Typing tool
|
|
|
|
|
|
Typing tool
|
Complete norovirus genomes
| OP686904 | GII.8 | |
|
|---|---|---|---|
| GII.P8 |
ORF1: 5..5104
ORF2: 5085..6698
ORF3: 6698..7471
LOCUS OP686904 7533 bp RNA linear VRL 25-OCT-2022
DEFINITION Norovirus GII isolate Hu/US/2020/GII.8[P8]/CA-RGDS-1153, complete
genome.
ACCESSION OP686904
VERSION OP686904.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norovirus norwalkense.
REFERENCE 1 (bases 1 to 7533)
AUTHORS Pan,C.-Y., Hatada,A., Morales,C., Montmayeur,A.M., Chhabra,P. and
Vinje,J.
TITLE Direct Submission
JOURNAL Submitted (20-OCT-2022) Viral and Rickettsial Disease Laboratory,
California Department of Public Health, 850 Marina Bay Parkway,
Richmond, CA 94804, USA
COMMENT ##Assembly-Data-START##
Assembly Method :: Geneious v. R10; SPAdes v. 3.6
Sequencing Technology :: Illumina
##Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..7533
/organism="Norovirus GII"
/mol_type="genomic RNA"
/strain="CA-RGDS-1153"
/isolate="Hu/US/2020/GII.8[P8]/CA-RGDS-1153"
/isolation_source="stool"
/host="Homo sapiens"
/db_xref="taxon:122929"
/geo_loc_name="USA: CA"
/collection_date="Feb-2020"
/note="Amplicon sequencing:first 35 nt does represent
primer sequence;
genotype: GII.8[P8]"
gene 5..5104
/gene="ORF1"
CDS 5..5104
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="UYL06246.1"
/translation="MKMASNDASAAAGNFNIANNSESTPPPIKEEASVLSNVKVGFKK
ILGAVPKQPKPPEVKTKDQPRVLVNGKALEVPPPPPNGEDVVYYNSKDDTVHGLPNLT
TVSCEGENLPYTVPPLSEREHRAAPEPLPGTILEMWDGEFYHYAIYVSGGKAIGVHKP
PAAISLATIELTPISLYWRPVYVPNYLVHPDTLKSLAGEKFPYTAFSNNCYNFCCWVL
DLKDSWLNRRSITRTTGFFKPYQTWNKKPLPTVDDGKIKKVANAVLCALGSLFSKPIK
DLIGKLKPLNFLNLLASCDWTFSGVVETVILAAELFGVFWTPPDVSNFIASLIGDFEL
QGPEDLAVELVPIIMGGIGMVLGFTAEKIGRMLSSAASTLRACKDLGNYALDILKLVM
KWFFPKKEEKAEMETLRAIEDAVLDMEAIGNNHLTALLKDRDSLLTYMKTLDLEEEKA
RKLSTKSSSPDIVGTINAILARIAAARSLLHRAKEEMYSRPRPVVVMISGRPGVGKTH
MARHLAKSVAGTMSGDQRVGLIPRNGVDHWDAYRGERVVLWDDYGMGNPVKDALALQE
LADTCPVTLNCDRIENKGKMFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEA
PTIEKAKKDFPGQPDMWKEHFKADFSHLKLTLAPQGGFDKNGNTPHGKGTMKTLTQGS
LTARVAGLVHERKDEFQLQGGELQVYNFDTNKVSAFRKLAADNNYGFLETMRVGTSLK
DVKTVEDLKCALKSVSFKECEIIYRNVKYRISSDGCGKVSIEKLADNNSQTTREIITA
VTRLRQARARYYISCFQDLVYTLLQVAGASFVINRIVKKFNWERWVKTPETDEPTPSN
DKPDTEEEWEIAPKDVDSEGKKGKNKKGRGRKHTAFSSKGLSDEEYDEFKRLREEKQG
RYTIEEYLQDRDRYYEELAVARATEENFCEEEEIKIRQRIFRPTKKQRKEERGVLGLV
TGADIRKRRPDDFQPKGKLWADDSRSVDYNEKIEFEAPPSVWSRIVPLGTGWGFWVSS
NLLITTTHVLPKGIKELFGVDIKQVQVHKSGEFCRFRFPKPVRPDVSGLVLEEGAPEG
TVCSVLIKRSTGEMIPLAVRMGTHASMKIQGRTVGGQMGMLLTGANAKNMDLGTGPGD
CGCPYIYKRGNDIVVAGVHTAAARGGNTVICATQGPDGEAVLEGGEDHGTYCGAPILA
PGKAPKLSTKTKFWRSSPDSLPPGTYEPAYLGGKDPRVEKGPSLQQVMRDQLKPFTEP
RGKPPRPSVLEEAKKTVMNVLEQTIEPAKPWTYSQACASLDKTTSSGSPHHVRKNEHW
