Typing tool
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Typing tool
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Complete norovirus genomes
| MW305713 | GII.7 | |
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| GII.P7 |
ORF1: 1..5027
ORF2: 5008..6630
ORF3: 6630..7403
LOCUS MW305713 7456 bp RNA linear VRL 06-JUL-2021
DEFINITION Norovirus GII isolate CMH-S040-16 nonstructural polyprotein (ORF1)
gene, partial cds; and VP1 (ORF2) and VP2 (ORF3) genes, complete
cds.
ACCESSION MW305713
VERSION MW305713.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7456)
AUTHORS Tohma,K., Lepore,C.J., Martinez,M., Degiuseppe,J.I., Khamrin,P.,
Saito,M., Mayta,H., Nwaba,A., Ford-Siltz,L.A., Galeano,M.E.,
Zimic,M., Stupka,J.A., Gilman,R.H., Maneekarn,N., Ushijima,H.,
Green,K.Y. and Parra,G.I.
TITLE Genome-wide analyses of human noroviruses reveal coexistence of
viral populations evolving under recombination constraints
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 7456)
AUTHORS Tohma,K., Lepore,C.J., Martinez,M., Degiuseppe,J.I., Khamrin,P.,
Saito,M., Mayta,H., Nwaba,A., Ford-Siltz,L.A., Galeano,M.E.,
Zimic,M., Stupka,J.A., Gilman,R.H., Maneekarn,N., Ushijima,H.,
Green,K.Y. and Parra,G.I.
TITLE Direct Submission
JOURNAL Submitted (23-NOV-2020) CBER/OVRR/DVP/LHV, U.S. Food and Drug
Administration, 10903 New Hampshire Avenue, Silver Spring, MD
20993, USA
COMMENT ##Assembly-Data-START##
Assembly Method :: High-performance Integrated Virtual
Environment (HIVE) v. 2
Sequencing Technology :: Illumina
##Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..7456
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="CMH-S040-16"
/isolation_source="feces"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="Thailand"
/collection_date="03-Feb-2016"
/note="genotype: GII.7[GII.P7]"
gene <1..5027
/gene="ORF1"
CDS <1..5027
/gene="ORF1"
/codon_start=3
/product="nonstructural polyprotein"
/protein_id="QPJ59475.1"
/translation="ATPSNKEEVGAFSNIKVGLKKMLGAVPKGTKAPSSGQHCPTVKI
GPKTLTIPPEPPNGEDTVQFDAKSETIIGLPDLTTVQNEHENTPYTVPPLSEREHRPA
TEPLPGTILEMWDGEFYHYSVYVSDGKALGVHKPPAAISLATIELTPISLYWRPVYTP
NYLVSPDTLKGLAGEKFPYTAFSNNCYNFCCWVLELNDTWLNRRCISRTTGFFKPYQS
WNRKPLPTVDDGKIKKVANAILCALGSLFSKPIKDLLGKLKPLNLLHLLASCDWTFAG
IVETVILMAELFNVFWTPPDVSNFVASLIGDFELQGPEDLAVELVPVVMGGIGMVLGF
TAEKIGRMLSSAASTLRACKDLGNYALDILKLVMKWFFPKKEEKAEMETLRAIEDAVL
DMEAIGNNHLTTLLKDKDSLTAFMKTLDLEEEKARKLSTKSSSPDIVGTINAILARIA
AARSLLHKAKEEMFSRIRPVVVMISGRPGIGKTHMARHLAKSIANTMSGDQRVGLVPR
NGVDHWDAYRGERVVLWDDYGMGSPVKDALTLQELADTCPVTLNCDRIENKGKMFDSD
VIIITTNLVNPAPLDYVNFEACSRRVDFLVYAESPEIEKVKRDFPGQPDMWKDHFKPD
FSHIKLTLAPQGGFDKNGNTPHGKGTMRSLTQGSLTARVAGLVHERRDEFQLQGNDLQ
IYNFDTNRVSAFRKLAADNKYGIMETMRVGTALKNVKTLEDLKIALRDVKFNECEIIY
KNSKYRVSSNGKGSVSVDKVEDNASQTVNEVQSAILRLRQARARYYISCFQDLVYTLI
