Typing tool

Complete norovirus genomes

MK641589  GII.14
 GII.P7

Length: 7,529 | 3 CDS

ORF1: 5..5098
ORF2: 5079..6689
ORF3: 6689..7483
LOCUS       MK641589                7529 bp    RNA     linear   VRL 23-MAR-2019
DEFINITION  Norovirus GII isolate CA-RGDS-1023, complete genome.
ACCESSION   MK641589
VERSION     MK641589.1
KEYWORDS    .
SOURCE      Norovirus GII
  ORGANISM  Norovirus GII
            Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
            Picornavirales; Caliciviridae; Norovirus.
REFERENCE   1  (bases 1 to 7529)
  AUTHORS   Pan,C.-Y., Huynh,T., Newsum,M., Fitzpatrick,K., Castro,C.J.,
            Ng,T.F., Marine,R.L. and Wadford,D.A.
  TITLE     Norovirus GII.P7-GII.14 genome from a school outbreak, Arizona 2018
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 7529)
  AUTHORS   Pan,C.-Y., Huynh,T., Newsum,M., Fitzpatrick,K., Castro,C.J.,
            Ng,T.F., Marine,R.L. and Wadford,D.A.
  TITLE     Direct Submission
  JOURNAL   Submitted (15-MAR-2019) 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..7529
                     /organism="Norovirus GII"
                     /mol_type="genomic RNA"
                     /isolate="CA-RGDS-1023"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:122929"
                     /country="USA: AZ"
                     /collection_date="Feb-2018"
                     /note="genotype: GII.P7-GII.14"
     gene            5..5098
                     /gene="ORF1"
     CDS             5..5098
                     /gene="ORF1"
                     /codon_start=1
                     /product="nonstructural polyprotein"
                     /protein_id="QBM30993.1"
                     /translation="MKMASNDATAALGSQKSVNDSNIATPSNKEEVGTFSNIKVGFKK
                     MLGAVPKGTKAPSSDQHCPTVKIRPKTLTIPPEPPNGEDTVQFDAKSETVIGLPDLTT
                     VQNEHENTPYTVPPLSEREHRPATEPLPGTILEMWDGEFYHYSVYVSDGKALGVHKPP
                     AAISLATIELTPISLYWRPVYTPNYLVSPDTLKGLAGEKFPYTAFSNNCYNFCCWVLE
                     LNDTWLNRRCISRTTGFFKPYQSWNRKPLPTVDDGKIKKVANAILCALGSLFSKPIKD
                     LLGKLKPLNLLHLLASCDWTFAGIVETVILMAELFNVFWTPPDVSNFIASLIGDFELQ
                     GPEDLAVELVPVVMGGIGMVLGFTAEKIGRMLSSAASTLRACKDLGNYALDILKLVMK
                     WFFPKKEEKAEMETLRAIEDAVLDMEAIGNNHLTTLLKDKDSLTAFMKTLDLEEEKAR
                     KLSTKSSSPDIVGTINAILARIAAARSLLHKAKEEMFSRIRPVVVMISGRPGIGKTHM
                     ARHLAKSIANTMSGDQRVGLVPRNGVDHWDAYRGERVVLWDDYGMGSPVKDALTLQEL
                     ADTCPVTLNCDRIENKGKMFDSDVIIITTNLVNPAPLDYVNFEACSRRVDFLVYAESP
                     EIEKVKRDFPGQPDMWKDHFKPDFSHIKLTLAPQGGFDKNGNTPHGKGTMRSLTQGSL
                     TARVAGLVHERKDEFQLQGNDLQTYNFDTNRVSAFRKLAADNKYGIMETMRVGAALKS
