Typing tool
|
Complete norovirus genomes
MH188080 | GII.4 Sydney | ||
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GII.P4 New Orleans |
ORF1: 1..4692 ORF2: 4673..6295 ORF3: 6295..7044LOCUS MH188080 7044 bp RNA linear VRL 11-JUN-2018 DEFINITION Norovirus sp. clone NSP_VP1_VP2/413-7456/ST5/AU/2017 non-structural polyprotein gene, partial cds; VP1 gene, complete cds; and VP2 gene, partial cds. ACCESSION MH188080 VERSION MH188080.1 KEYWORDS . SOURCE Norovirus sp. ORGANISM Norovirus sp. Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus. REFERENCE 1 (bases 1 to 7044) AUTHORS Vibin,J., Chamings,A., Collier,F., Klaassen,M., Nelson,T.M. and Alexandersen,S. TITLE Metagenomics detection and characterisation of viruses in faecal samples from Australian wild birds JOURNAL Sci Rep 8 (1), 8686 (2018) REMARK Publication Status: Online-Only REFERENCE 2 (bases 1 to 7044) AUTHORS Vibin,J., Chamings,A., Collier,F., Klaassen,M., Nelson,T.M. and Alexandersen,S. TITLE Direct Submission JOURNAL Submitted (10-APR-2018) School of Medicine, Geelong Centre for Emerging Infectious Diseases, 285 Ryrie Street, Geelong, Victoria 3220, Australia COMMENT ##Assembly-Data-START## Assembly Method :: Ion Torrent Suite v. 5.6.0; Integrative Genomics Viewer v. 2.3.93; MEGA v. 7.0.26 Assembly Name :: ST4-ST5-ST6-Aug 2017 Coverage :: 2-189 Sequencing Technology :: IonTorrent ##Assembly-Data-END## FEATURES Location/Qualifiers source 1..7044 /organism="Norovirus sp." /mol_type="genomic RNA" /isolation_source="feces" /host="Homo sapiens" /db_xref="taxon:1938392" /clone="NSP_VP1_VP2/413-7456/ST5/AU/2017" /country="Australia" /collection_date="Jun-2017" CDS <1..4692 /note="ORF1" /codon_start=1 /product="non-structural polyprotein" /protein_id="AWR88306.1" /translation="IYHYGLYVERGLVLGVHKPPAAISLAKVELAPLSLYWRPVYTPQ YLISPDTLKKLSGETFPYTAFDNNCYAFCCWVLDLNDSWLSRRMIQRTTGFFRPYQDW NRKPLPTMDDSKIKKVANIFLCALSSLFTRPIKDIIGKIRPLNILNILASCDWTFAGV VESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVELVPVVMGGIGLVLGFT KEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEANELAIVRSIEDAVLD LEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLSTKSASPDIVGTINALLARIAA ARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREVAKRIAASLTGDQRVGLIPRN GVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCPLTLNCDRIENKGKVFDSDV IIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRDFPGQPDMWKNAFSSDF SHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLHERLDEFELQGPALTT FNFDRNKVLAFRQLAAENKYGLMDTMRVGKQLKDVRTMPELKQALKNVSIKKCQIVYS GCTYMLESDGKGNVKVDRIQSAAVQTNNELAGALHHLRCARIRYYVKCVQEALYSIIQ IAGAAFVTTRIAKRMNIQDLWSKPQVENTEETTSKDGCPKPKDDEEFVISSDDIKTEG KKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEEYLQDRDKYYEEVAI ARATEEDFCEEEEAKIRQRIFRPTRKQRKEERVSLGLVTGSEIRKRNPDDFKPKGKLW ADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSPSLFITSTHVIPQGAKEFFGV PIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVVTLLIKRPTGELMPLAAR MGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCGCPYIYKRGNDYVVIGVHT AAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILGPGSAPTLSTKTKFWRSSTAP LPPGTYEPAYLGGKDPRVKGGPSLQQVMREQLKPFTEPRGKPPKPSVLEAAKKTIINV LEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCWNGESFTGKLADQASKANLMF