Typing tool
|
|
|
|
|
|
Typing tool
|
Complete norovirus genomes
| MN897754 | GII.4 Sydney | |
|
|---|---|---|---|
| GII.P31 |
ORF1: 5..5104
ORF2: 5085..6707
ORF3: 6707..7513
LOCUS MN897754 7576 bp RNA linear VRL 09-JAN-2020
DEFINITION Norovirus GII isolate Hu/US/2018/GII.4 Sydney[P31]/Chippewa0181,
complete genome.
ACCESSION MN897754
VERSION MN897754.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7576)
AUTHORS Montmayeur,A.M., Tim,D., Tatusov,R.L., Chhabra,P. and Vinje,J.
TITLE Direct Submission
JOURNAL Submitted (03-JAN-2020) Division of Viral Diseases, Centers for
Disease Control and Prevention, 1600 Clifton Road NE, Atlanta, GA
30329, 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..7576
/organism="Norovirus GII"
/mol_type="genomic RNA"
/strain="Chippewa0181"
/isolate="Hu/US/2018/GII.4 Sydney[P31]/Chippewa0181"
/isolation_source="stool"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="USA"
/collection_date="09-Mar-2018"
/note="genotype: GII.4 Sydney[P31]"
gene 5..5104
/gene="ORF1"
CDS 5..5104
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="QHB18521.1"
/translation="MKMASNDASAAAVANSNNDIAKSSSDGVFSNMAVTFKRALGARP
KQPPPKEIPPRPPRPPTPELVKKIPPPPPNGEDELVVSYNAKDGVSGLPELTTVRQPE
ETNTAFSVPPLNQRESRDAKEPLTGTIIEMWDGEIYHYGLYVERGLILGVHKPPAAIS
LAKVELAPLSLFWRPVYTPQYLISPDTLRRLHGESFPYTAFDNNCYAFCCWVLDLNDS
WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCTLSSLFTRPIKDIIGK
LKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED
LAVELVPIVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
KKEEANELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLTTYMRTLDLEEEKARKLST
KSASPDIVGTINSLLARIAAARSLVHRAKEELSSRPRPVVVMISGRPGIGKTHLAREL
AKKIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC
PLTLNCDRIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK
AKRDFPGQPDMWKNAFSPDFSHIKLSLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA
SGLLHERLDEYELQGPALTTFNFDRNKILAFRQLAAENKYGLMDTMRVGKQLKDVKTM
SDLKQALKNIAIKKCQIVYNGGTYTLEADGKGSVKVDKVQSATVQTNNELAGALHHLR
CARIRYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQNLWSKPQVEDTEEMANKDGC
LKPKDDEEFVVSSDDIKTEGKKGKNKSGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
KYSIEEYLQDRDRYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV
TGSEIRKRNPEDFKPKGKLWADDDRSVDYNEKLNFEAPPSIWSRIVNFGSGWGFWVSP
SLFITSTHVIPQGAKEFFGVPIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG
TVATLLIKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDSKGTYCGAPILG
PGSAPKLSTKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP
RGKPPRPNVLEAAKKTIINVLEQTIDPPQKWSFAQACASLDKTTSSGHPHHMRKNDCW
NGESFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKVYGKVKKRLLWGSDL
ATMIRCARAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFEKHSRYRYHYDADYSRWD
STQQRDVLAAALEIMVKFSPEPHLAQIVAEDLLSPSVMDVGDFQVSISEGLPSGVPCT
SQWNSIAHWLLTLCALSEVTDLSPDIVQANSLFSFYGDDEIVSTDIKLDPERLTAKLK
EYGLKPTRPDKTEGPLVISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP
NHEDPFETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQE
PMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE"
mat_peptide 5..994
/gene="ORF1"
/product="p48"
mat_peptide 995..2092
/gene="ORF1"
/product="NTPase"
mat_peptide 2093..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..6707
/gene="ORF2"
CDS 5085..6707
