Typing tool

Complete norovirus genomes

MH130046  GI.7
 GI.PNA2

Length: 7,734 | 3 CDS

ORF1: 95..5404
ORF2: 5388..7028
ORF3: 7028..7678
LOCUS       MH130046                7734 bp    RNA     linear   VRL 08-APR-2018
DEFINITION  Norovirus GI strain Hu/BD/2011/GI.Pg-GI.7/Dhaka1882, complete
            genome.
ACCESSION   MH130046
VERSION     MH130046.1
KEYWORDS    .
SOURCE      Norovirus GI
  ORGANISM  Norovirus GI
            Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
            Picornavirales; Caliciviridae; Norovirus.
REFERENCE   1  (bases 1 to 7734)
  AUTHORS   Nelson,M.I., Mahfuz,M., Chhabra,P., Haque,R., Seidman,J.C.,
            Hossain,I., McGrath,M., Ahmed,A.Shamsir., Knobler,S., Vinje,J. and
            Ahmed,T.
  TITLE     Genetic diversity of noroviruses circulating in a pediatric cohort
            in Bangladesh
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 7734)
  AUTHORS   Nelson,M.I., Mahfuz,M., Chhabra,P., Haque,R., Seidman,J.C.,
            Hossain,I., McGrath,M., Ahmed,A.Shamsir., Knobler,S., Vinje,J. and
            Ahmed,T.
  TITLE     Direct Submission
  JOURNAL   Submitted (27-MAR-2018) 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. 8
            Sequencing Technology :: Illumina
            ##Assembly-Data-END##
FEATURES             Location/Qualifiers
     source          1..7734
                     /organism="Norovirus GI"
                     /mol_type="genomic RNA"
                     /strain="Hu/BD/2011/GI.Pg-GI.7/Dhaka1882"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:122928"
                     /country="Bangladesh"
                     /collection_date="06-Jul-2011"
                     /note="genotype: GI.Pg-GI.7"
     gene            95..5404
                     /gene="ORF1"
     CDS             95..5404
                     /gene="ORF1"
                     /codon_start=1
                     /product="nonstructural polyprotein"
                     /protein_id="AVT56082.1"
                     /translation="MARIRGRIGPQRGETTTKIKDANMALDLLRRSQTPSPSRQDSPP
                     KSQRDRPPRTVSEVKKVMGWDAEPEHQESTAKAWCDLSKEEKEEIMRNNERLFDAGGV
                     TPSTLPSTFERAELSNTSTEQQTVSWSASDGVNIGVNDLTTVRGPFWNMCPLPPLDAR
                     NNGPAKEPLIGDMIEFYEGHIFHYAIYMGQGKTIGVHSPQAAFSIPRITIHPLVAWWR
                     VCYTPTSQQRLTYDQLKELENEPWPYASITNNCYEFCCRVMALDDTWLQRRLVSAGKF
                     NHPTQEWSQDTPDFHQDSKLEMVRDAVLSAINGLVSQPFKNILSKIKPLNVLNLLSNC
                     DWTFMGVVELIVLLAELFDIFWTPPDISSFIASLLPEFHLQGPEDLARDLVPLVLGGI
                     GLAIGFTRDKITKVMKSAVDGLRSATQLGQYGLEIFSIIKKYFFGGDQTEKTLRGIED
                     AVIDMEVLSSTNVTQLVKDKKLARAYMNVLDNEEEKARKLSVRSADPHIVTSVNNLIS
                     RISMARSALAKAQAEMTSRPRPVVIMMCGPPGIGKTKAAEHLAGRLAAEIRPGGKVGL