                     VKTLEDLKVALRDVKFNECEIIYKNSKYRVSSNGKGSVSIDKVEDNASQTVNEVHSAL
                     LRLRQARARYYISCFQDLVYTLIQVAGASFVVSRISRRFCWERWVKPTETQEVNESEK
                     EAAQGRWEIEPKDTEPEGKKGKNKKGRGKKHTAFSSKGLSDEEYDEFKRIREERNGKY
                     SIEEYLQDRDRYYEEVAVARATEEDFCEEEEAKIRQRIFRPTRKQRKEERGVLGLVTG
                     SDIRKRRPDDFQPKGNLWADDTRSVDYNERLDFEAPPSVWSRIVPLGTGWGFWVSSNL
                     LITTTHVLPKGIRELFGVEIKQIQIHKSGEFCRFRFPRPIRPDVTGLVLEEGAPEGTV
                     CSVLVKRPTGEMIPLAVRMGTHASMKIQGRTVGGQMGMLLTGANAKNMDLGTGPGDCG
                     CPYIYKRGNDIVVAGVHTAAARGGNTVICATQGQDGEAVLEGNEDLGTYCGAPILGPG
                     KAPKLSTKTKFWRSSPDALPPGTYEPAYLGGKDPRVEKGPSLQQVMRDQLKPFTEPRG
                     RLPRPAILEEAKKTVMNVLEQTIDPAKPWSYSQACASLDKTTSSGSPHHVKKNDHWNG
                     ESFTGPLADQASKANLMYEQAKHVQPVYTAALKDELVKTDKIYKKIKKRLLWGSDLGT
                     MIRCARAFGGLMDSMKASCIALPCRVGMNMNEDGPIIFDKHSKYRYHYDADYSRWDST
                     QQRCILSAAMEVMVRFSAEPELAQVVAEDLLAPSQLDVGDFVISVQEGLPSGVPCTSQ
                     WNSIAHWILTLSAMAEVSGLSPDVIQAHSCFSFYGDDEIVSTDINLDPMKLTQKLREY
                     GLVPTRPDKTEGPLVITEDLTGLTFLRRSIARDPAGWFGKLDQDSILRQLYWTRGPNH
                     ENPYESMVPHSQRATQLMALLGEASLHGPQFYKKVSKMVINEIKSGGLEFYVPRQEAM
                     FRWMRFSDLSTWEGDRNLAPEGVNEDGVE"
     mat_peptide     5..1006
                     /gene="ORF1"
                     /product="p48"
     mat_peptide     1007..2104
                     /gene="ORF1"
                     /product="NTPase"
     mat_peptide     2105..2623
                     /gene="ORF1"
                     /product="p22"
     mat_peptide     2624..3022
                     /gene="ORF1"
                     /product="VPg"
     mat_peptide     3023..3565
                     /gene="ORF1"
                     /product="Pro"
     mat_peptide     3566..5095
                     /gene="ORF1"
                     /product="RdRp"
     gene            5079..6689
                     /gene="ORF2"
     CDS             5079..6689
                     /gene="ORF2"
                     /note="major capsid protein"
                     /codon_start=1
                     /product="VP1"
                     /protein_id="QBM30994.1"
                     /translation="MKMASNDATPSDDGAAGLVPEINNEVMALEPVAGASLAAPVVGQ
                     QNIIDPWIRNNFVQAPAGEFTVSPRNSPGELLLDLELGPELNPYLAHLARMYNGHAGG
                     MEVQIVLAGNAFTAGKILFAAIPPSFPYENLSPAQLTMCPHVIVDVRQLEPVLLPMPD
                     IRNVFYHYNQNNSPKLRLVAMLYTPLRANNSGDDVFTVSCRVLTRPSPDFQFTFLVPP
                     TVESKTKNFTLPVLRVSEMTNSRFPVVLDQMYTSRNENIIVQPQNGRCTTDGELLGTT