NGESFTGPLADQASKANLMYEEGKHMDPMYTAALKDELVKTDKIYKKIKKRLLWGSDL
GTMVRCARAFGGLLDSMKESCISLPCRVGMNINEDGPLIFEKHSKYTYHYDADYSRWD
STQQRAVLSAAMEVMVKFSAEPELAQVVAEDLLAPSRLDVGDFVVSVQEGLPSGVPCT
SQWNSIAHWILTLSAMSEVSGLSPEVVQANSCFSFYGDDEIVSTDINLDPEKLTRKLR
EYGLVPTRPDKTEGPLVITQDLNGLTFLRRTIVRDPAGWFGKLDRDSILRQLYWTRGP
NHENPFESMIPHSQRATQLMALLGEASLHGPQFYKKVSKMVINEIKSGGLEFYVPRQE
AMFRWMRFSDLSTWEGDRNLAPENVNEDGVE"
mat_peptide 5..1009
/gene="ORF1"
/product="p48"
mat_peptide 1010..2107
/gene="ORF1"
/product="NTPase"
mat_peptide 2108..2629
/gene="ORF1"
/product="p22"
mat_peptide 2630..3028
/gene="ORF1"
/product="VPg"
mat_peptide 3029..3571
/gene="ORF1"
/product="Pro"
mat_peptide 3572..5101
/gene="ORF1"
/product="RdRp"
gene 5085..6698
/gene="ORF2"
CDS 5085..6698
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="UYL06247.1"
/translation="MKMASNDAAPSNDGAAGLVPEINHEVMAIEPVAGASLAAPVVGQ
LNIIDPWIRNNFVQAPAGEFTVSPRNAPGEFLLDLELGPELNPYLAHLARMYNGHAGG
MEVQIVLAGNAFTAGKILFAVIPPGFPYENLSPAQLTMCPHVVVDVRQLEPILLPMPD
IRNTFFHYNQSNGPKLRLVAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFEFNFLVPP
SVESKTKAFTLPILKTSEMTNSRFPIPVDQMYTSRNENIVVQPQNGRVTLDGELQGTT
TLQPVSICGFRGTLQTRLADQPNYTYQVHLENLDGSPVDPTDEVPAPLGTPDFQAQLF
GVVSQRSSDNATRAHEARVNTNDPTFAPQIAQVRFKSPSHDFFDNEPIKFTPVGISVD
SENSYNQWLLPRYGGHLTNNTHLAPSVSPMFPGEQILFFRSFMPGASGHTDGAIDCLL
PQEWVAHFYQEAATAQTDVALIRFVNPDTGRVLFEGKLHKQGFITISNSGDHPIVMPA
NGYFRFEAWVNQFYSLAPVGTGSGRRRIQ"
gene 6698..7471
/gene="ORF3"
CDS 6698..7471
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="UYL06248.1"
/translation="MAGAFLAGLAGDVVTSGIGSLINAGANAVNQKVEYDFNRQLQEA
SFKHDKEMLNAQINATTKLQRDMIAIKQGVLTAGGFSPTDAARGSINAPTTKILDWNG
SRYWAPGSMRTTAYSGNFISQGVKQPTPIVKSVEPQVQQSPAPSSVYSVGSVKSQSTQ
STQLTGSGTVSRAPTPSTTTTLSRTSEWVRSQNDRLSPFMGGALQTAFITPPSSKASS
SSGTVSTVPREILDSWTPVFNTRRQPLFAHMRRRGESRA"
ORIGIN
1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgct ggcaacttta acattgccaa
61 caacagtgaa agcactcccc ctcccattaa ggaagaggcg agtgtcctat ccaacgtaaa
121 agttggattc aagaaaatat tgggggctgt gcctaagcag cccaagccac cagaagtgaa
181 aaccaaagat caacccaggg tgctggtcaa tggtaaggcc ctggaggtgc cgcccccacc
241 accaaatggt gaagacgtgg tttactataa cagcaaggat gacactgtgc acggcctacc
301 aaatctaaca acagtcagct gtgaaggtga aaaccttccg tacacagttc ctcctctcag
361 cgagagagag cacagggcag caccagaacc attacctggc accatactag agatgtggga
421 tggtgaattc taccattatg cgatatatgt ctctggtggt aaggccatag gggtgcacaa
481 acccccagct gcaatcagcc ttgctaccat cgagcttaca cccatatcgc tttactggag
541 gcctgtctat gtccccaatt acttggtcca ccctgacaca ctcaagagct tagctggtga
601 aaaatttcca tacaccgcat ttagcaacaa ttgttacaat ttctgttgct gggttcttga
661 cttgaaagac tcgtggctta accgcaggtc aataactaga acaaccggtt tcttcaagcc