EEGKNMTPVYTAALKDELVKTDKIYGKIKKRLLWGSDLATMIRCARAFGGLMDELKAH CVTLPIRVGMNMNEDGPIIFERHSRYTYHYDADYSRWDSTQQRAVLAAALEIMVKFSP EPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCTSQWNSIAHWLLTLCALSEVT NLSPDTIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLREYGLKPTRPDKTEGPLAISE DLNGLTFLRRTITRDPAGWFGKLEQSSILRQMYWTRGPNHGDPSETMIPHSQRPIQLM SLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQEPMFRWMRFSDLSTWEGDRNL APSFVNEDGVE" CDS 4673..6295 /note="major capsid protein" /codon_start=1 /product="VP1" /protein_id="AWR88307.1" /translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKVIFAAVPPNFPTEGLSPSQVTMFPHIVVDVRQLEPVLIPLPD VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFSIPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT QLSPVNICTFRGDVTHITGSHNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML TQTTRADGSTRGHKATVYTGSADFAPKLGRVQFETDTSNDFEASQNTKFTPVGVIQDG STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD CLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKAGYVTVAHTGQHDLV IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRVV" CDS 6295..>7044 /note="minor structural protein" /codon_start=1 /product="VP2" /protein_id="AWR88308.1" /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN APMTKVLDWSGTRYWAPDARTTTYNAGRFSTPQSPGALPGRANLRDAVPARGSSSKSS NSSTATSVYSNQTTSTRLGSTAGSGTSVSSLPSTARTRSWVEDQSRNLSPFMRGAHNI SFVTPPPSRSSSQGTVSTVPKEILDSWTGAFN" ORIGIN 1 atctaccatt atggcctgta tgtggaacga ggtcttgtgc taggtgtgca caaaccgcca 61 gctgccatca gccttgctaa ggttgagctg gcaccactct ccttgtactg gagacctgtg 121 tacactcctc agtacctcat ctctccagac actctcaaga aattgtccgg agagacgttc 181 ccctacacag cctttgataa taactgctat gccttttgtt gctgggttct ggacctaaat 241 gactcgtggc tgagtagaag aatgatccag agaacaactg gtttctttag gccctatcag 301 gactggaata ggaaacccct tcctactatg gatgactcca aaataaagaa ggtagctaac 361 atatttctgt gtgccctgtc ctcgctattc accagaccca taaaagatat aatagggaag 421 ataaggcctc ttaatatcct caacatcttg gcctcatgtg actggacctt tgcgggtgta 481 gtggagtccc tgatactctt ggcagaactc tttggagttt tctggacacc cccagatgtg 541 tctgcgatga ttgccccctt acttggtgac tatgagctac aaggacctga ggaccttgca 601 gtagagctcg tccccgtggt gatgggggga attggtttgg tgctaggatt caccaaagag 661 aaaattggaa aaatgttgtc atctgctgcg tccactttga gagcttgcaa agaccttggt 721 gcatatgggc tagagatcct aaagttagtc atgaagtggt tcttcccaaa gaaggaggag 781 gcaaatgaac tggctatagt gaggtccatc gaggacgcag tcctggatct cgaggcaatt 841 gaaaacaatc atatgaccac cttgcttaaa gataaagaca gtctggcaac ctacatgaga 901 acacttgacc ttgaagagga gaaagccaga aaactctcaa ccaagtctgc ctcacccgac 961 atcgtgggta caatcaacgc cctcctggcg agaatcgctg ccgcacgctc tctggtgcat 1021 cgagcgaaag aggagctttc cagcagacca agacctgtgg tgttgatgat atctggcagg 1081 ccaggaatag ggaagaccca ccttgctagg gaagtggcta agagaatcgc agcctccctt 1141 acaggagatc agcgtgtggg cctcatccca cgcaatggtg tcgaccattg ggatgcgtac 1201 aagggggaga gggtcgtcct gtgggacgat tatggaatga gcaaccctat tcacgatgcc 1261 ctcaggctgc aagaactcgc tgacacttgt cccctcactc tgaactgtga caggattgaa 1321 aataaaggaa aggtttttga cagcgatgtc atcattatca ccactaatct ggccaaccca 1381 gcaccactgg actatgtcaa ctttgaagca tgctcgaggc gcattgactt cctcgtgtat 1441 gcagaagccc ctgaagttga aaaggcgaag cgtgacttcc caggccagcc tgacatgtgg 1501 aagaacgctt tcagttctga tttctcacac ataaaactag cactggcccc acagggtggt 1561 ttcgataaga acgggaacac cccacacgga