                     VPRESIDHWDGYHGEDVLLWDDYGMSKITEDCNKLQAIADTAPLSLNCDRIENKGMQF
                     SSDAIIITTNAPGPAPVDFVNLGPVCRRVDFLVYCSAPEIEQMRRTHPGDASAIKDLY
                     KRDYTHLKMELAPQGGFDNQGNTPFGKGVMKPTTLNRLLIQATALAMERQDEFQLQGA
                     IYNFDEDRVAAFTNLARANGLGLISMATLGKRLRTVKTMEGLRNALVGYKIEECDIIW
                     NTRAYSIKSDGNTVTIKEKQAPTSPQHQAICTATLALSRLRAARALAYASCLQSAVLS
                     ILQVAGSAVVVSRAVKRMFGTRTDQPVLEGKHKEHSCRVHRAEAAGHGPIGHDGVIER
                     YGLCESEQEEEEDQTMELPTANKEGKNKGKTKKGRGRKSNFNAFSRRGLSDEEYEEYK
                     KIREEKSGNYSIQEYLEDRQRYEEELAEVQAGGDGGIGETEAEIRHRVFYKSKSGMRK
                     QRQEERRQLGLVSGSEIRKRKPIDWTPPKNDWSEDTRTVNYDEHISFEAPPSIWSRVV
                     KFGSGWGFWVSSTVFITTTHVIPPGAKEIFGESLSNVAIHRVGEFTQFRFSKKMRPDL
                     TGMVLEEGCPEGTVCTIMIKRDSGELLPLAVRMGAVASMKIQGKLMHGQSGMLLTGAN
                     AKGMDLGTIPGDCGAPYVHKRGNDWVVCGVHAAATKSGNTVVCAIQGGEGEATLEGGG
                     QNKGHYAGHPILRYGNGPSLSTKTKFWKSTPQPLPPGTYEPAYLGGRDPRVEGGPSLQ
                     QVLRDQLKPFAEPRGRLPEAGLLEAAVETVTNVLEQVMDTPVAWSFNDACMSLDKTTS
                     SGFPHHKKKNDDWNGSAFVRELGDQAAHANNMYELGKPMKPVYTAALKDELVKPDKVY
                     NKIKKRLLWGADLGTVIRAARAFGPFCEAIKPHVIKLPIKVGMNAIEDGPLIYAEHSK
                     YKFHYDADYTAWDSTQNREIMMESFNIMCKLTANPSLAAVVAQDLLSPSEMDVGDYVI
                     SVKDGLPSGFPCTSQVNSMNHWILTLCALSEVTGLSPDVIQSQSYFSFYGDDEIVSTD
                     IEFDPNKLTQVLKEYGLKPTRPDKTDGPIIVRQQVDGLVFLRRTISKDAIGYQGRLDR
                     NSIERQLWWTRGPNHDDPFETLVPHSQRKVQLVSLLGEAALHGEKFYRKIASRVIQEV
                     KEGGLEIYIPGWQAMFRWMRFHDLSLWTGDRDLLPDYVNDDGV"
     mat_peptide     95..1219
                     /gene="ORF1"
                     /product="p48"
     mat_peptide     1220..2308
                     /gene="ORF1"
                     /product="NTPase"
     mat_peptide     2309..2908
                     /gene="ORF1"
                     /product="p22"
     mat_peptide     2909..3328
                     /gene="ORF1"
                     /product="VPg"
     mat_peptide     3329..3871
                     /gene="ORF1"
                     /product="Pro"
     mat_peptide     3872..5401
                     /gene="ORF1"
                     /product="RdRp"
     gene            5388..7028
                     /gene="ORF2"
     CDS             5388..7028
                     /gene="ORF2"
                     /note="major capsid protein"
                     /codon_start=1
                     /product="VP1"
                     /protein_id="AVT56083.1"
                     /translation="MMMASKDAPSNMDGTSGAGQLVPEANTADPIPLEPVVGAATAAA
                     TAGQVNMIDPWIMNNFVQSPEGEFTISPNNTPGDILFDLQLGPHLNPFLQHLSQMYNG