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="QHB18522.1"
/translation="MKMASSDVNPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKVIFAAVPPNFPTEGLSPSQVTMFPHIVVDVRQLEPVLIPLPD
VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHITGSHNYTMNLASQNWSNYDPTEEIPAPLGTPDFVGKIQGML
TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTNNDFEANQNTKFTPVGVIQDG
GTTHRNEPQQWVLPSYSGRNTPNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGAGRRRAL"
gene 6707..7513
/gene="ORF3"
CDS 6707..7513
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="QHB18523.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKRLQQEMMKVKQAMLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANFRDAVPARGSSSKSS
NSSTATSVYSNQTTSTRLGSTAGSGTSVSSFPSTARTRSWVEDQSRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEILDSWAGAFNTRRQPLFAHIRKRGESRV"
ORIGIN
1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgct gttgccaaca gcaacaacga
61 catcgcaaaa tcttcaagtg acggtgtatt ttctaacatg gctgtcactt ttaagcgggc
121 cctcggggcg cggcctaaac agccgccccc gaaggaaata ccacccagac ccccgcgacc
181 acccacacca gaattggtca aaaagatccc tcctccccca cccaacgggg aggatgaact
241 agtggtctct tacaacgcca aagatggcgt ttccggactg cctgagctca ccactgtcag
301 acaaccggaa gaaaccaaca cggcgttcag tgtcccccca ctcaaccaaa gggagagcag
361 ggacgccaag gagccactaa ctggaacaat cattgaaatg tgggatggag aaatctacca
421 ttacggcctg tacgtggaac gaggtcttat acttggtgtg cacaagccac cagcagccat
481 cagcctcgct aaggtcgagc tggcaccgct ctctttgttc tggagacctg tatacacccc
541 ccagtacctt atctctccag acactcttag gagattacat ggagagtcat tcccctacac
601 tgcatttgac aacaattgct acgccttttg ttgttgggta ttagacctaa acgactcatg
661 gctaagcagg agaatgattc agagaacaac aggcttcttt aggccgtacc aggattggaa
721 caggaaaccc ctccccacta tggatgattc caaattaaag aaggtagcca acatattttt
781 gtgcactttg tcttcactat tcaccaggcc cattaaggac ataataggga agttgaaacc
841 tctcaacatc cttaatattc tggctacatg tgattggacc ttcgcaggca tagtggaatc
901 cttaatactc ctggcagaac tctttggagt tttctggaca cccccagatg tgtctgcgat
961 gatcgccccc ttgctaggtg attatgaact gcaaggaccc gaggaccttg cagtggaact
1021 ggtcccaata gtgatggggg ggataggttt ggtgctagga tttaccaaag agaagatcgg
1081 aaagatgctg tcatccgctg catccacttt aagagcttgt aaagaccttg gtgcatacgg
1141 actggaaatc ttaaaattgg tcatgaagtg gttcttccca aagaaagagg aagcaaatga
1201 actggctatg gtgagatcca tcgaggatgc agtactagac ctcgaggcaa ttgaaaacaa
1261 ccacatgacc accctgctca aagacaaaga cagcttgaca acctacatga gaacccttga
1321 ccttgaggag gagaaagcca gaaaactctc aaccaaatct gcttcacccg atattgtggg
1381 cacaatcaac tctcttctgg caagaatcgc tgctgcacgc tccctagtgc atcgggcgaa
1441 agaagagcta tccagcaggc cgagacctgt cgttgtaatg atatcgggaa gaccagggat
1501 aggaaaaact caccttgcca gggagctggc caagaagatc gcggcctccc tcacagggga
1561 ccagcgtgtg ggccttatcc cacgcaatgg tgtcgaccac tgggacgcat acaagggcga
1621 aagggttgtc ctatgggacg actatggaat gagcaacccc atccatgatg cccttaggtt
1681 gcaggagctt gctgacactt gccccctcac gctaaattgt gacagaattg agaacaaagg
1741 aaaagtcttt gacagtgatg ccataattat caccaccaac ctggccaacc cagcaccact
1801 ggattatgtc aactttgaag cgtgctcgag acgcattgat ttcctcgtgt acgcagaagc
1861 ccctgaggtg gagaaggcaa agcgcgactt cccaggtcag cctgacatgt ggaagaacgc
1921 tttcagtcct gacttctcac acataaaact gtcattggct ccacagggtg gttttgacaa
1981 gaacggcaac accccacatg gaaaaggggt catgaagacc ctcaccactg gctccctcat
2041 cgcccgagca tcagggttac tccatgagag gctagatgaa tatgaattac aaggcccagc