QVAGASFVVSRISRRFCWERWVKPTETQEVNDSEKEVAQGRWEIEPKDTEPEGKKGKN
KKGRGKKHTAFSSKGLSDEEYDEFKRIREERNGKYSIEEYLQDRDRYYEEVAVARATE
EDFCEEEEAKIRQRIFRPTKKQRKEERGVLGLVTGSDIRKRRPDDFQPKGNLWADDTR
SVDYNERLDFEAPPSVWSRIVPLGTGWGFWVSSNLLITTTHVLPKGVKEFFGVEIKQI
QVHKSGEFCRFRFPRPIRPDVTGLVLEEGAPEGTVCSILIKRPTGEMIPLAVRMGTHA
SMKIQGRTVGGQMGMLLTGANAKNMDLGTGPGDCGCPYIYKRGNDIVVAGVHTAAARG
GNTVICATQGQDGEAVLEGNEDLGTYCGAPILGPGKAPKLSTKTKFWRSSPDALPPGT
YEPAYLGGKDPRVEKGPSLQQVMRDQLRPFTEPRGKPPRPAVLEEAKKTVMNVLEQTI
DPAKPWSYSQACASLDKTTSSGSPHHVKKNDHWNGESFTGPLADQASKANLMYEQAKH
VQPVYTAALKDELVRTDKIYKKIKKRLLWGSDLGTMIRCARAFGGLMDSMKASCIALP
CRVGMNMNEDGPIIFDKHSKYRYHYDADYSRWDSTQQRSILSAAMEVMVRFSAEPELA
QVVAEDLLAPSQLDVGDFVISVQEGLPSGVPCTSQWNSIAHWILTLSAMAEVSGLSPD
VVQAHSCFSFYGDDEIVSTDINLDPMKLTQKLREYGLVPTRPDKTEGPLVITEDLTGL
TFLRRSIARDPAGWFGKLDQDSILRQLYWTKGPNHENPYESMVPHSQRATQLMALLGE
ASLHGPQFYKKVSKMVINEIKSGGLEFYVPRQEAMFRWMRFSDLSTWEGDRNLAPEGV
NEDGVE"
mat_peptide <1..935
/gene="ORF1"
/product="p48"
mat_peptide 936..2033
/gene="ORF1"
/product="NTPase"
mat_peptide 2034..2552
/gene="ORF1"
/product="p22"
mat_peptide 2553..2951
/gene="ORF1"
/product="VPg"
mat_peptide 2952..3494
/gene="ORF1"
/product="Pro"
mat_peptide 3495..5024
/gene="ORF1"
/product="RdRp"
gene 5008..6630
/gene="ORF2"
CDS 5008..6630
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="QPJ59476.1"
/translation="MKMASNDAAPSNDGAAGLVPEINNEVMPLEPVAGASLATPVVGQ
QNIIDPWIRNNFVQAPAGEFTVSPRNSPGEILLDLELGPELNPYLAHLARMYNGHAGG
MEVQIVLAGNAFTAGKIIFAAIPPGFPYENLSPSQITMCPHVIIDVRQLEPVLLPMPD
IRNNFFHYNQGNDPKLRLVAMLYTPLRANNSGDDVFTVSCRVLTKPSPDFEFTFLVPP
TVESKTKQFTLPILKISEMTNSRFPVPVEMMYTARNENQVVQPQNGRVTLDGELLGTT
PLLAVNICKFKGEVIAKNGDVRSYRMDMEITNTDGTPVDPTEDTPGPIGSPDFQGILF
GVASQRNKNEQNPATRAHEANINTGGDQYAPKLAQVKFFSESQDFEVHQPTVFTPVGV
AGDTSHPFRQWVLPRYGGHLTNNTHLAPAVAPLFPGEQILFFRSQIPSSGGHELGYMD
CLVPQEWVQHFYQEAATAQSEVALIRFINPDTGRVLFEAKLHKQGFITVAHTGDNPIV
MPPNGYFRFEAWVNQFYSLAPVGTGNGRRRIQ"
gene 6630..7403
/gene="ORF3"
CDS 6630..7403
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="QPJ59477.1"
/translation="MASAFLANLAGGVASNGISSLINAGANAINQKVEFDYNKQLQNA
SFSHDKEMLQAQIEATKRLQQEMIDIKQGVLTAAGFSPTDAARGSVGAPMTKLVDWSG
TRYWAPGAMRTTGYSGTFTHLPPVQSASYVNNQNRQSLKVDSFPPSSSGSSVSSVKTQ
STTLSGTSRVGSSSQSTLSTRPSTRTSDWVRSQNERLSPFMDGALQTTYVTPPSSRAS
SVSTVSTVPKEVLDSWTPMFNTHRQPLFAHLRKRGESQI"
ORIGIN
1 acgccacccc ttctaataaa gaagaggttg gtgcattctc caacataaaa gttggactca
61 agaaaatgct gggtgccgtt cccaagggca ccaaagcacc cagcagtggt caacattgcc
121 ccacagttaa gatcgggcct aaaacattga caatcccccc tgagccccca aatggtgaag
181 acaccgtaca gtttgatgca aagtcagaaa ctataattgg gttgccggac ttaacaacgg
241 tgcaaaatga acatgaaaac accccataca ctgtccctcc attaagtgag agggaacaca
301 gaccggctac tgaaccactt cctggcacaa tattggaaat gtgggatggt gagttttacc
361 attattctgt gtacgtcagc gacggcaaag ctctgggggt ccacaaacca ccggcagcta