                     WVGNMRVRILLAGNAFSAGKIIICCVPPGFTAQNISIAQATMFPHVIADVRVLEPIEI
                     PLDDVRNVLFHTNENRPTMRLLCMLYTPLRAGGASAGTDPFVIAGRVLTCPSPDFNFL
                     FLVPPSVEQKTRQLTVPNIPLNNLSNSRVPAMINKMAISPDANQVVQFQNGRCTTDGQ
                     LLGTTPISASQVARIRGKVFSTSSGKGLNLSELDGSPYHAFESPAPVGFPDLGHCDWH
                     VSSFKADQNSRDDPISRLDIKQGASFAPHLGSIEYTTSQNPDGDQLGTLTWISSPSED
                     TPGHGTINLWKIPSYGSTVTESVHLAPPIYPPGFGETLVYFMSNFPIGHTSSSMAQVP
                     CTLPQEFVAHFVNEQAPVRGDAALLHYVDPDTHRNLGEFKLYPEGYITCVPNTGGGGP
                     QSLPTNGVFIFSSWVSRYYQLKPVGTAGPARRLGVRRV"
     gene            7028..7678
                     /gene="ORF3"
     CDS             7028..7678
                     /gene="ORF3"
                     /note="minor capsid protein; small basic protein"
                     /codon_start=1
                     /product="VP2"
                     /protein_id="AVT56084.1"
                     /translation="MAQAIFGAIAATAAGSAVGAGIQAGTEAALQYQRYQQDLTLQQN
                     SFKHDERMLGLQIEGSNALLQKNLSTRYNLLLNSGMSSADAARTIVGAPASKVVDWNG
                     VRIAAPTSTATTLRSGNFMNIPVFQKTKQQSSSVLSSGYSNPNYDSSTLVSRTTQWVE
                     SQNSSRSLPPFHPSALRTTWVTPPGSTSTSTYSSVSSAPRFFNTERLPLFANNGRK"
ORIGIN      
        1 gtgaatgatg atggcgtcta acgacgctat tgccgttgct gatgtcagca ataacaatgc
       61 taacaccaac aatgaaaaca ttggatcccg ccttatggcg aggatccgtg ggcgtatagg
      121 cccacaacgt ggtgaaacaa ccacaaagat caaggatgcc aacatggcgc tcgatttgtt
      181 gcgccggtca caaacaccct ctccgtcccg acaggacagc ccccccaaga gtcaaagaga
      241 ccgacctcca cgaactgtct cagaggtaaa gaaggtgatg gggtgggatg ctgaaccgga
      301 acaccaagaa agtacggcta aagcgtggtg tgacctatcg aaagaagaaa aggaggaaat
      361 aatgcgcaac aatgaaaggc ttttcgatgc tggaggggtc accccatcca ccctacctag
      421 cacgtttgaa agagctgaat tgagcaacac ctcaactgaa cagcaaaccg tgtcttggtc
      481 agccagtgat ggggttaaca ttggtgtaaa tgacttgacc accgtccgtg ggccattctg
      541 gaacatgtgc cccctaccgc cactggatgc ccgcaacaat ggccctgcca aagagcctct
      601 cattggggac atgatagagt tctatgaagg tcacatattc cattatgcca tatatatggg
      661 ccagggcaaa accattggag tgcactcgcc gcaggccgcc ttctctatac ctagaataac
      721 aatccatccc ttggtggctt ggtggcgtgt gtgttacact cccacaagcc agcaacgcct
      781 cacatatgac cagctcaaag aattggaaaa cgagccatgg ccttatgcct ccatcaccaa
      841 taattgctat gagttttgtt gcagagtgat ggcacttgat gatacctggc tccagaggag
      901 actggttagt gctgggaaat ttaaccaccc cacacaagag tggtcacaag acaccccaga
      961 ctttcaccaa gattccaagc ttgagatggt aagagacgct gtattgtcag ccatcaacgg
     1021 cctcgtgtca cagcccttca aaaacatctt atcaaaaatt aaaccactta acgtgcttaa
     1081 tctcttatca aattgtgatt ggacttttat gggggttgtg gagctgatcg tactcttggc
     1141 tgagttattt gatatctttt ggactccgcc agatatttca agcttcatag cctcattgct