2101 cctcaccact ttcaactttg accgcaacaa gatacttgct tttagacagc ttgctgctga
2161 aaacaagtat gggctgatgg acacaatgag agttggaaaa cagctcaagg atgtcaagac
2221 tatgtcagac ctcaaacagg cactcaagaa catcgcgatc aagaagtgcc agatagtgta
2281 caatggtggc acctacacac ttgaggctga tggcaagggc agtgtgaaag ttgacaaagt
2341 gcaaagtgcc actgtgcaga ccaacaatga actagccggt gccctacacc acctaagatg
2401 cgctagaatc agatactatg ttaagtgcgt ccaggaggca ctgtactcca tcatccaaat
2461 cgctggggct gcattcgtca ccacgcgcat cgctaagcgc atgaatatac agaatctctg
2521 gtccaagcca caggtggaag acacagaaga gatggccaac aaagatggtt gcctaaaacc
2581 caaagatgat gaagagtttg tcgtttcatc cgacgacatc aaaactgagg gcaagaaagg
2641 gaagaacaag tccggccgtg gcaagaagca cacagccttt tcaagtaaag ggctcagtga
2701 tgaggagtac gatgagtaca agagaatcag agaagaaagg aatggtaagt actccataga
2761 agagtacctt caggacagag acaggtacta cgaggaggtg gccattgcca gggcaaccga
2821 agaggacttc tgtgaagaag aagaggccaa aatccggcag aggattttca gaccaacacg
2881 gaaacaacgc aaagaagaga gggcttctct cggcttggtc acaggctctg aaatcaggaa
2941 gagaaaccca gaagacttca aacccaaggg aaagctgtgg gctgatgacg acagaagtgt
3001 tgactacaat gagaaactca actttgaggc cccaccaagc atctggtcgc ggatagtcaa
3061 ctttggttca ggctggggct tctgggtctc ccccagtctg tttataacat caacccatgt
3121 cataccccaa ggtgcaaagg agttcttcgg agtccctatc aagcaaatcc agatacacaa
3181 gtcaggtgaa ttctgccgat tgagattccc aaagccaatc agaaccgatg tgacgggcat
3241 gattctagaa gaaggtgcgc ccgaggggac cgtggccaca ctgcttatca agagaccaac
3301 tggagagctc atgcctctgg cagccagaat ggggacccat gcaaccatga aaattcaggg
3361 gcgcacagtt ggagggcaaa tgggtatgct cctgacagga tccaacgcca agagtatgga
3421 cctaggcaca acaccaggcg actgcggctg cccctacatc tacaagaggg ggaatgacta
3481 cgtggtcata ggggtccata cggccgctgc ccgtggagga aacactgtca tatgtgccac
3541 ccagggaagt gagggagagg ccacacttga aggaggtgac agtaaaggga catactgtgg
3601 cgcgccaatc ttgggcccag ggagcgctcc gaagctcagc accaagacta agttttggag
3661 atcatccaca acaccactcc cacctggcac ctacgaacca gcctacctcg gtggcaaaga
3721 ccctagagtc aaaggtggcc cttcattgca acaagttatg agggaccagc tgaagccatt
3781 cacagaaccc agaggcaaac caccaagacc aaatgtgttg gaagctgcca agaaaaccat
3841 catcaatgtt cttgagcaaa caattgatcc accccaaaaa tggtcatttg cgcaagcttg
3901 cgcatccctt gacaaaacca cctccagcgg ccacccgcac cacatgcgga aaaacgactg
3961 ttggaatggg gagtccttca caggaaagtt ggctgaccaa gcctccaagg ccaacctaat
4021 gtttgaagag ggaaagaaca tgactccagt ctacacaggt gcacttaaag atgagttggt
4081 aaagaccgat aaagtttatg gtaaggtcaa gaagaggctt ctatggggtt cagatctggc
4141 gaccatgata cggtgcgccc gagcttttgg aggcctcatg gatgaactca aggcacactg
4201 tgtcacactc cctgtcagag ttggtatgaa catgaatgag gatggcccca tcatcttcga
4261 gaaacactcc agatatagat atcattatga tgctgactat tcccggtggg actcaacaca
4321 acaaagggat gtgctagcag cagcactaga aatcatggtt aagttctctc cagaaccaca
4381 cctggcccag atagttgcag aagacctcct ttcccctagc gtgatggatg tgggtgactt
4441 tcaagtatca ataagtgagg gtctcccctc tggggtgcct tgcacctccc agtggaattc
4501 catcgcccac tggctcctca ctctgtgtgc actctctgaa gtcacggatc tgtcccctga
4561 tatcgttcag gccaactccc ttttctcctt ctatggtgat gatgagattg taagcacaga
4621 cataaagttg gacccagaga ggctgacagc aaaactcaag gagtacgggc tgaaaccaac
4681 ccgccccgac aaaactgaag gaccccttgt catctctgaa gacctggatg gtctgacatt
4741 cctccggaga actgtgaccc gtgatccagc tggctggttt ggaaaattgg aacaaagttc