                     ILQSVSICNFKGTMQAKLNEEPRYQLQLTNLDGSPIDPTDDMPAPLGTPDFQAMLYGV
                     ASQRSSRDNATRAHDAQVDTAGDTFAPKIGQVRFKSSSNDFDLHDPTKFTPIGVNVDD
                     QHPFRQWSLPNYGGHLALNNHLAPAVTPLFPGEQILFFRSYIPSAGGHTDGAMDCLLP
                     QEWIEHFYQEAAPSQSDIALVRFINPDTGRVLFEAKLHKQGFLTIAASGDHPIVMPTN
                     GYFRFEAWVNPFYTLAPVGTGSGRRRIQ"
     gene            6689..7483
                     /gene="ORF3"
     CDS             6689..7483
                     /gene="ORF3"
                     /note="minor structural protein; small basic protein"
                     /codon_start=1
                     /product="VP2"
                     /protein_id="QBM30995.1"
                     /translation="MAGAFLAGLAGDVVASSLGSLVGAGANAINQKVEYDFNRQLQEA
                     SFRHDKDMLKAQVAATAGLQQAMIDIKREALTAGGFSPADAARGAVKAPMTQILDWNG
                     SRYWAPNSMKTTGYSGTFTSQGIRSSPHLSNQTPSAVKPTRPLPSISSSSSVYSSPST
                     APSQSTQSTTLSAGTGSSRPNTVSTKTSTLSRTSDWVRGQNEMLGPFMSGALQTAYVT
                     PPSSKASSQGTVSTVPKAVLDSWTPMFNTHRQPLFAHLRRRGESQI"
ORIGIN      
        1 gtgaatgaag atggcgtcta acgacgctac cgctgccctt ggcagtcaaa aatctgtcaa
       61 tgacagtaat atagccaccc cttctaacaa agaagaggtt ggtacattct ccaacattaa
      121 agttggattc aagaaaatgc tgggtgccgt acccaaaggt accaaggcac ccagcagtga
      181 tcagcattgc cccacagtta agatcaggcc taaaacattg acaatccccc ccgaaccccc
      241 aaatggtgaa gacaccgtac aatttgatgc aaagtcagaa actgtaattg ggctaccgga
      301 cttgacaacg gtgcaaaacg aacacgaaaa tactccatac actgtccccc cattaagtga
      361 gagggagcac agaccggcca ctgaaccact tcctggcaca atattggaga tgtgggatgg
      421 tgagttttac cattactccg tgtacgtcag cgatggtaaa gctctagggg tccacaaacc
      481 accggcggct ataagtctcg cgacgataga actcaccccc atatcacttt actggagacc
      541 cgtctacacc cccaactact tggtctcccc agacacatta aaaggcctcg ctggtgaaaa
      601 gttcccctac acggccttca gcaacaactg ttacaacttc tgttgttggg tgcttgagct
      661 caacgacacg tggcttaaca gaagatgcat ctccagaact accggcttct ttaaaccata
      721 ccagtcttgg aataggaaac ccctcccaac tgttgatgat ggaaagatca aaaaggtggc
      781 caacgcgatc ctctgtgcac tcggctcgct gttttcaaaa ccaatcaaag atctattagg
      841 taaactcaaa ccattgaatc tactacactt gcttgcgtcc tgtgattgga cgtttgcggg
      901 tatagtagag acagtcatct taatggcgga gcttttcaat gtgttctgga ccccgccaga
      961 tgtctctaat tttatagcct ccctgatagg tgattttgaa ttgcaaggtc ctgaagactt
     1021 ggctgtggag ctcgttcccg tggttatggg tggcataggg atggttctcg gcttcaccgc
     1081 tgagaagata ggccgcatgc tgtcgtccgc ggcatcaaca ctacgggcgt gcaaagactt
     1141 agggaactat gcccttgaca tactcaaatt ggtcatgaaa tggttcttcc caaagaagga