     1201 acctgagttc catctgcaag gcccggaaga cctggctagg gacttggtcc cccttgtgct
     1261 aggtggcatt ggcttagcga ttggcttcac gagagataag ataacaaaag ttatgaaaag
     1321 tgctgttgac ggcctacgat cagcaacaca gcttggacaa tatggactgg aaatattctc
     1381 aattataaag aaatacttct ttggggggga tcaaacagaa aagaccctaa gaggtattga
     1441 ggatgcagtt atagacatgg aggtgttatc cagcactaat gtaactcaat tggtcaagga
     1501 caagaaacta gctagagcat acatgaatgt gctggacaac gaggaggaga aggcccgaaa
     1561 actctcagtc cgcagtgctg acccgcacat agtgacttct gttaacaact tgatatcacg
     1621 catttcaatg gcaaggtcag cgctagctaa ggcccaagct gagatgactt ctcgcccccg
     1681 accagtggtt ataatgatgt gtggaccccc tggcattggg aagacaaagg ccgccgagca
     1741 tctagcaggc cgcctagctg ccgagattag gcctggggga aaggttggcc ttgtacctag
     1801 agaatccata gaccactggg atggatacca tggcgaggat gtcctgctct gggatgacta
     1861 tggtatgtca aagataacag aagattgcaa caaattgcag gctatagctg acaccgcccc
     1921 gttgtcactc aactgtgata ggatagaaaa caagggtatg cagttctcat ctgatgcaat
     1981 cattattacc accaatgccc ctggcccggc cccagttgac tttgttaatt tgggtcccgt
     2041 gtgtaggcga gtggactttt tagtctattg ctctgcccct gagattgaac agatgcgaag
     2101 aacccaccca ggtgatgcca gcgccatcaa ggacttgtac aagagggatt acacccacct
     2161 aaaaatggaa ctagccccac agggcggctt tgacaatcag ggcaatacac catttgggaa
     2221 aggtgttatg aagcccacga ccctcaacag actgttaatc caggctacag cactagccat
     2281 ggagcggcag gatgagtttc agctccaagg ggccatttac aactttgatg aggacagagt
     2341 agcagccttc actaacctag ctcgtgccaa tggcttgggg ctcataagca tggccacact
     2401 aggtaaaagg ttaaggactg ttaagaccat ggaagggcta cgcaatgcac tggtgggtta
     2461 caaaatagag gagtgtgaca taatttggaa taccagagca tattcaatca agagtgacgg
     2521 gaacactgtc acgatcaagg agaaacaggc cccaacctca ccccaacacc aagctatctg
     2581 tacggccacc ctcgcccttt ccaggctgcg ggctgctagg gcccttgcat atgcctcctg
     2641 cttacaaagt gcagtgctgt caatactcca agtggcaggt tccgctgtgg tggtaagcag
     2701 ggctgtgaaa cgcatgtttg gcacacgcac tgaccaacct gtactggaag gcaagcacaa
     2761 ggagcatagt tgcagggtgc atcgagcaga agctgctgga cacggtccta ttggccatga
     2821 tggagtcatc gagcgctatg gcctatgtga aagtgaacag gaagaagagg aagatcagac
     2881 tatggaattg cccactgcta ataaggaagg caagaataag ggtaaaacta aaaagggccg
     2941 cggccgtaag tctaacttca atgccttctc aaggcgcggc cttagtgatg aagagtatga
     3001 ggagtataag aaaatcaggg aagaaaagag tggcaactac agcatacagg aatatcttga
     3061 agaccgccaa cgctatgagg aggagctcgc tgaggtccag gcaggtggag atggtggaat
     3121 cggcgaaact gaagcggaga tccgtcaccg agttttctac aagtcaaagt ctggcatgag
     3181 aaagcagcgc caagaggaac gacgccagtt aggccttgtg agcgggtccg agatccggaa
     3241 acgcaagcct atagactgga ctccccccaa aaatgattgg tcagaggaca ccagaacagt
     3301 taattatgat gaacacatta gttttgaagc cccaccctca atctggagta gggtagtaaa
