaaacc caagggaaag ctgtgggccg atgatgacag aagcgttgac
3001 tacaacgaga aactcaactt tgaggcccca ccaagcatct ggtcgcggat agtcaacttt
3061 ggttcaggtt ggggcttctg ggtctccccc agtttgttta taacatcaac ccatgtcata
3121 ccccaaggta caaaagagtt cttcggagtc cccatcaaac aaatccagat acacaaatca
3181 ggtgaattct gtcggctgag attcccaaaa ccaatcagaa ctgatgtgac gggcatgatt
3241 ctagaagagg gtgcgccaga gggaaccgtg gccacactgc tcatcaagag gccaactgga
3301 gagcttatgc ccttggcagc cagaatggga actcatgcaa ccatgaaaat tcaggggcgc
3361 acagttggag gacaaatggg tatgctcttg acagggtcca acgccaagag tatggacttg
3421 ggcacaacac caggtgactg cggctgtccc tacatctata aaagagggaa cgactatgtg
3481 gtcataggag tccatactgc tgctgcccgt ggaggaaaca ctgtcatctg tgccacccag
3541 ggtagtgagg gggaagccac ccttgaaggg ggtgacaaca aaggaacgta ctgtggtgca
3601 ccaatcttgg gcccagggag cgctccgaaa cttagcacca aaactaggtt ttggaggtca
3661 tccacaacgc cactcccacc aggcacctac gaaccagcct acctcggcgg caaggatccc
3721 agagtcaaag gtggcccttc attgcaacaa gtcatgaggg accagctaaa gccattcaca
3781 gaacccagag gcaaaccacc aagaccaaat gtattggaag ccgccaagaa aaccatcatt
3841 aatgtccttg agcaaacaat tgacccaccc caaaaatggt cattcgcgca agcttgcgca
3901 tcccttgaca aaaccacctc cagcggccat ccgcaccaca tgcggaaaaa cgattgctgg
3961 aatggggact cctttacagg aagattggca gatcaggcct ccaaggccaa cctaatgttt
4021 gaggagggaa agaacatgac tccagtctac acaggtgcac ttaaagatga attggtaaag
4081 actgacaaga tttatggtaa gatcaagaag aggcttttgt ggggctcgga cttggcgacc
4141 atgatacggt gcgcccgggc ttttggaggc cttatggatg agctcaaggc acactgtgtc
4201 acccttccag tcagagttgg tatgaacatg aatgaagatg gccccataat ctttgagaag
4261 cactccagat acaagtatca ctatgatgct gattactcca ggtgggactc aacacaacaa
4321 agggatgtgc tagcagcagc actagaaatc atggttaagt tctctccaga accacacttg
4381 gcccaggtgg ttgcagaaga cctcctttcc cctagtgtaa tggatgtagg tgactttcag
4441 atatcaataa gtgaggggct cccctccggg gtgccttgca cttcccagtg gaattccatc
4501 gcccactggc tcctcaccct ttgtgcgctc tctgaagtca cggacctgtc ccctgatatc
4561 attcaggcca attccctttt ctccttctac ggtgatgatg agattgtgag tacagacata
4621 aaattggacc cagagaagct gacagcaaaa ctcaaggagt acggattgaa gccgacccgt
4681 cccgacaaaa ctgaaggacc ccttgttatc tctgaagatt tggatggcct gacattcctc
4741 cggaggactg tgacccgtga cccagctggc tggtttggaa aattggaaca aagctcaatc
4801 ctcaggcaaa tgtactggac caggggtccc aatcatgaag atccatctga aacaatgata
4861 ccacactccc aaagacccat acaattgatg tccttgctag gtgaggctgc actccacggc
4921 ccagcatttt atagcaaaat tagcaagttg gttattgcag agttgaagga aggtggcatg
4981 gatttttacg tgcccagaca agagccaatg ttcagatgga tgagattctc agatctgagc
5041 acgtgggagg gcgatcgcaa tctggctccc agttttgtga atgaagatgg cgtcgagtga
5101 cgccaaccca tctgatgggt ccgcagccaa cctcgtccca gaggtcaaca atgaggttat
5161 ggctctggag cccgttgttg gtgccgccat agcggcacct gtagcgggcc agcaaaatgt
