Typing tool

Complete norovirus genomes

MN400355  GII.4 Hong Kong
 GII.P31

Length: 7,556 | 3 CDS

ORF1: 5..5104
ORF2: 5085..6707
ORF3: 6707..7510
LOCUS       MN400355                7556 bp    RNA     linear   VRL 21-JAN-2020
DEFINITION  Norovirus GII isolate Hu/HK/2019/GII.4 Hong Kong[P31]/CUHK-NS-2200,
            complete genome.
ACCESSION   MN400355
VERSION     MN400355.2
KEYWORDS    .
SOURCE      Norovirus GII
  ORGANISM  Norovirus GII
            Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
            Picornavirales; Caliciviridae; Norovirus.
REFERENCE   1  (bases 1 to 7556)
  AUTHORS   Tse,E.H.Y., Zhang,L.Y., Lau,S.L. and Chan,M.C.
  TITLE     Genome Sequence of a Human Norovirus GII.4 Hong Kong[P31] Variant
            in Hong Kong, China
  JOURNAL   Microbiol Resour Announc 9 (3), e01391-19 (2020)
   PUBMED   31948964
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 7556)
  AUTHORS   Zhang,L.-Y., Lau,S.L. and Chan,M.C.-W.
  TITLE     Direct Submission
  JOURNAL   Submitted (02-SEP-2019) Department of Microbiology, The Chinese
            University of Hong Kong, Room 38022, 1/F, Department of
            Microbiology, Hong Kong 852, China
COMMENT     On Oct 31, 2019 this sequence version replaced MN400355.1.
            
