Typing tool
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Typing tool
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Complete norovirus genomes
| MH260510 | GII.6 | |
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| GII.P7 |
ORF1: 1..4962
ORF2: 4943..6586
ORF3: 6586..7193
LOCUS MH260510 7193 bp RNA linear VRL 16-JUN-2018
DEFINITION Norovirus GII isolate ST287 nonstructural polyprotein (ORF1) gene,
partial cds; VP1 (ORF2) gene, complete cds; and VP2 (ORF3) gene,
partial cds.
ACCESSION MH260510
VERSION MH260510.1
DBLINK BioProject: PRJNA338014
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7193)
AUTHORS Casto,A.M., Adler,A., Huang,M.-L., Makhsous,N., Xie,H., Zerr,D. and
Greninger,A.
TITLE The limits of epidemiology: Real-time metagenomic sequencing during
norovirus outbreak reveals discrete transmission clusters and
elucidates long-term sequelae of hospital acquired infections
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 7193)
AUTHORS Casto,A.M., Adler,A., Huang,M.-L., Makhsous,N., Xie,H., Zerr,D. and
Greninger,A.
TITLE Direct Submission
JOURNAL Submitted (25-APR-2018) Department of Laboratory Medicine,
University of Washington, 1100 Fairview Ave. N, E5-110, PO Box
19024, Seattle, WA 98109, USA
FEATURES Location/Qualifiers
source 1..7193
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="ST287"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="USA"
/collection_date="2017"
/note="genotype: GII"
gene <1..4962
/gene="ORF1"
CDS <1..4962
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="AWT08386.1"
/translation="MLGAVPKGTKAPSSDQHCPSVKIGTKTLTVPPEPPNGEDAVQFD
AKSETVRGLPDLTTVQNEHENTPYTVPPLSEREHRPATEPLPGTILEMWDGEFYHYSV
YVSGGKALGVHKPPAAISLATIELTPISLYWRPVYTPNYLVCPDTLKGLAGEKFPYTA
FSNNCYNFCCWVLELNDTWLSRKSISRTTGFFKPYQSWNRKPLPTVDDGKIKKVANAI
LCALGSLFSKPIKDLLGKLKPLNLLHLLASCDWTFAGIVETVILMAELFGIFWTPPDV
SSFIASLIGDFELQGPEDLAVELVPVVMGGIGMVLGFTAEKIGRMLSSAASTLRACKD
LGNYALDILKLVMKWFFPKKEEKAEMETLRAIEDAVLDMEAIGNNHLTTLLKDKDSLT
AFMKTLDLEEEKARKLSTKSSSPDIVGTINAILARIAAARSLLHKAKEEMFSRIRPVV
VMISGRPGIGKTHMARHLAKSIANTMSGDQRVGLVPRNGVDHWDAYRGERVVLWDDYG
MGNPVKDALTLQELADTCPVTLNCDRIENKGKMFDSDVIIITTNLVNPAPLDYVNFEA
CSRRVDFLVYAESPEIEKVKRDFPGQPDMWKDHFKPDFSHIKLTLAPQGGFDKNGNTP
HGKGTMRSLTQGSLTARVAGLVHERRDEFQLQGNDLQTYNFDANRVSAFRKLAADNKY
GIMETMRVGTALKGVKTLEDLKAALRDVKFNECEIIYRNSKYRVSSNGKGSVSVDKVE
DQTSQTANEVGAAILRLRQARARYYVSCFQDLVYTLIQVAGASFVVNRISKRFCWERW
VKPTETQETSESEKEVARGRWEIEPKDTEPEGKKGKNKKGRGKKHTAFSSKGLSDEEY
DEFKRIREERNGKYSIEEYLQDRDRYYEEVAVARATEEDFCEEEEAKIRQRIFRPTKK
QRKEERGVLGLVTGTDIRKRRPDDFQPKGNLWADDTRSVDYNERLDFEAPPSVWSRIV
PLGTGWGFWVSSNLLITTTHVLPKGINELFGVEIKQIQIHKSGEFCRFRFPRPIRPDV