     1201 agagaaagct gagatggaga ccttgagggc gattgaagat gctgtccttg acatggaagc
     1261 tatagggaat aaccatctca caacccttct caaggacaaa gacagcctca cggctttcat
     1321 gaaaaccctg gatctagaag aggagaaagc aaggaaactg tccactaaat catcttcacc
     1381 ggacatagtc ggcaccatta acgccatact agctaggata gctgctgcta gatccctact
     1441 acataaggcc aaagaggaaa tgtttagcag aatcagacca gtagttgtca tgatctcagg
     1501 cagacctggc attggaaaaa ctcatatggc aagacacttg gctaagagca tcgccaacac
     1561 catgagtggc gaccaaaggg tcggactcgt cccacgcaac ggtgtcgatc actgggatgc
     1621 ctacagagga gagagagtag tcttgtggga tgactacggc atggggagcc ctgtcaaaga
     1681 cgccctgaca ctgcaagaat tggccgacac atgtccagtc actttaaatt gtgataggat
     1741 tgagaataag gggaagatgt ttgatagtga tgtcatcata atcacgacca acttagtcaa
     1801 ccccgcgccc ctcgactatg tgaacttcga ggcgtgttcc aggagagttg atttcctggt
     1861 ttatgcagag tcaccagaaa ttgaaaaggt caagagagat ttccccggcc agcctgacat
     1921 gtggaaagac cattttaagc cagacttctc ccacattaag ctgactctag ccccccaggg
     1981 tggatttgac aagaatggta acaccccaca tggcaagggc accatgcggt ccctaaccca
     2041 ggggtcccta accgcgagag ttgcaggcct tgtccatgaa aggaaggacg agttccagct
     2101 ccaaggaaat gaccttcaaa catacaattt tgacaccaac agagtctccg catttagaaa
     2161 attggccgca gacaacaagt atgggatcat ggagacgatg agagttggcg cagcgctcaa
     2221 gagcgtgaag accttggaag atcttaaagt tgcattgagg gatgtaaaat tcaatgagtg
     2281 tgaaataatt tacaagaatt ctaagtaccg agtctcttcc aacggtaaag gctcagtctc
     2341 tattgacaaa gttgaagaca atgcttccca gacagtgaac gaggtgcatt cagccctcct
     2401 cagactcagg caggcgaggg ccagatacta catcagctgc ttccaagacc tcgtctacac
     2461 tctcatacag gttgccgggg catcatttgt tgttagtagg atctccagga ggttctgctg
     2521 ggaaaggtgg gtcaaaccga ccgagaccca ggaggtgaat gagtccgaaa aggaagcggc
     2581 ccaaggcaga tgggaaattg agcccaagga cacagaacca gaaggcaaga agggtaagaa
     2641 caagaaagga aggggcaaga aacacacagc cttctctagc aaaggtctga gtgatgaaga
     2701 gtatgatgag ttcaagagga tcagggaaga aagaaatgga aagtactcca ttgaggaata
     2761 cctgcaggac cgagaccgct attatgaaga agtagcagtt gctcgagcga cagaggagga
     2821 cttctgtgaa gaggaagagg ccaagataag acaaagaatt ttccgcccga caaggaagca
     2881 gaggaaggag gaaaggggcg tactcggctt ggtcaccggc tcagacatca ggaagaggag
     2941 accagacgat tttcaaccaa aaggcaatct atgggctgat gacaccagaa gtgtggacta
     3001 caatgagagg cttgattttg aagcaccccc gagtgtctgg tcaagaatag tcccactagg
     3061 cactggttgg gggttttggg tgtcatccaa ccttctgatc acaacaacac acgtcctgcc
     3121 taaagggatt agggaacttt ttggagttga aatcaaacaa atccaaattc ataagtctgg
     3181 agagttttgc aggtttagat tcccaagacc tatcaggcca gatgtcacag gactcgtgct
     3241 ggaggagggc gccccagagg gcactgtctg ttctgtgctc gtgaaaagac ccacaggtga