     3361 atttggcagt ggctggggct tctgggtgag ctcaacagtg ttcatcacca caacacatgt
     3421 cataccacct ggcgctaaag agatctttgg tgaaagcctc agcaatgtgg ccattcacag
     3481 ggttggtgaa ttcactcaat ttcgattctc caaaaagatg agacccgacc tcaccggtat
     3541 ggttctagaa gaaggttgcc cagaaggcac ggtgtgtact ataatgataa agagggattc
     3601 tggtgagttg ctgccactag ctgtccgcat gggagcagtg gcttcaatga agatccaagg
     3661 gaagctcatg catggacaat caggaatgct gctcactggc gccaatgcca agggcatgga
     3721 tttaggaact atacctgggg actgtggggc accatacgtc cacaaaaggg ggaatgactg
     3781 ggtagtctgt ggtgttcatg cggccgccac gaaatcaggt aatactgtgg tgtgtgctat
     3841 tcagggtggt gagggtgaag ccacattgga gggtggtggc caaaataagg gtcattatgc
     3901 agggcaccca atactgaggt atgggaatgg cccttcattg tcaactaaga caaagttctg
     3961 gaagtcaacc ccccaaccat tgcctccagg cacctatgaa ccagcttatc ttggtggtag
     4021 ggaccccagg gtcgaagggg gaccgtccct acagcaagtg ctaagagacc aactaaaacc
     4081 atttgctgaa ccccgtggca gattgccgga ggcaggcttg ttagaagctg cggttgaaac
     4141 agtcaccaat gtgcttgaac aagttatgga cacaccagtg gcatggagct tcaatgatgc
     4201 ctgtatgtca ttagataaaa caaccagttc aggctttccc catcacaaga aaaagaatga
     4261 tgattggaat gggagtgcat ttgtgagaga acttggagac caggcggccc atgccaacaa
     4321 catgtatgag cttggtaagc ccatgaaacc tgtatacacg gcagccctca aggatgaact
     4381 cgtcaagcca gataaagtgt acaacaagat taagaaaagg ctactttggg gggcagatct
     4441 tggcactgtc atccgcgctg caagagcctt tgggccattc tgcgaagcca taaaacctca
     4501 tgtgatcaag ctgcccatca aagtgggcat gaatgccata gaggatggcc ctctgatcta
     4561 cgcagaacat tccaagtaca aatttcatta tgatgctgat tacacggcat gggattcaac
     4621 acaaaacagg gaaatcatga tggagtcctt caacattatg tgcaaattga cagccaatcc
     4681 ctctctggct gcagtggtgg cgcaagatct tctttctccc tctgagatgg atgttggtga
     4741 ctatgtaatc agtgtcaagg atggcctacc gtctggtttc ccatgtacct cacaagtaaa
     4801 tagcatgaat cattggatct tgaccctgtg tgctctatca gaggtgactg gactctcccc
     4861 cgatgtgata cagtcacaat cctacttctc tttctatggt gatgatgaga tagtgtccac
     4921 agacattgag tttgacccta ataaattaac ccaagtgcta aaagaatatg gcttgaaacc
     4981 cacaagaccc gacaaaactg atggccctat cattgttaga caacaggtgg atggcttggt
     5041 ctttctccgg cgcaccatat caaaagatgc cattgggtat caggggcggc tcgaccgcaa
     5101 ctctattgag agacagttgt ggtggactcg cggacccaat catgatgatc cattcgaaac
     5161 tctggttcca cattcgcaga gaaaagtcca gttggtgtct ttgttaggtg aagctgctct
     5221 ccatggtgaa aagttttata ggaaaatagc cagcagagtt attcaagaag tcaaggaagg
     5281 ggggcttgag atctacatac ccgggtggca ggccatgttc cgctggatgc ggttccatga
     5341 tttgagtttg tggacaggag atcgcgatct cttgcccgat tatgtaaatg atgatggcgt
     5401 ctaaggacgc cccttcaaac atggacggca ctagtggtgc tggtcagctg gtaccagagg
     5461 caaatacagc tgatcctatt cctttagaac ctgtagtggg ggctgcaact gcagccgcta
     5521 cggcaggtca agttaatatg attgacccct ggattatgaa taattttgta cagtcaccag