TGLVLEEGAPEGTVCSILVKRPTGEMIPLAVRMGTHASMKIQGRTVGGQMGMLLTGAN
AKNMDLGTGPGDCGCPYIYKRGNDIVVAGVHTAAARGGNTVICATQGQDGEAVLEGNE
NLGTYCGAPILGPGKAPKLSTKTKFWRSSPDALPPGTYEPAYLGGKDPRVEKGPSLQQ
VMRDQLKPFTEPRGKPPRPAVLEEAKKTVMNVLEQTIDPAKPWTYSQACASLDKTTSS
GSPHHVRKNDHWNGESFTGPLADQASKANLMYEQAKHVQPVYTAALKDELVKTDKIYK
KIKKRLLWGSDLGTMIRCARAFGGLMDSMKASCIALPCRVGMNMNEDGPIIFDKHSKY
RYHYDADYSRWDSTQQRNILSAAMEVMVRFSAEPELAQVVAEDLLAPSQLDVGDFVIS
VQEGLPSGVPCTSQWNSIAHWILTLSAMAEVSGLSPDVVQAHSCFSFYGDDEIVSTDI
NLDPMKLTQKLREYGLVPTRPDKTEGPLVITEDLTGLTFLRRSIARDPAGWFGKLDQD
SILRQLYWTRGPNHENPYESMVPHSQRATQLMALLGEASLHGPQFYKKVSKMVISEIK
SGGLEFYVPRQEAMFRWMRFSDLSTWEGDRNLAPEGVNEDGVE"
mat_peptide <1..870
/gene="ORF1"
/product="p48"
mat_peptide 871..1968
/gene="ORF1"
/product="NTPase"
mat_peptide 1969..2487
/gene="ORF1"
/product="p22"
mat_peptide 2488..2886
/gene="ORF1"
/product="VPg"
mat_peptide 2887..3429
/gene="ORF1"
/product="Pro"
mat_peptide 3430..4959
/gene="ORF1"
/product="RdRp"
gene 4943..6586
/gene="ORF2"
CDS 4943..6586
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="AWT08384.1"
/translation="MKMASNDAAPSNDGAANLVPEATNEVMALEPVVGASIAAPVVGQ
QNIIDPWIRENFVQAPQGEFTVSPRNSPGEMLLNLELGPELNPYLGHLSRMYNGYAGG
MQVQVVLAGNAFTAGKIIFAAVPPHFPVENISAAQITMCPHVIVDVRQLEPVLLPLPD
IRNRFFHYNQENTPRMRLVAMLYTPLRANSGEDVFTVSCRVLTRPAPDFEFTFLVPPT
VESKTKPFTLPILTLGELSNSRFPAPIDMLYTDPNEAIVVQPQNGRCTLDGTLQGTTQ
LVPTQICSFRGTLISQTSRSADSTDSAPRVRNHPLHVQLKNLDGTPYDPTDEVPAVLG
AIDFKGTVFGIASQRNTTGSSIGATRAHEVHIDTTNPRYTPKLGSVLMYSESNDFDDG
QPTRFTPIGMGADDWRQWELPEYSGHLTLNMNLAPAVAPAFPGERILFFRSVVPSAGG
YGSGHIDCLIPQEWVQHFYQEAAPSQSAVALIRYVNPDTGRNIFEAKLHREGFITVAN
SGNNPIVVPPNGYFRFEAWVNQFYTLTPMGTGQGRRRVQ"
gene 6586..>7193
/gene="ORF3"
CDS 6586..>7193
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="AWT08385.1"
/translation="MAGAFLAGLAGDAITSGVGSLINAGANAINQKVEYDFNKQLQLA
SFKHDKEMLQSQVLATKQLQQEMMNIRQGVLSAGGFSPTDAARGAVNAPMTKILDWNG
TRYFAPNSMKTTSYSGQFSSNPMHRQPTLPRSAPPKIKANSDSASVYSSASTAPSQST
HSTALTVGSGSSRTTSSSAVASNLSRTSDWVRGQNERLSPFM"
ORIGIN
1 atgctgggtg ccgttcccaa ggggaccaaa gcacccagta gtgatcagca ctgcccctca
61 gttaagatcg ggaccaagac attaacagtt ccccctgagc ccccaaatgg tgaagacgcc
121 gtgcagtttg atgcgaagtc ggaaactgtg cgcgggttgc cagacttgac aacggtgcag
181 aatgaacacg aaaacacacc atacactgtc cccccactga gtgaaaggga gcacagacca
241 gctactgaac cgcttcctgg cacaatactg gagatgtggg atggtgaatt ctaccattac
301 tctgtgtacg tcagcggtgg caaagcccta ggggttcaca aaccccctgc agcgataagc
361 ctcgcgacga tagagctcac acccatatct ctttattgga ggcccgttta cacccccaac
421 tatctagtct gcccagacac gttgaagggc cttgctggtg agaagttccc ctacacggcc
481 ttcagcaaca actgttacaa cttctgttgc tgggtgcttg agctcaatga cacgtggctt