     3301 aatgatcccc cttgcagtga ggatgggcac acacgcatcc atgaaaatac agggtaggac
     3361 cgttggtggc cagatgggaa tgctcctcac aggagcaaac gcaaagaaca tggatcttgg
     3421 caccggccct ggtgactgcg gttgccccta tatctataag cgtggcaacg acatcgttgt
     3481 tgcgggcgtc cacaccgcag cagcccgggg aggcaacact gtgatatgtg ctacccaggg
     3541 gcaagatggg gaagcagtcc ttgagggaaa tgaggacctt ggcacctact gtggtgcccc
     3601 aattctgggc cctggtaagg cgcctaaact cagcacgaag accaagtttt ggcgctcatc
     3661 accagatgcc ctgccacctg gcacatatga acctgcttac ctaggaggca aagaccctag
     3721 agtggaaaaa ggtccctccc tgcagcaagt catgagagat cagctgaagc ccttcacaga
     3781 acccagaggc agactaccta gacctgcaat tttagaggaa gccaaaaaga cagtaatgaa
     3841 tgttctagag caaaccattg accccgccaa gccatggtcc tattcgcagg catgtgcctc
     3901 attggacaaa accacttcaa gtggtagccc ccatcacgtt aagaaaaatg accactggaa
     3961 tggagagtcc ttcactggtc ctcttgcaga ccaggcttcc aaagccaacc tcatgtatga
     4021 gcaggctaaa catgtgcagc ccgtgtatac ggctgcgctg aaagatgagc ttgttaagac
     4081 tgacaagatc tacaagaaga taaagaagag gcttctatgg gggtcagacc ttggcacaat
     4141 gatcaggtgc gccagggctt ttggcggtct catggacagc atgaaggcaa gttgtatagc
     4201 tcttccttgt agggtaggaa tgaacatgaa tgaagatggc cccatcatat ttgacaaaca
     4261 ctctaagtac aggtaccact atgatgctga ctattctagg tgggactcaa cccaacaaag
     4321 gtgtatcctc tctgccgcta tggaagtgat ggtgcggttt tctgctgagc cagaattggc
     4381 acaagtggtt gcagaggacc ttttggcacc tagccagctt gatgttggcg actttgtcat
     4441 ctcagtccag gagggcctgc catcaggagt cccatgcaca tcgcaatgga attcaatagc
     4501 acactggata ctcactttga gtgcgatggc agaagtgtca ggcctctcac cagatgttat
     4561 ccaagctcac tcttgttttt cattttatgg ggatgatgag atcgtcagca ctgacatcaa
     4621 ccttgacccc atgaagttaa cacaaaaact tagggagtat ggcctggttc ccacccggcc
     4681 tgacaaaact gaaggtcccc tcgtcataac tgaagacctc accggcctga cgttccttcg
     4741 taggtcgatt gctcgggacc cagctggctg gtttggaaaa ctagaccaag attcaatcct
     4801 caggcaactg tactggacga gggggcctaa ccatgagaac ccgtacgaga gcatggtccc
     4861 tcattctcag cgggctacac aactcatggc ccttcttggt gaggcctcac tgcatggtcc
     4921 tcagttttac aagaaagtta gcaaaatggt catcaatgaa attaagagtg gtggtctgga
     4981 gttttacgtg cccagacaag aggccatgtt cagatggatg aggttctctg acctcagcac
     5041 gtgggagggc gatcgcaatc ttgctcccga aggtgtgaat gaagatggcg tcgaatgacg
     5101 ctactccatc tgatgatggt gcagccggcc tcgtaccaga gatcaacaat gaggttatgg
     5161 ctcttgaacc cgtcgctggg gcctcccttg cagcccctgt agtcggtcaa cagaatataa
     5221 ttgatccctg gattagaaac aattttgtac aagcccctgc tggtgaattt acagtttccc
     5281 ctagaaactc tcctggagaa ctcctacttg atttggaatt gggtcctgaa cttaacccct
     5341 atcttgcaca tttggccagg atgtacaatg ggcacgcagg aggaatggaa gtgcagatag
     5401 tactggctgg gaatgcgttc acagctggta agatcctatt tgccgccatc ccacctagct