421 taagcctcgc gacgatagag ctcaccccca tatcacttta ctggaggccc gtttataccc
481 ccaattactt ggtctccccg gacacattaa agggtctcgc tggtgagaag tttccctata
541 cggcctttag taacaactgt tataactttt gctgttgggt gcttgagctc aacgacacgt
601 ggcttaacag aagatgcatt tccagaacta ccggcttctt caagccatac cagtcttgga
661 acagaaaacc tctcccaacc gttgatgatg gaaagattaa aaaggtggcc aacgcaatcc
721 tctgtgcact cggttcactg ttctcaaaac caatcaaaga cctgttaggt aaactcaagc
781 cattgaatct gctgcacttg cttgcgtctt gtgattggac gtttgcgggt atagtggaga
841 cagtcatctt gatggcggag cttttcaatg tcttttggac ccccccagat gtctctaatt
901 ttgtagcctc cctaataggt gattttgaat tacaagggcc tgaggacctg gctgtggagc
961 tcgtccccgt ggttatgggc ggcataggga tggttcttgg tttcaccgcc gagaaaatag
1021 gccgcatgct gtcgtccgct gcatcaacac tgcgggcgtg caaagacctt gggaactacg
1081 cccttgacat actcaaattg gtcatgaagt ggttcttccc gaagaaggaa gagaaagctg
1141 agatggaaac cttgagggcg attgaagatg ccgtcctaga tatggaagcc atagggaaca
1201 accacctcac aacccttctc aaggacaaag atagcctcac ggctttcatg aagaccctgg
1261 atctggaaga ggagaaggcg aggaaactgt ccaccaaatc atcttcaccg gacatagtcg
1321 gcaccatcaa tgccatactg gctaggatag ctgctgctag atcccttcta cataaggcca
1381 aagaggagat gttcagcagg attaggccag tggttgttat gatctcaggc aggcctggca
1441 ttggaaaaac ccacatggcg aggcatttgg ctaagagcat cgccaacacc atgagtggcg
1501 accagagagt cgggctcgtt ccgcgcaacg gcgtcgacca ctgggatgcc tacagaggag
1561 agagggtggt cttgtgggat gactacggca tggggagccc cgttaaggac gctctaacac
1621 tacaagagct ggccgacaca tgcccagtca ctttaaattg tgacaggatt gagaacaagg
1681 ggaagatgtt tgacagtgat gtcatcataa tcacgaccaa cctagtcaac cccgcgcccc
1741 tcgactatgt aaacttcgag gcgtgttcta ggagagttga cttcctggtc tatgcagagt
1801 caccagaaat tgaaaaggtc aagagagact tccctggcca gcctgacatg tggaaagacc
1861 attttaaacc agacttctcc cacatcaagc tgactctagc cccccagggt gggtttgaca
1921 aaaatggcaa caccccacac ggtaagggaa ccatgcggtc cctaacacag gggtccctga
1981 ctgcgagagt tgcaggcctt gtccatgaga ggagagatga attccagctc caaggaaatg
2041 acctccaaat atacaatttt gacaccaaca gagtctccgc attcagaaaa ttggctgcag
2101 ataacaagta tgggatcatg gagacaatga gggtgggtac ggcactcaag aacgtgaaga
2161 ccctggaaga tcttaaaatt gcattgaggg atgtaaaatt taatgagtgt gaaataatct
2221 acaagaactc taagtatcgg gtctcttcca acggtaaagg ctcagtttct gttgataaag
2281 ttgaggacaa tgcatcccag actgtgaacg aggtacaatc agcaattctc aggctcaggc
2341 aagcgagggc cagatattac atcagctgct tccaagacct cgtctacact ctcatacagg
2401 ttgccggagc atcattcgtt gtcagcagga tctctagaag gttctgctgg gaaaggtggg
2461 tcaaaccgac cgagacccag gaggtgaatg attccgaaaa ggaagtggca caaggcagat
2521 gggaaattga acccaaggat acagaaccag aaggtaagaa gggtaagaac aagaaaggaa
2581 ggggtaagaa acacacagct ttctccagta aaggcctgag tgatgaagag tatgacgagt
2641 tcaagagaat cagggaagaa agaaacggaa agtactccat tgaggaatac ctgcaagacc
2701 gggaccgcta ttatgaagaa gtggcagttg cccgggcgac agaggaggac ttttgtgaag