541 agcaggaaaa gcatctctag gaccaccggc ttcttcaaac cataccagtc ttggaatagg
601 aaaccccttc caaccgttga tgatggaaag atcaaaaagg tggccaacgc aattctctgt
661 gcactcggat cactgttttc aaaaccaatc aaggacctat tgggcaaact taaaccattg
721 aacttgctgc acttgctcgc atcatgtgac tggacgtttg cgggcatagt agagacagtc
781 atcctaatgg cggaactctt cggcatcttt tggacaccgc cagatgtttc cagcttcata
841 gcctccctga taggtgattt tgaattgcaa gggcctgagg acctggctgt ggagcttgtg
901 cccgtggtca tgggtggcat aggaatggtt ctcggcttta ctgctgagaa gataggccgc
961 atgctgtcgt ctgctgcatc aacactgcgg gcgtgcaaag acttggggaa ttatgctctt
1021 gacatattga aactggttat gaagtggttc ttcccaaaga aagaagagaa agccgagatg
1081 gaaaccctga gggcgattga ggatgccgtc ctggacatgg aagctatagg aaataaccat
1141 ctcacgaccc tcctcaagga caaggatagc ctcacggctt tcatgaagac tttagaccta
1201 gaagaagaga aggcaaggaa gctgtccacc aagtcatcct cgccagacat tgtcggcacc
1261 attaatgcca tactggctag aatagctgct gccaggtccc tcttgcacaa ggctaaagaa
1321 gaaatgttca gcaggatcag acccgtggtt gtcatgatct cgggtagacc tggtattggc
1381 aaaacccaca tggcaagaca cctggccaag agtatcgcca acaccatgag cggcgaccag
1441 agagtggggc tcgtcccacg caacggggtt gatcattggg atgcctacag gggagagagg
1501 gtggttttat gggatgacta tggcatggga aaccctgtca aagatgccct aacgttgcaa
1561 gagctggccg acacctgccc agtaactcta aactgtgata ggattgagaa caaggggaag
1621 atgtttgaca gtgatgtcat cataatcacg accaatttag tcaacccagc gcccctcgat
1681 tatgtaaact tcgaggcgtg ctccagaagg gttgactttc tggtctatgc agagtcacca
1741 gaaattgaga aggttaagag agactttccc ggccaacctg acatgtggaa ggaccatttt
1801 aagccagact tttcccacat aaaactgact ctagccccac aaggtgggtt tgacaagaat
1861 ggcaacaccc cgcatggtaa gggcaccatg cgatccctaa cccaggggtc cctgactgca
1921 agggttgcag gtcttgttca tgagaggaga gacgagtttc agctccaggg gaacgacctt
1981 caaacatata actttgatgc caacagagtc tctgcattta ggaagctggc cgcagacaac
2041 aagtatggga tcatggagac tatgagagtg ggcacagcgc ttaagggtgt caagaccttg
2101 gaggatctga aagctgcact gagggacgtg aagttcaatg agtgtgagat aatttacaga
2161 aactctaaat accgagtctc ttccaatggt aaaggttctg tctctgttga caaagttgag
2221 gaccagacat cccagaccgc aaacgaagtg ggtgcagcaa tccttaggct cagacaggca
2281 agagccagat actatgtcag ctgcttccaa gacctcgttt acactctaat acaggtcgcc
2341 ggagcatcat tcgttgtcaa caggatctct aaaaggttct gctgggagag atgggtcaaa
2401 ccaaccgaga cccaggaaac gagtgagtcc gaaaaggaag tggcccgagg cagatgggag
2461 attgagccca aggacacaga accagaaggt aagaagggta agaacaagaa aggaagaggc
2521 aagaaacaca cagctttctc cagtaaaggc ttgagtgatg aggagtatga cgagttcaag
2581 agaatcagag aagaaaggaa cggaaaatac tccattgagg aatacctgca agaccgggat
2641 cgctactatg aggaagtggc agttgcccgg gcgacagagg aggacttctg tgaagaggag
2701 gaggccaaga taagacaaag aatctttcgc cccacaaaga aacagaggaa ggaagaaagg