721 ttatcaaacc tggaacaaga aaccactccc gacggtggat gatggaaaaa tcaagaaagt
781 cgccaatgca gtcctgtgtg cccttggttc actattctca aaacctatta aggacttgat
841 cgggaagctg aaaccattga atttcttgaa tctcctcgct tcgtgcgatt ggacattctc
901 cggagtggtt gagaccgtca tactagctgc tgaactattc ggagtgtttt ggacccctcc
961 cgacgtgtcg aacttcatcg cgtcactcat cggggacttt gagttgcagg gtccagagga
1021 tttagctgtg gagttggtgc cgattatcat gggcggcatc gggatggtgc tgggattcac
1081 cgccgagaag atcggccgaa tgctatcatc agctgcgtcg acccttaggg cctgtaaaga
1141 cctaggtaac tatgcccttg acatacttaa attggtcatg aagtggttct tcccaaagaa
1201 ggaggaaaag gcagagatgg agaccttgag ggccatagag gatgctgttt tggacatgga
1261 ggcgattgga aataatcacc tcactgctct gttgaaagac agggacagtc tcctaaccta
1321 catgaagact ctagacctcg aagaggaaaa ggcaagaaag ttatccacaa aatcatcttc
1381 ccctgacatc gtgggtacca tcaatgccat actagccaga attgccgcgg ctaggtctct
1441 cctacacaga gctaaagaag aaatgtacag cagacctagg cctgtcgtgg tgatgatatc
1501 aggaagacca ggggttggca aaacccatat ggctagacac ctcgccaaga gtgtggcggg
1561 caccatgagc ggtgaccaaa gggtgggcct catcccccgt aatggagttg atcactggga
1621 tgcctacagg ggggaacgag tagtcttgtg ggacgactat ggcatgggca acccagtgaa
1681 ggacgccctt gctctgcaag aactagcaga cacttgtcca gtcaccctca attgtgacag
1741 gatagagaat aagggaaaga tgtttgatag cgaggtaata attataacaa ccaatctggc
1801 caaccccgcc ccgcttgatt atgtcaactt tgaggcatgt tcccgcagaa ttgacttcct
1861 cgtctacgca gaggccccga ccattgagaa ggcgaagaaa gatttccccg gacaaccaga
1921 catgtggaag gagcacttca aagcagactt ctctcatctc aaactcacac tggccccaca
1981 aggcggtttt gacaagaacg gcaacacgcc acatgggaag gggactatga agaccttgac
2041 acagggttcc ctcacagcaa gagtggctgg gcttgtgcat gaaaggaaag acgagttcca
2101 gttacagggt ggagagttgc aggtctacaa ctttgacaca aacaaggtat cggctttcag
2161 gaagcttgct gcagacaaca actatgggtt tctggagaca atgagagtcg gcacctcact
2221 caaggacgtc aagacagtgg aagaccttaa atgtgcactc aagagtgtca gtttcaaaga
2281 atgtgaaata atctacagga atgtcaagta ccgcatatca tcagacggtt gcggtaaggt
2341 cagcatagag aaactggcag ataacaactc ccaaacaacc agagagatta tcacggccgt
2401 cactagacta cgacaggctc gtgctaggta ctacattagc tgcttccaag acctagtcta
2461 cacactcttg caggttgccg gagcctcatt tgtcattaat agaatagtta agaagttcaa
2521 ctgggaacga tgggtcaaga ccccagaaac ggatgaaccc acaccaagta atgacaagcc
2581 cgacactgaa gaggaatggg agatcgcccc caaagatgtg gactctgagg gtaaaaaggg
2641 gaagaacaag aagggcagag gacgtaagca cactgcattc tccagcaaag ggcttagtga
2701 tgaggagtat gatgaattca aaaggctgag ggaagagaaa cagggccgct acacaataga
2761 ggagtacctc caggacagag accggtacta tgaagagctg gcagtggccc gggccactga
2821 agagaacttc tgtgaagagg aagagataaa gatcaggcaa agaatattcc gccccaccaa
2881 aaagcagagg aaggaggaga ggggggttct gggactcgtc acaggagcag acatcaggaa
2941 acggagaccc gatgatttcc aaccaaaagg aaaactgtgg gcagatgatt ctaggagcgt