     5461 tcccttatga aaatttgtca cccgcccaat tgactatgtg cccccatgtg atagtggatg
     5521 tgaggcaatt ggaaccagtg ctcttgccaa tgccagatat aagaaatgtt ttctatcatt
     5581 ataatcagaa caacagtccc aaacttaggc ttgtggctat gctttacact cctctgaggg
     5641 ctaataattc aggtgatgat gtgttcacgg tgtcttgtcg cgttctaacg cgaccttctc
     5701 cagatttcca gttcactttc ctggtcccac ctacagttga gtctaaaact aagaacttca
     5761 cccttcccgt tctcagagtc tcagagatga caaactcaag gttccccgtt gttttggacc
     5821 aaatgtacac aagcaggaat gaaaacatca ttgtccaacc ccaaaacggc agatgcacaa
     5881 ctgatggtga gctgcttggt accactatct tacaatctgt gtctatttgc aatttcaaag
     5941 gaacaatgca ggcgaagctg aatgaagagc cacgatacca attgcaactc accaacttgg
     6001 atgggtcacc catagatcca acagatgata tgcctgcccc tcttggcaca ccagacttcc
     6061 aggccatgtt atatggcgtt gcaagccaac gctcttccag agacaatgcc accagggcac
     6121 atgatgcaca ggttgacact gcgggtgaca cattcgcccc gaagattggc caggttcgat
     6181 ttaaatcaag ctccaatgat tttgacctac atgaccctac aaaattcaca cctattggtg
     6241 tcaatgtgga tgaccagcac ccttttagac agtggtccct gccaaactac ggtggtcacc
     6301 ttgccctgaa caatcattta gccccagctg tgacgccgct cttccctggc gagcaaatct
     6361 tgttctttag gtcatacatt ccaagcgccg gaggccatac agacggtgct atggactgtt
     6421 tgctgcccca agagtggata gagcacttct accaggaggc ggctccttcc caatctgaca
     6481 tcgcactggt aaggttcatc aaccctgaca caggaagagt gctctttgaa gctaaattgc
     6541 ataaacaagg tttcctcaca attgcagcat ctggagacca ccctattgtg atgcccacca
     6601 atggttactt taggtttgaa gcttgggtta atcctttcta tactctcgcc cccgtgggaa
     6661 ctgggtctgg gcgcaggagg attcaataat ggctggagct ttccttgcag gtttggcagg
     6721 tgacgttgtg gcttccagct tgggctcact cgtgggtgct ggagccaacg ccatcaatca
     6781 gaaagtggag tatgacttca acaggcaact ccaggaggca tcttttagac atgacaagga
     6841 tatgctcaaa gcccaggttg cagcaacagc aggccttcaa caggccatga tagacatcaa
     6901 gcgggaggca ttgactgcag gcggcttttc ccccgctgat gctgcaagag gtgcagtcaa
     6961 agcgcctatg acgcagatcc ttgattggaa tggttctaga tattgggctc ctaactccat
     7021 gaagacaact ggctattcag gtacatttac ttctcaaggc attagaagtt cccctcatct
     7081 gtctaatcaa accccaagtg ctgttaaacc tactagacct ttaccatcta tatctagttc
     7141 ttctagtgtg tatagttctc cctctactgc cccttcacaa tcaacacaat caacaacgct
     7201 gtctgcaggg acagggtcct ccagacctaa cactgtgtcc acaaagacct ccacattgtc
     7261 gaggacaagt gattgggtca gaggccaaaa tgagatgctt ggcccgttca tgagtggtgc
     7321 actccaaact gcttatgtca caccaccatc gagcaaggcc tcatcacaag ggacggtctc
     7381 gaccgtaccc aaggctgttt tggactcctg gactcccatg tttaacaccc acaggcagcc
     7441 tctcttcgcc cacttgcgta ggcgagggga gtcacagatt tagtgaaaag gatgattagg
     7501 gttccttcct tcccccttct tattctttt
//