2761 ggggtgcttg gtttggttac tggcacagac atcaggaaga gaagaccaga cgattttcaa
2821 ccgaaaggca acctgtgggc agacgacact aggagcgtgg actacaacga gaggcttgat
2881 ttcgaggctc ccccgagtgt ctggtcaaga atagtcccat tgggcactgg ctggggcttc
2941 tgggtctcat caaacctcct gatcacaaca acgcacgtcc tacctaaggg gattaatgag
3001 ctctttggag ttgagatcaa acagatccag atccataagt ctggagagtt ctgcaggttc
3061 agatttccaa gaccaattag accagatgtc acagggctcg tgttggagga aggcgctcca
3121 gaaggcactg tctgctccat actcgtaaag agacctacag gtgagatgat ccccctggca
3181 gtgaggatgg gcacgcatgc atccatgaaa atacagggta ggaccgttgg tggccagatg
3241 ggaatgctcc tcacaggggc aaatgcgaag aacatggatc ttggcaccgg tcctggtgac
3301 tgcggttgcc cttacatcta caaacgcggc aatgatatag ttgtcgcggg tgtccacacc
3361 gcagcagccc ggggaggcaa cactgtcata tgtgccactc aagggcaaga tggggaagca
3421 gtccttgagg gaaatgagaa ccttggcact tactgcggtg ctccaatcct gggtccaggc
3481 aaggcgccca aactcagcac gaagaccaag ttctggcgtt catcaccaga cgctttgcca
3541 ccaggcactt atgagcctgc ctacttgggg ggtaaggacc ctagagtgga aaaaggacca
3601 tccctgcagc aagtcatgag ggaccagcta aaacctttca cagagcccag gggcaagcca
3661 cctagacctg cagtcttaga agaagctaaa aagacagtga tgaatgttct agagcaaacc
3721 attgatcctg ctaaaccgtg gacctattcc caagcatgtg cctcactgga caagaccact
3781 tccagtggta gcccccatca tgtcaggaaa aatgaccatt ggaatgggga atccttcact
3841 ggccccctcg cagaccaagc atccaaagcc aacctcatgt acgagcaggc taaacatgtg
3901 cagcctgtgt acacggccgc actcaaagat gaactagtca aaactgataa gatctacaag
3961 aagataaaga aaaggctctt atgggggtcg gatcttggta caatgatcag gtgtgccagg
4021 gcctttggcg gtctcatgga tagcatgaag gcaagctgca tagccctccc gtgtagggta
4081 ggaatgaaca tgaatgaaga tggccccatc atatttgaca aacattctaa gtataggtac
4141 cattatgatg ctgattattc caggtgggac tcaacccagc aaaggaacat tctctcggcc
4201 gctatggaag tgatggtgcg gttctctgct gaaccagagc tggcacaagt ggttgcagag
4261 gacctcctgg cacccagcca actagatgtt ggcgatttcg ttatctcagt ccaggagggc
4321 ctgccatcag gggtcccatg cacatcacaa tggaattcaa tagcacactg gatcctaacc
4381 ttgagcgcaa tggcagaagt atcgggtctc tcaccagatg ttgttcaagc ccactcctgt
4441 ttctcattct atggtgatga tgagatcgtc agcactgaca tcaaccttga ccccatgaag
4501 ttgacacaga agctcagaga gtatggtctg gtccccactc gacctgacaa aactgagggt
4561 cccctcgtaa taactgaaga tctcaccggc ctaacgttcc tgcgtaggtc aattgcacgg
4621 gacccagctg ggtggtttgg aaaattggac caagactcaa tcctcagaca gttgtactgg
4681 acaagaggcc ccaaccatga gaacccatat gagagcatgg tccctcattc ccagcgggcc
4741 acacaactca tggccctcct cggtgaggct tcactgcatg gtcctcagtt ttacaagaaa
4801 gttagcaaga tggttattag tgagatcaaa agtggtggtc tggaattcta tgtacccaga
4861 caagaggcca tgttcagatg gatgagattc tctgacctca gcacatggga gggcgatcgc
4921 aatcttgctc ccgagggtgt gaatgaagat ggcgtcgaat gacgctgctc catcgaatga