3001 cgactacaat gagaagatcg agtttgaagc tcctcctagc gtctggtcaa gaatcgtccc
3061 gcttgggact ggttggggat tctgggtctc atccaactta ctaatcacca ccacacatgt
3121 gctgcccaaa ggcattaaag agctttttgg ggtggacatc aaacaagtcc aagtccacaa
3181 atcaggtgaa ttttgcagat tcaggttccc aaaaccagtg aggccagatg tctctgggtt
3241 ggtactagaa gaaggggccc ccgaaggcac agtgtgctct gttctcatca agaggtcaac
3301 aggagagatg atcccccttg cagtcaggat gggcacccac gcctctatga agatccaggg
3361 gcgcactgtt ggcggccaga tgggcatgct gctcactgga gccaacgcta agaacatgga
3421 tttaggcacc ggccccgggg attgtggttg cccgtacata tacaagaggg gcaatgacat
3481 cgtggtggcc ggcgtccaca cagcagcagc gcgcgggggc aacacggtca tctgcgcaac
3541 ccaaggacct gatggtgagg cagtgttgga agggggagag gaccacggca cttattgtgg
3601 agctccaata ttggcccctg gtaaagcgcc gaagcttagc acaaagacta agttttggcg
3661 ctcatcccct gattcccttc cccctgggac gtatgaacca gcttaccttg ggggtaagga
3721 tccccgtgtg gagaaagggc cgtcactcca acaagtgatg cgagaccaac taaaaccctt
3781 cacagaaccc aggggcaagc cacctaggcc gtcagtgctg gaggaagcca agaagacagt
3841 catgaatgta ctggagcaga ccatagaacc agctaagcca tggacctact ctcaagcctg
3901 tgcttcattg gataaaacaa catccagtgg cagtcctcac cacgtcagga agaatgaaca
3961 ctggaacggg gagtctttca ctgggcctct tgcagatcaa gcctcaaaag ccaacctgat
4021 gtatgaggag ggtaaacaca tggaccctat gtacacagca gccctcaagg acgagttggt
4081 gaaaactgac aaaatctata agaaaatcaa gaagaggttg ttgtgggggt ctgatctggg
4141 gacaatggta aggtgtgctc gagcgtttgg aggattgctc gacagcatga aagagagttg
4201 catctcctta ccctgtaggg ttggcatgaa cataaacgaa gatggaccac tcatatttga
4261 aaaacattcc aaatacacct atcactatga tgctgactac tctaggtggg actcaacgca
4321 acagagggct gtcctgagtg cagccatgga ggtaatggtg aagttctctg ctgagccgga
4381 actggctcag gtggttgccg aagacctcct tgcacccagc cgtcttgacg tgggtgactt
4441 cgtcgtctcc gtccaagaag gtcttccatc gggtgtcccc tgcacgtcac agtggaactc
4501 aatcgctcac tggatcctga ctcttagtgc tatgtctgag gtctctggtc tttcccctga
4561 ggttgtgcaa gccaactcct gtttctcatt ctatggggat gatgaaatag tcagcacaga
4621 tataaaccta gacccagaaa aactcaccag gaaactgagg gagtatggcc tcgtcccaac
4681 aaggccagac aaaactgagg gcccacttgt gatcactcag gatttgaatg gtctcacatt
4741 cttgaggcgg accatagtgc gggaccccgc aggttggttt ggaaaattgg atcgtgattc
4801 cattctaagg cagttatact ggaccagagg acccaatcat gagaacccct ttgaaagtat
4861 gattccccac tcccagagag caacccagtt aatggccctt cttggggaag cctcgttgca
4921 tggtccccaa ttttacaaga aggtgagtaa aatggtcatc aatgagatca agagtggtgg
4981 tctggagttt tacgtgccca gacaggaggc catgtttaga tggatgagat tttcagacct
5041 cagcacgtgg gagggcgatc gcaatctggc tcccgagaat gtgaatgaag atggcgtcga
5101 atgacgcagc tccatcgaat gatggcgcgg ctggcctcgt accagagatc aaccatgagg
5161 tcatggccat agagcctgtt gcaggggcct ctctagcagc ccctgtcgta ggacaactta
5221 atataattga tccctggatt agaaataatt ttgtacaagc ccctgctgga gaattcactg