aagggcgtca tgaagaccct caccactggc 1621 tcccttattg cccgagcatc agggctgctc catgagaggc tggatgaatt tgagctgcag 1681 ggcccagctc tcaccacctt caacttcgat cgcaataaag tgcttgcctt tagacagctt 1741 gctgctgaaa acaaatatgg attgatggac acaatgaggg ttgggaaaca gctcaaggat 1801 gtcagaacca tgccagaact caaacaggca ctcaaaaatg tctcaatcaa gaagtgccaa 1861 atagtgtata gtggttgcac ttacatgctt gagtctgatg gcaagggcaa tgtgaaggtt 1921 gacagaatcc aaagcgccgc cgtgcagacc aacaatgagc tggctggtgc cctgcaccac 1981 ttgaggtgcg ccagaatcag atactatgtc aagtgtgtcc aggaagccct gtattccatc 2041 atccaaatcg ctggggctgc atttgtcacc acgcgcattg ccaagcgcat gaatatacaa 2101 gacctatggt ccaagccaca agtggaaaac acagaggaga ctaccagcaa ggacgggtgc 2161 ccaaagccta aggatgatga ggagttcgtc atttcatccg acgacatcaa aactgagggc 2221 aagaaaggga agaacaagac tggccgtggc aagaagcaca cagcattttc aagcaaaggc 2281 ctcagtgatg aagagtatga tgaatacaag aggattagag aagagaggaa tggcaagtac 2341 tctatagaag agtaccttca ggacagggac aaatactatg aggaggtggc tattgccagg 2401 gcgaccgagg aagacttctg tgaagaggag gaggccaaga tccggcaaag gatctttagg 2461 ccaacaagga aacaacgcaa ggaggaaaga gtctctcttg gtctggtcac aggctctgaa 2521 attaggaaaa gaaacccaga tgacttcaaa cccaagggaa aattgtgggc tgacgatgac 2581 aggagtgtgg actacaatga gaaactcagc tttgaggccc caccaagcat ttggtcgaga 2641 atagtcaact ttggttcagg ctggggattc tgggtctctc ccagtttgtt cataacatca 2701 acccatgtca taccccaggg cgcaaaggag ttctttggag tccccatcaa acaaatacag 2761 gtacacaagt caggcgagtt ctgtcgcttg agatttccta aaccaatcag gactgatgta 2821 acgggcatga tcttggaaga aggcgcacct gagggcaccg tggtcacact actcatcaaa 2881 aggcccactg gggaactcat gcccctagca gctaggatgg ggacccatgc gaccatgaag 2941 atccaagggc gcactgttgg aggccagatg ggcatgcttc tgacaggatc caacgccaag 3001 agcatggacc tgggtactac accaggtgat tgtggctgcc cctacatcta caagagaggc 3061 aatgactatg tggtcattgg agtccacacg gctgccgcac gtgggggaaa cactgtcata 3121 tgtgccaccc aagggagtga aggggaggct acacttgagg gtggtgacaa caaggggaca 3181 tactgtggtg caccaatcct gggtccaggg agtgccccaa cacttagcac caagaccaaa 3241 ttctggagat cgtccacagc accacttcca cctggcacct atgaaccagc ctatcttggt 3301 ggcaaggacc ctagagtcaa gggtggccct tcactgcagc aagtcatgag ggaacagttg 3361 aagccattca cagagcccag gggcaagcca ccaaaaccaa gtgtgttaga agctgccaag 3421 aagaccatca ttaatgtcct tgaacaaaca attgacccac ctgagaaatg gtcgttcgca 3481 caagcttgcg cgtcccttga caagaccact tccagtggcc atccgcacca tatgcggaaa 3541 aacgactgct ggaacgggga atcctttacg ggcaagctgg cagaccaagc ttccaaggcc 3601 aacctgatgt ttgaagaagg gaagaacatg accccagtct acacagctgc gctcaaggat 3661 gagttagtta aaactgacaa aatttatggt aagatcaaga agaggcttct ctggggctcg 3721 gatttggcaa ccatgattcg gtgtgctcga gcattcggag gcctaatgga tgaactcaaa 3781 gcgcactgtg tcacactccc cattagagtt ggcatgaata tgaatgagga tggccccatc 3841 atcttcgaga ggcattccag gtacacgtac cactatgatg ctgactactc tcggtgggat 3901 tcaacacaac agagagccgt gttggcagca gctctagaaa tcatggttaa attctcccca 3961 gaaccacatt tggctcaggt ggtcgcggaa gaccttcttt cccccagcgt ggtggacgtg 4021 ggcgacttca caatatcaat caatgagggt cttccctctg gggtgccctg cacctcccaa 4081 tggaactcca ttgcccactg gctcctcacc ctctgtgcgc tctctgaagt cacaaacctg 4141 tcccctgata ccatacaggc taattccctc ttctcttttt atggtgatga tgaaattgtt 4201 agcacagaca taaaattgga cccagagaaa ttgacagcaa aactcagaga gtatgggtta 4261 aaaccaaccc gccctgacaa aactgaagga ccccttgcca tctctgaaga cctgaatggt 