4981 tggtgctgcc aacctcgtac cagaggccac caatgaggtt atggcacttg agccggtggt
5041 gggagcctca attgctgctc ctgtcgtcgg ccaacaaaat ataattgacc cctggattag
5101 agaaaatttt gttcaggcac cacagggtga gtttactgtt tcaccaagga actcaccagg
5161 tgagatgctt ctaaatcttg aattaggccc tgagctcaac ccttatctgg gtcatttgtc
5221 ccgcatgtac aatggctatg ctggtggtat gcaggttcag gtggtcctag ctgggaatgc
5281 gttcacagct ggtaaaatca tctttgccgc cgtcccacca catttccctg ttgagaacat
5341 tagtgcagcc caaattacaa tgtgccccca tgtaattgtt gatgtaagac agcttgagcc
5401 agtgcttttg cccctccctg acataaggaa tagattcttt cattataatc aggaaaatac
5461 cccccggatg agacttgtgg ctatgttgta tacacccctt agagcaaatt ctggtgagga
5521 tgtgtttacg gtgtcttgca gagttctgac ccgccctgcc cccgactttg agttcacgtt
5581 tttggtgcca ccaaccgtgg agtcaaagac taaacccttt acacttccta ttctgactct
5641 tggagagctg tccaactcta gattccccgc tccgatagac atgttgtaca ctgaccccaa
5701 tgaggcaatt gtggtgcaac cacaaaatgg caggtgcact ctagatggaa cacttcaggg
5761 gaccacccaa ctggtgccca cccaaatttg ctccttcagg ggcacgctaa ttagtcagac
5821 gtcgaggtct gcagactcaa ctgattcagc cccacgggtg aggaaccacc ctctccacgt
5881 tcagctgaag aacctcgatg ggacaccata tgacccaaca gatgaggtgc cagcagtttt
5941 gggtgccata gatttcaaag gaactgtgtt tgggatcgct agccaaagaa acaccacagg
6001 gagctctata ggagcgaccc gcgcccatga agtgcacata gacaccacaa accctagata
6061 caccccaaag cttggctctg tgttgatgta ttctgaatca aatgattttg atgatggaca
6121 acctacccgc tttaccccca ttggcatggg agccgatgat tggcgccaat gggaattgcc
6181 cgaatattct ggtcacctca ctcttaacat gaatttggcc cccgcagttg cccctgcttt
6241 tcctggtgag cgcattctct tcttcaggtc agtggtgcca tctgctggtg gctatggatc
6301 aggtcacata gattgcctca tcccacagga gtgggttcag catttctatc aggaggccgc
6361 tccatcacaa tccgcggtgg ctctcatcag atatgtcaac cctgacactg gaagaaacat
6421 ctttgaggca aaactgcata gagaagggtt catcactgtg gcaaattctg gaaacaatcc
6481 catagttgtg cccccaaatg gctacttcag gtttgaggcc tgggtcaatc aattctacac
6541 actcaccccc atgggaactg gacaggggcg cagaagagtt caataatggc aggagctttc
6601 ttagctggat tagcaggtga cgccataaca agtggtgtcg ggtccctaat taatgctggg
6661 gccaatgcaa ttaaccaaaa ggtagaatat gactttaata aacagctcca attggcatcc
6721 ttcaaacatg ataaagagat gttgcagtca caagtactgg ccactaaaca gctccagcag
6781 gagatgatga acataaggca aggggtcttg tccgctggcg gcttttcccc tacagatgcc
6841 gcgagaggtg ctgtgaacgc gccgatgaca aaaattttgg attggaatgg aacaaggtac
6901 tttgccccaa atagtatgaa aacaaccagt tattcgggcc agttttccag caaccctatg
6961 cataggcaac ccactttacc ccgttctgca cccccaaaaa ttaaggctaa tagtgattct
7021 gctagtgtgt atagttctgc atctactgct ccttcacaat caactcactc aacggctctg
7081 actgtggggt ctggctcatc taggacaaca tcctcttctg cagtagcttc caacctatct
7141 aggactagtg actgggtgag aggacaaaat gaaaggctta gcccgttcat gga
//