5221 aattgacccc tggattagaa ataattttgt acaagcccct ggtggagagt ttacagtgtc
5281 tcctagaaac gctccaggtg aaatactatg gagcgcgccc ttaggccctg atttaaatcc
5341 ctacctatcc catttggcca gaatgtacaa tggttatgca ggtggctttg aagtgcaggt
5401 aattctcgcg gggaacgcgt tcaccgccgg gaaggtcata tttgcagcag tcccaccaaa
5461 tttcccaact gaaggcttaa gtcccagcca ggtcaccatg ttcccccaca tagtagtaga
5521 tgttaggcaa ctagaacctg tgttgattcc cttacccgat gttaggaaca atttttacca
5581 ctacaatcaa tcaaatgacc ccactatcaa gttgatagca atgttgtata caccacttag
5641 ggctaataat gctggggatg atgtcttcac agtttcttgc cgggtcctca cgagaccatc
5701 ccccgatttt gatttcatat ttttggtgcc acccacagtt gagtcaagaa ctaagccatt
5761 ctctatccca gttttaactg ttgaggagat gaccaattca agattcccca ttcctttgga
5821 gaagttattc acgggtccca gcagcgcctt tgttgttcaa ccacaaaacg gcaggtgcac
5881 gactgatggc gtgctcctag gcaccaccca actgtctcct gtcaacatct gtaccttcag
5941 aggggatgtc acccatatca caggcagtca taactacaca atgaatttgg cttctcaaaa
6001 ttggaacaat tatgacccaa cagaagaaat tccagcccct ctaggaactc cagattttgt
6061 ggggaagatc caaggcatgc tcacccaaac cacaaggaca gatggctcaa cacgcggcca
6121 caaagctaca gtgtacaccg ggagcgccga cttcgctcca aaactgggta gagttcaatt
6181 tgaaactgac acaaacaatg actttgaagc caaccaaaac acaaagttca ccccagtcgg
6241 tgtcatccaa gatggtagca ccacccaccg aaatgaaccc caacagtggg tgctcccaag
6301 ctattcaggc agaaacactc ataatgtaca tctggccccc gctgtggccc ccacttttcc
6361 aggtgagcag cttctctttt tccgatccac catgcccgga tgcagcgggt accccaacat
6421 ggatctggat tgtctcctcc cccaagaatg ggtgcagcac ttctaccaag aggcagcccc
6481 agcacaatct gatgtggccc tgctgagatt tgtgaaccca gacacaggta gggttttatt
6541 tgagtgtaaa ctccacaaat caggttatgt tactgtggct cacactggcc aacatgattt
6601 ggttatcccc cccaatggtt attttaggtt tgattcctgg gtcaaccagt tctacacgct
6661 tgcccccatg ggaaatggag cggggcgtag acgtgtagta taatggctgg agctttcttt
6721 gctggattgg catctgatgt ccttggctct ggacttggtt ccctcatcaa tgctggggct
6781 ggggccatca atcaaaaagt tgagtttgaa aataacagaa aattacaaca agcatccttc
6841 caatttagca gcaatctgca acaggcctcc ttccaacatg acaaagatat gctccaagca
6901 caaattgaag ccaccaaaaa gttacaacag gaaatgatga aggtcaagca ggcaatgctc
6961 ctagagggtg ggttctctga gacagatgca gcccgcgggg caatcaacgc ccccatgaca
7021 aaagctctgg actggagcgg gacaaggtac tgggcccccg atgctaggac tacaacatac
7081 aatacaggcc gcttttccac ccctcaacta tcgggggcac cgccaggaag agctaatctt
7141 agggatgctg tccctgctcg gggttccccc aataaaactt ctaattcttc tactgctact
7201 tctgtgtatt cgaatcaaac tacttcaacg agacttggtt ctacagctgg ttctggcacc
7261 agtgtctcga gcctcccgtc aactgcaagg actaggagct gggttgagga tcaaagtagg
7321 aatttgtcac ctttcatgag gggggcccac aacatttcgt atgtcacccc accatctagt
7381 agatcctcca gccaaggcac agtctcaacc gtgcctaaag aggttttgga ctcctggact
7441 ggc
//