5281 tttcgcctag aaatgctcca ggtgaatttt tgttagattt agagttaggt ccagaattga
5341 atccttatct tgctcacctt gcacgcatgt ataatgggca tgcaggtggt atggaggtgc
5401 agatagtgct tgctgggaat gcgttcacag cgggcaaaat actgtttgca gtcataccac
5461 ctggattccc ctatgaaaat ttgtcacctg cacaattgac catgtgccca cacgtagtgg
5521 tggatgtgag gcagctagaa ccaatactgc tgcccatgcc agacatccgt aatacattct
5581 tccattacaa tcagagcaat gggccaaaac tcagattagt agctatgctt tacacacccc
5641 taagggctaa caatgctggt gatgatgtct tcacagtctc ctgcagggtt ctgactcgtc
5701 catcaccaga ttttgaattc aactttcttg tccccccatc tgttgaatct aagactaaag
5761 ctttcactct tccaattctt aagacatctg agatgacaaa ttcaagattt cccataccag
5821 ttgaccagat gtatactagt aggaatgaaa atatagttgt tcaaccacag aatggcaggg
5881 tgacacttga tggagagtta cagggcacaa ccacactcca accggtgtcc atttgtggct
5941 ttcgggggac gctgcagacc aggctggcag atcaaccaaa ttacacatac caagtgcacc
6001 ttgagaattt ggacggctca cccgtcgatc cgacagatga agtcccagcc cccctgggga
6061 cgccagattt tcaggcccaa ctgtttggag ttgtcagcca aaggagtagt gataatgcca
6121 ccagggcaca tgaggctagg gtcaacacca acgatcctac cttcgcgccc cagatcgccc
6181 aggtgcgttt caaatcacca tcccacgact tctttgacaa tgaacccatc aagttcacac
6241 cagttggaat tagtgttgat agcgaaaaca gctacaacca atggctcctt cccaggtatg
6301 gcgggcactt gacaaacaac actcacctgg ccccctctgt gtccccaatg ttccccggcg
6361 agcagattct cttcttccgc tcgttcatgc caggtgccag tggtcatact gatggcgcta
6421 ttgactgcct tttaccacaa gagtgggttg cccacttcta tcaggaggcc gcaactgccc
6481 aaacagatgt ggctctgatt agatttgtga accccgacac aggcagagtg ctatttgaag
6541 ggaagctaca caagcagggc tttataacca tctccaacag tggggaccac cccattgtta
6601 tgcctgctaa tggatacttc aggtttgagg catgggtcaa ccaattttac tctctcgccc
6661 ccgtgggaac cggaagtggg cgcagaagga ttcaataatg gctggagctt ttcttgcggg
6721 tctggctggt gatgtggtga cctctggcat cgggtcgctc atcaatgcag gtgccaatgc
6781 agtaaaccaa aaggttgaat atgatttcaa taggcaactt caagaagctt cttttaaaca
6841 tgacaaggag atgttgaatg ctcaaattaa tgccactacc aaattgcaga gggacatgat
6901 tgccatcaag cagggggttt tgaccgctgg cggcttttcc cccactgatg ctgcaagagg
6961 ttccatcaat gctccaacca ccaaaattct tgactggaat ggatctaggt actgggcgcc
7021 aggatcaatg agaacaacag catactctgg caatttcata tcacagggag ttaagcagcc
7081 tacacccatt gttaaatctg tggaacccca agtacagcaa tctcctgccc cttcttctgt
7141 ttattctgta ggttctgtta agtcacaatc aacacaatca actcaattaa cagggtcagg
7201 gactgtgtca agggcaccca ccccctcaac aaccacaaca ctgtccagaa caagtgagtg
7261 ggtgaggagc cagaatgata ggctgagccc ctttatggga ggcgcactcc agacagcttt
7321 catcacgccc ccatcgagta aggcttcatc ctcatcagga acagtctcaa ccgttcctag
7381 agaaattttg gactcctgga ctcctgtatt taacacacgc aggcagccgc tcttcgccca
7441 catgcgtagg cgaggggagt cacgggctta gtgaaaagaa tgatttggtt agattatatc
7501 tttttcttac ctattctatc ttttaaaaaa aaa
//