2761 aggaagaggc caagataaga caaagaattt tccgcccgac aaagaaacag aggaaggagg
2821 agaggggtgt gcttggctta gtcaccggct cagacatcag gaagaggaga ccagatgact
2881 tccaaccaaa aggcaaccta tgggcagatg acaccagaag cgtggactac aacgagaggc
2941 ttgattttga agcgcccccg agtgtttggt caagaatagt cccattaggc actggttggg
3001 gattctgggt ttcatccaac cttctgatca caacaacaca cgtcctgcct aaaggagtta
3061 aggagttctt tggagttgaa attaagcaaa tccaagttca taagtctgga gagttttgca
3121 ggttcagatt cccaagacct atcaggccag atgtcacagg actcgtgttg gaggaaggcg
3181 ccccagaagg cactgtttgt tctatactca taaaaaggcc cacaggtgag atgatcccct
3241 tagcagtgag gatgggcaca catgcatcca tgaaaataca gggcaggact gttggtggcc
3301 agatgggaat gcttctcaca ggagcaaacg cgaagaacat ggacctcggt accggtcctg
3361 gtgactgcgg ttgtccttac atctacaaac gtggcaacga cattgttgtc gcaggtgttc
3421 acaccgcagc agcacgagga ggcaacactg ttatatgtgc cacccaaggg caagacgggg
3481 aagcagtcct tgaggggaac gaggaccttg gcacctattg tggcgcccca attttgggcc
3541 ccggcaaggc gcctaaactc agcacgaaga ccaagttttg gcgctcatca ccagatgcct
3601 taccacctgg cacatatgaa cctgcttacc tagggggcaa agaccctaga gtggaaaaag
3661 gtccttccct tcaacaagtc atgagagatc agttgagacc cttcacagaa cccaggggca
3721 aaccacctcg acctgcagtt ttggaggaag ccaaaaagac agtgatgaat gttctagaac
3781 aaaccattga ccccgccaag ccatggtcct actcgcaggc atgtgcctca ctggacaaaa
3841 ccacctccag tggtagtccc catcatgtta agaaaaacga ccactggaat ggggagtctt
3901 tcaccggccc acttgcagat caggcatcta aagccaacct catgtatgag caggctaagc
3961 atgtgcagcc cgtgtatacg gccgcgctca aagatgagct tgttaggact gacaagatct
4021 acaaaaagat aaagaagagg ctcctgtggg ggtcggacct tggcacaatg atcaggtgcg
4081 ccagggcctt tggtggtctc atggacagca tgaaggcaag ttgtatagct cttccttgta
4141 gggtaggaat gaacatgaat gaagatggcc ctattatatt tgacaaacat tctaagtaca
4201 ggtaccacta tgatgctgac tattctaggt gggactcaac ccaacaaagg agcattcttt
4261 ctgccgctat ggaagtgatg gtgcggttct ctgctgaacc agaattggca caagtggttg
4321 ctgaggacct tctagcacct agccagcttg acgttggcga ttttgtcatc tcggtccagg
4381 agggtctacc atcaggagtc ccatgcacat cacaatggaa ttcaatagca cactggatcc
4441 taactttgag tgcaatggca gaagtatcag gtctctcacc agatgtcgtc caagctcatt
4501 cttgtttttc cttttatggg gacgatgaga tcgtcagtac tgatatcaac cttgacccca
4561 tgaagttgac acagaaactc agggagtatg gcctggttcc cactcggcct gataaaactg
4621 aaggtcccct cgtcataact gaagacctca ccggcctgac gttcctccgt aggtcgattg
4681 ctcgggaccc agctggttgg tttggaaagc tggaccaaga ctcaatcctc aggcagctgt
4741 actggacaaa ggggcctaac catgagaacc catacgagag catggttcct cattctcagc
4801 gggccacaca actcatggcc cttcttggtg aggcctcact acatggtccc cagttttaca
4861 agaaagttag caagatggtc atcaatgaga ttaagagtgg tggtctggag ttttatgtgc
4921 ccagacaaga ggccatgttc aggtggatga gattctctga cctcagcaca tgggagggcg
4981 atcgcaatct tgctcccgaa ggtgtgaatg aagatggcgt cgaatgacgc agctccatcg
5041 aatgatggtg cagcaggcct cgtaccagag atcaacaatg aggtcatgcc ccttgagccc