4801 aattcttagg caaatgtact ggaccagggg tcccaaccat gaagacccat ttgaaacaat
4861 gataccacac tcccaaagac ccatacaatt gatgtccttg ctgggcgagg ctgcactcca
4921 cggcccggca ttctacagca aaattagcaa attagtcatt gcagagttga aggaaggtgg
4981 catggatttt tacgtaccca gacaagagcc aatgttcagg tggatgagat tctcagatct
5041 gagcacgtgg gagggcgatc gcaatctggc tcccagtttt gtgaatgaag atggcgtcga
5101 gtgacgtcaa cccatctgat gggtccgcag ccaacctcgt cccagaggtc aacaatgagg
5161 ttatggctct ggagcccgtt gttggtgccg ccattgcggc acctgtagcg ggccaacaaa
5221 atgtaattga cccctggatt agaaacaatt ttgtacaagc ccctggtgga gagtttacag
5281 tgtcccctag aaacgctcca ggtgaaatac tatggagcgc gcccttgggc cctgatttaa
5341 atccctactt gtctcatttg gccagaatgt acaatggtta tgcaggtggt tttgaagtgc
5401 aggtaattct cgcggggaac gcgtttaccg ccgggaaggt catatttgca gcagtcccac
5461 caaattttcc aactgaaggc ttgagcccca gccaggtcac tatgttcccc catatagtag
5521 tagatgttag gcaactagaa cctgtgttga ttcccttacc cgatgttagg aataatttct
5581 atcactacaa tcaatcaaat gaccccacca ttaagttgat agcaatgttg tatacaccac
5641 ttagggctaa taatgctggg gatgatgttt tcacagtttc ttgccgagtt ctcacgagac
5701 catcccccga ttttgacttc atatttctag tgccacccac agttgagtca agaactaaac
5761 cattctctgt cccagttttg actgttgagg agatgaccaa ttcaagattc cccattcctt
5821 tggaaaagtt gttcacgggt cccagcagtg cctttgttgt ccaaccacaa aacggtaggt
5881 gcacgactga tggcgtgctc ctaggcacca cccaactgtc tcctgtcaac atctgcacct
5941 ttagaggaga tgtcacccat atcacaggta gtcataacta tacaatgaat ttggcttctc
6001 aaaattggag caactacgac ccaacagaag aaatcccagc ccctctaggg actccagact
6061 ttgtggggaa gattcaaggc atgcttaccc aaaccacaag gacagatggc tcaacacgcg
6121 gccacaaagc cacagtgtac actgggagcg ccgactttgc tccaaaactg ggtagagttc
6181 aatttgaaac tgacacaaac aatgattttg aagctaacca aaacacaaag ttcaccccag
6241 ttggtgtcat ccaagatggt ggcaccaccc atcgaaatga gccccaacag tgggtgctcc
6301 caagttactc aggcaggaac actcctaatg tgcatctggc ccccgctgtg gcccccactt
6361 ttccgggtga gcaactcctc ttctttagat ccaccatgcc cggatgcagc gggtacccca
6421 acatggattt ggattgtctg ctcccccagg aatgggtgca gtacttctac caggaggcag
6481 ccccagcaca atctgatgtg gctctgctaa gatttgtgaa tccagacaca ggtagggttt
6541 tgtttgaatg taagcttcat aaatcaggct atgttacagt ggctcacact ggccaacatg
6601 atttggttat cccccccaat ggttatttta ggtttgattc ctgggtcaac cagttttaca
6661 cgcttgcccc catgggaaat ggagcggggc gtagacgtgc actataatgg ctggagcttt
6721 ctttgctgga ttggcatctg atgtccttgg ctctggactt ggttccctta tcaatgctgg
6781 ggctggggcc atcaaccaaa aagttgagtt tgaaaataac agaaaattgc aacaagcatc
6841 cttccaattt agcagcaatc tacaacaggc ttcctttcaa catgacaaag agatgctcca
6901 agcacaaatt gaggctacca aaaggttaca acaggaaatg atgaaagtta agcaggcaat
6961 gctcctagag ggtgggttct ctgagacaga tgcagcccgc ggggcaatca acgcccctat
7021 gacaaaagcc ttggactgga gcgggacaag gtactgggct cctgatgcta ggactacaac
7081 atacaatgca ggccgctttt ccacccccca accatcgggg gcgctgccag gaagagctaa
7141 ttttagggat gctgtccctg ctcggggttc ctctagtaag tcttctaact cttctactgc
7201 tacttctgtg tattcaaatc aaaccacttc aacgagactt ggttctacag ctggttctgg
7261 taccagtgtc tcgagcttcc cgtcaactgc aaggactagg agctgggttg aggaccaaag
7321 taggaatttg tcacctttca tgaggggggc ccacaacata tcgtttgtca ccccaccatc
7381 tagcaggtcc tctagccaag gcacagtctc aaccgtgcct aaagagattt tggactcctg
7441 ggctggcgct ttcaacacgc gcaggcagcc actcttcgct cacattcgta agcgagggga
7501 gtcacgggtg taatgtgaaa agacaaaatt gattatcttt cttttcttta gtgtctttta
7561 aaaaaaaaaa aaaaaa
//