     5581 agggcgagtt cacaatttcc ccaaacaaca cgcctggtga cattttattt gatttacaat
     5641 tgggccccca tttgaatcca ttcctgcagc atctatcaca aatgtacaat ggctgggttg
     5701 gcaacatgag ggttagaatt ttgctagcag ggaatgcgtt ttctgctggc aagataataa
     5761 tctgttgtgt gccacctggc tttaccgccc agaatatctc tattgctcaa gccacaatgt
     5821 tcccacatgt cattgctgat gttcgagttt tagagcccat tgagattccc cttgatgatg
     5881 ttcggaatgt gctcttccac acaaatgaga atagacccac aatgcgctta ttgtgcatgc
     5941 tctatacccc attgcgggcc gggggcgcgt ctgcgggcac ggatccgttc gtgattgcag
     6001 ggcgcgtctt aacgtgccct tctccagact ttaatttctt gtttctagtc ccccccagtg
     6061 ttgaacagaa aactaggcaa ttaactgtcc ccaacatccc attaaacaat ctatcaaatt
     6121 ctagagtgcc cgccatgatc aataagatgg ctatttcccc agatgctaat caggttgtcc
     6181 aatttcaaaa tggcaggtgc actacagatg gtcagctgtt gggcacaacc ccaatctctg
     6241 cgagtcaagt ggcccgcatc cgcggcaaag tcttttctac ttcatcaggc aaaggattga
     6301 atctgtctga gctggatggc agtccatacc atgcctttga aagccctgcc ccggttggtt
     6361 tccctgatct tgggcattgt gattggcatg tctcttcctt caaggcagat caaaactcca
     6421 gagatgatcc catttcacgc ctagatataa aacaaggggc ttcctttgcc ccacacctgg
     6481 gttctattga atacaccact tcgcaaaacc cagatggtga tcagttaggc accctaacct
     6541 ggatctcatc cccatcagaa gatactcctg gtcatggtac aatcaaccta tggaagattc
     6601 cttcctatgg ttccacagtc actgagtcag tccatcttgc acccccaata taccctccag
     6661 ggtttgggga gacacttgtt tattttatgt ctaactttcc aattgggcac actagttcca
     6721 gtatggcaca agtcccatgc accctccctc aggaatttgt ggcacacttt gttaatgaac
     6781 aggcccctgt tcgaggggat gcagcattgc ttcactatgt ggaccctgac acacacagaa
     6841 atcttggtga gttcaaatta taccctgaag gttacataac ctgtgtgcca aacacgggtg
     6901 gtggtggccc ccaaagtctc ccaaccaatg gagtatttat cttctcatct tgggtatcca
     6961 gatattatca acttaagcct gtgggaacgg ctggaccagc caggaggctt ggagttagaa
     7021 gggtataatg gcccaagcaa tctttggagc aatagctgcc actgccgcag gcagtgcggt
     7081 gggagcagga attcaagcag ggactgaggc tgcattgcaa taccaaaggt atcaacaaga
     7141 tttgaccctc caacaaaatt catttaaaca tgatgaaaga atgctaggcc tgcaaattga
     7201 ggggtctaat gccctattgc aaaagaatct gtcaactagg tataatcttt tacttaattc
     7261 aggtatgtcg tcagctgatg ctgcccgcac cattgtcggt gctcccgcct caaaggttgt
     7321 ggactggaat ggtgttagga ttgcagcccc aacatcgacc gctaccacac tgcggtcagg
     7381 caactttatg aacatacctg tctttcaaaa gactaaacag cagtcatctt ctgtgctgtc
     7441 ttctggatat tctaacccta attatgattc ctctactctt gtgtctagaa ctactcaatg
     7501 ggttgaatca cagaattcat ctagaagctt gcctcccttt catccttcag ctttaaggac
     7561 cacgtgggtt acaccacctg gttcaacctc aacttctact tattcatctg tgtcttcagc
     7621 gccccggttt ttcaacaccg agcgccttcc tttattcgca aataatggta ggaagtgaat
     7681 ttttgtaata taatgtgggc atcatattca ttattggcaa ttttaattgg tttt
//