5101 gtggctggtg catcgttggc gacaccagtt gtcgggcaac aaaatataat tgatccctgg
5161 ataagaaata attttgtaca agctcctgca ggtgagttca cagtctcccc tagaaactcc
5221 cctggtgaaa ttttacttga tttggagttg ggaccagaac tgaaccccta tctcgctcat
5281 ctggcccgta tgtacaatgg gcacgctggt ggcatggaag tgcaaattgt gttggctggg
5341 aatgcgttca cagctggcaa gatcatattt gctgccatcc ctccagggtt cccatatgaa
5401 aatttgtcac cttcacaaat cacaatgtgc cctcatgtta taattgatgt cagacaatta
5461 gaaccagttc tattgcctat gccagatatt aggaataatt tcttccatta caatcagggt
5521 aatgacccaa aattgagatt ggtagccatg ctctacaccc ctttaagggc taacaattct
5581 ggtgatgatg tgttcacagt ttcctgtagg gtcctcacta aaccgtcacc tgattttgaa
5641 ttcacatttc tggtcccccc tacggttgaa tctaagacca aacagttcac attgcccatc
5701 ctcaaaatat cagagatgac caactcaaga ttcccagttc cagtggaaat gatgtacaca
5761 gccaggaatg agaaccaagt tgtccagcca cagaatggta gggtcacact tgatggcgag
5821 ctattaggca ccacaccctt gttggctgtc aacatctgca aattcaaggg ggaggttata
5881 gctaagaatg gagatgtgag atcctatagg atggacatgg aaatcaccaa cactgatggc
5941 accccagttg accccacaga agacacacct ggtcccatag gttcacctga ctttcaaggt
6001 atactctttg gcgttgccag tcaacgcaat aagaatgaac agaaccctgc cacgagagcc
6061 catgaagcca acattaacac tggtggggac caatatgccc ccaaattggc ccaagtgaaa
6121 ttcttttcag agtcccagga tttcgaggta caccagccca cagttttcac cccagttggt
6181 gtggcaggcg acacctccca ccctttcaga cagtgggtcc tgcctcgata cggtggacat
6241 ctcaccaaca acacccattt ggctccagca gtggcccccc tgtttccagg tgagcagatt
6301 ctattcttta gatcacaaat acccagctca ggcggccatg aattgggtta catggactgc
6361 cttgtcccac aagagtgggt ccaacacttc taccaagaag ctgccacagc tcagtctgag
6421 gtggcactca taaggttcat taacccagac actggcagag tcctttttga ggccaagttg
6481 cacaagcaag gctttataac tgtggctcac accggtgaca acccaattgt catgccacca
6541 aatgggtact ttagatttga agcctgggtt aatcagtttt actcactcgc ccccgtggga
6601 actgggaatg ggcgcaggag gattcaataa tggccagtgc tttccttgca aatttggcag
6661 gaggcgttgc ctccaatgga attagttcac tcataaatgc tggggctaat gctattaacc
6721 aaaaggttga atttgattat aataaacaac tccaaaatgc atccttctcc catgacaagg
6781 aaatgctcca agcccaaatt gaagccacca aacgtctaca acaagagatg attgacataa
6841 aacaaggggt gctgacagct gcgggattct cccctacgga tgccgcaagg ggttctgtcg
6901 gcgcgccgat gacaaaatta gttgattgga gtggcactag atattgggcg cctggtgcca
6961 tgaggacaac aggttattca gggactttca ctcacttgcc ccctgtgcag tctgcctcat
7021 atgttaataa tcaaaataga caatctctta aagtagattc ttttcctcct tcttcgagtg
7081 gttcttctgt ctcttctgtc aagacacaat caaccaccct ctcaggcact tcaagggtgg
7141 gctcctcatc tcagtcaacc ctctcgacca ggccgagcac aaggacatct gattgggtgc
7201 gcagccagaa tgaaaggttg agtcccttca tggatggagc gttgcaaaca acgtatgtaa
7261 cgccaccgtc cagtagggca tcaagtgtca gcacagtctc gaccgtgccg aaagaggttt
7321 tggactcctg gacgcctatg tttaatactc acaggcagcc actcttcgcc catttgcgta
7381 agcgagggga gtcacagatt tagtgaaaag attggttagg aaagttgatt agtctgttct
7441 tctctactat tccttt
//