4321 ctgactttcc tgcggagaac tataacccgc gacccagctg gttggtttgg aaaactggag 4381 cagagttcaa tactcaggca aatgtactgg actaggggtc ccaaccatgg agacccatct 4441 gaaacaatga ttccacactc ccaaagaccc atacagttga tgtccctact gggggaggcc 4501 gctctccacg gcccagcatt ttacagcaaa attagcaaat tggtcattgc agagctaaaa 4561 gaaggtggca tggattttta cgtgcccaga caagagccaa tgttcagatg gatgagattc 4621 tcagatctga gcacgtggga gggcgatcgc aatctggctc ccagttttgt gaatgaagat 4681 ggcgtcgagt gacgccaacc catctgatgg gtccgcagcc aacctcgtcc cagaggtcaa 4741 caatgaggtt atggctctgg agcccgttgt tggtgccgct attgcggcac ctgtagcggg 4801 ccaacaaaat gtaattgacc cctggattag gaataatttt gtacaagccc ctggtggaga 4861 gtttacagta tcccctagaa acgctccagg tgaaatacta tggagtgcac ccttaggccc 4921 tgatctaaat ccctacctat cccatttggc cagaatgtac aatggttatg caggtggttt 4981 tgaagtgcag gtaattctcg cggggaacgc gttcaccgcc gggaaggtca tatttgcagc 5041 agtcccacca aatttcccaa ctgaaggctt aagccccagc caggtcacta tgttccccca 5101 catagtagta gatgttaggc aactagaacc tgtgttgatt cccttacccg atgttaggaa 5161 caatttctac cattataacc aatcaaatga ccccaccatt aagttgatag caatgttgta 5221 tacaccactt agggctaata atgctgggga cgatgtcttc acagtttctt gccgagttct 5281 tacaagacca tcccccgatt ttgatttcat atttttagta ccacccacag ttgagtcaag 5341 aactaaacca ttctctatcc cagttttaac agttgaggag atgaccaatt caagattccc 5401 cattcctttg gaaaagttgt tcacgggtcc cagcagcgcc tttgttgttc aaccacaaaa 5461 cggcagatgc acgactgatg gcgtgctcct aggcaccacc caactgtctc ctgtaaacat 5521 ctgcaccttc agaggggacg tcacccacat cacaggcagt cacaactaca caatgaattt 5581 ggcttctcaa aattggaaca attacgatcc aacagaagaa atcccagccc ctctaggaac 5641 cccagacttt gtggggaaga ttcaaggtat gctcacccaa accacaaggg cagatggctc 5701 aacacgcggc cacaaggcta cagtgtacac tgggagcgcc gacttcgctc ctaaactggg 5761 tagagttcaa tttgaaactg acacaagcaa tgattttgaa gctagccaaa acacaaagtt 5821 caccccagtc ggtgtcatcc aagacggtag caccacccac cgaaatgaac cccaacagtg 5881 ggtgctccca agttactcag gcagaaatac tcataatgtg catctggccc ccgctgtggc 5941 ccccactttc ccgggtgagc aacttctctt cttcagatcc accatgcccg gatgcagcgg 6001 gtaccctaac atggatttgg actgtctact ccctcaggaa tgggtacagc acttctacca 6061 agaggcagcc ccagcacaat ctgatgtggc tctgctaaga tttgtaaatc cagacacagg 6121 tagggttttg tttgagtgca agctccataa agcaggctat gtcacagtgg ctcacactgg 6181 ccaacacgat ttggtcatcc cccccaatgg ttattttagg tttgattctt gggtcaacca 6241 gttctacacg cttgccccca tgggaaatgg aacggggcgt agacgtgtag tataatggct 6301 ggagctttct ttgctggatt ggcatctgat gtccttggct ctggacttgg ttcccttatc 6361 aatgctgggg ctggggccat caaccaaaaa gttgagtttg aaaacaacag aaaattgcaa 6421 caagcatcat tccaatttag tagcaatctg caacaggctt cctttcaaca tgataaagag 6481 atgctccaag cacaaattga ggctaccaaa aagctacaac aggaaatgat gaaagttaag 6541 caggcaatgc tcctagaggg tggattctct gagacagatg cagcccgcgg ggcaattaac 6601 gcccccatga caaaagtttt ggactggagc gggaccaggt actgggctcc cgatgctaga 6661 actacaacat acaatgcagg ccgcttttcc acccctcaat caccaggggc actgccagga 6721 agagctaatc ttagggatgc tgtccctgct cggggttcct ccagcaaatc atctaactct 6781 tctactgcta cttctgtgta ttcaaatcaa actacttcaa cgagacttgg ttctacagct 6841 ggttctggta ccagtgtctc gagtctcccg tcaactgcaa ggactaggag ctgggttgag 6901 gatcaaagca ggaatttatc acctttcatg aggggggccc acaacatatc gtttgtcacc 6961 ccaccaccta gcagatcctc tagccaaggc acagtctcaa ccgtgcctaa agagattttg 7021 gactcctgga ctggcgcttt caac //