            ##Assembly-Data-START##
            Sequencing Technology :: Sanger dideoxy sequencing; Illumina
            ##Assembly-Data-END##
FEATURES             Location/Qualifiers
     source          1..7556
                     /organism="Norovirus GII"
                     /mol_type="genomic RNA"
                     /isolate="Hu/HK/2019/GII.4 Hong Kong[P31]/CUHK-NS-2200"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:122929"
                     /country="Hong Kong"
                     /collection_date="19-Aug-2019"
                     /note="genotype: GII.4 Hong Kong[P31]"
     primer_bind     1..22
     gene            5..5104
                     /gene="ORF1"
     CDS             5..5104
                     /gene="ORF1"
                     /codon_start=1
                     /product="nonstructural polyprotein"
                     /protein_id="QEL43935.2"
                     /translation="MKMASNDASAAAVAKSNNDIAKSSSDGVLSNMAVTFKRALGARP
                     KQPPPKEIPPRPPRPPTPELIKKIPPPPPNGEDELVVSYSAKDGVSGLPELTTVGQPD
                     ETNTAFSVPPLNQRENRDAKEPLTGTIIEMWDGEIYHYGLYVERGLILGVHKPPAAIS
                     FAKVELAPLSLYWRPVYTPQYLISPDTLRRLHGESFPYTAFDNNCYAFCCWVLDLNDS
                     WLSRRMINRTTGFFRPYQDWNRKPLPTVDDSKLKKVANIFLCTLSSLFTRPIKDIIGK
                     LKPLNILNILATCDWTFAGIVESLILMAELFGVFWTPPDVSAMIAPLLGDYELQGPED
                     LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
                     KKEEVSELAMVRSIEDAVLDLEAIENNHMTALLKDKDSLATYMRTLDLEEEKARKLST
                     KSASPDIVGTINALLARIAAARSLVHRAKEELSSRLRPVVVMISGKPGIGKTHLAREL
                     AKKIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC
                     PLTLNCDRIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPDVEK
                     AKRDFPGQPDMWKNAFSPDFSHLKLSLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA
                     SGLLHERLDEYELQGPTLTTFNFDRNKILAFRQLAAENKYGLVDTMRIGKQLKDVKTM
                     PDLKQALKNVSIKKCQIVYSGGTYTLEADGKGSVKVDKVQSATVQTNNELAGALHHLR
                     CARIRYYVKCVQEALYSIIQIAGAAFVTTRITKRMNIQNLWSRPQVEDTEETASKDGC
                     PKPKDDEEFVVASDDVKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
                     KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV
                     TGSEIRKRNPEDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP
                     SLFITSTHVIPQDAKEFFGVPIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG
                     TVATLLIKRPTGELMPLAVRMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
                     CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILG
                     PGSAPKLSTKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP
                     RGKPPRPSVLEAAKKTIINVLEQTIDPPQKWSFAQACASLDKTTSSGYPHHVRKNDCW
                     NGDSFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDL
                     ATMIRCARAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFEKHSRYRYHYDADYSRWD
                     STQQRDVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVMDVGDFQISINEGLPSGVPCT
                     SQWNSIAHWLLTLCALSEVTDLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLK
                     EYGLRPTRPDKTEGPLVISEDLDGLTFLRRTVTRDIAGWFGKLEQSSILRQMYWTKGP
                     NHEDPSETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQE
                     PMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE"
     gene            5085..6707
                     /gene="ORF2"
     CDS             5085..6707
                     /gene="ORF2"
                     /note="major capsid protein"
                     /codon_start=1
                     /product="VP1"
                     /protein_id="QEL43936.1"
                     /translation="MKMASNDANPSDGSTANLVPEVNNEVMALEPVVGAAIAAPVAGQ
                     QNLIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
                     FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHVIVDVRQLEPVLIPLPD
                     VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
                     TVESRTKPFTVPILTVEEMTNSRFPIPLEKLYTGPSTAFVVQPQNGRCTTDGVLLGTT
                     QLSAVNICTFRGDLTHIAGTRQFTMHLASPNWNNYDPTEEIPAPLGTPDFVGKIQGML
                     TQTTKGDGSTRGHKAIVSTGAADFAPKSGNIRFGTDTEDDLQSGTNTKFTPIGVVQDG
                     ENPHFSEPQQWVLPSYTGRTGHNVHLAPAVAPTYPGEQLLFFRSTMPGCSGYPNLDID
                     CLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGPHDLA
                     IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRVL"
     gene            6707..7510
                     /gene="ORF3"
     CDS             6707..7510
                     /gene="ORF3"
                     /codon_start=1
                     /product="VP2"
                     /protein_id="QFX67174.1"
                     /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
                     AFQFSSNLQQASFQHDKEMLQAQIEATQKLQQGMMKVKQAMLLEGGFSETDAARGAIN
                     APMTKALDWSGTRYWAPDARVTTYNAGRFSTPQPSGALPGRTNLRATLPTRGSSSVTS
                     ASSATSVYSNKTVSTRLGSSAGSGTSASSTPLTTRTRSWVEDQNRNLSPFMSGALNTS
                     FVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHVRRRGESRV"
ORIGIN      
        1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgct gttgccaaaa gcaacaacga
       61 catcgcaaaa tcttcaagtg acggtgtgtt atctaacatg gctgtcactt ttaaacgggc
      121 cctcggggcg cggcctaaac agccgccccc gaaggaaata ccacccagac ccccacgacc
      181 acccacacca gaattgatca aaaagatccc ccccccccca cccaacgggg aggatgaact
      241 agtggtttcc tacagtgcca aagatggcgt ttccggcctg cctgagctca ctactgtcgg
      301 acaaccggat gagaccaaca cggcgttcag tgttcccccg ctcaaccaga gggagaatag
      361 ggacgctaag gaaccactaa ctggaacaat cattgaaatg tgggatggag aaatatacca
      421 ttacggcctg tacgtggaac gaggtcttat acttggtgtg cacaagccac cggcagccat
      481 tagctttgcc aaggtcgagc tagcaccact ttctttgtac tggagacctg tatacacccc
      541 ccagtatctc atctctccag acactctcag gaggctgcat ggagagtcat tcccctacac
      601 tgcatttgac aacaattgct acgccttctg ttgttgggtg ttagacctaa acgactcatg
      661 gctaagcagg agaatgatta acagaacaac aggtttcttc agaccatacc aggattggaa
      721 caggaaaccc ctccccactg tggatgattc caaattgaaa aaggtagcca acatattctt
      781 gtgcactttg tcttcactat tcaccagacc cattaaggac ataataggga agttgaaacc
      841 ccttaacatc ctcaatattc tggccacatg cgactggacc ttcgcaggca tagtggagtc
      901 cttaatactc atggcagaac tctttggagt tttctggaca cccccagatg tgtctgcgat
      961 gatcgctccc ttactaggtg attatgaact gcaagggcct gaggaccttg cagtagaact
     1021 agtcccagtg gtgatggggg ggataggttt ggtgctagga ttcaccaaag agaaaattgg
     1081 aaagatgttg tcatccgctg catccacttt gagagcttgc aaagaccttg gtgcatacgg
     1141 actggaaatt ttgaaattgg tcatgaaatg gttcttccca aagaaagagg aagtgagtga
     1201 attggctatg gtgagatcca tcgaggacgc agtactggac ctcgaggcaa ttgaaaataa
     1261 ccacatgacc gcattgctca aggacaaaga cagtctggca acctatatga ggaccctcga
     1321 cctcgaggag gagaaagcca gaaaactttc aaccaaatct gcttcacccg acattgtggg
     1381 cacaatcaac gctcttctgg caaggatcgc tgctgcacgt tccctagtgc atcgggcgaa
     1441 agaagagctc tctagcaggc tgagacccgt tgttgtgatg atatcgggga agccagggat
     1501 agggaagact cacctcgcca gagagctggc caagaagatc gcggcctccc tcactgggga
     1561 ccagcgtgtg ggtctcatcc cgcgcaatgg tgttgatcac tgggatgcgt acaagggaga
     1621 aagagtggtt ctttgggacg actatggaat gagtaacccc atccatgatg ccctcagatt
     1681 gcaggaactt gctgacacct gtcccctcac actaaactgt gacaggattg agaataaagg
     1741 gaaggtcttt gacagtgatg ctataattat taccaccaac ctggccaacc cagcgccact
     1801 ggattatgtc aattttgaag catgctcgag gcgcattgac ttcctcgtgt acgcagaagc
     1861 tcctgatgtg gaaaaggcaa agcgcgactt cccaggccaa cctgacatgt ggaagaacgc
     1921 gttcagtcct gatttctcac acctgaaact gtcattggct ccacagggtg gttttgacaa
     1981 gaacggtaac accccgcatg gaaaaggcgt catgaagact ctcaccactg gctctctcat
     2041 cgctcgagct tcaggtttgc tccatgagag gctagacgag tatgaactac aaggcccaac
     2101 tctcaccact ttcaactttg accgtaacaa aatccttgct ttcaggcagc ttgccgctga
     2161 aaacaaatat gggctggtgg acacaatgag gattggaaaa cagctcaagg atgtcaagac
     2221 catgccagac ctcaaacagg cactcaagaa tgtctctatc aagaagtgcc agatagtgta
     2281 cagtggtggc acctacacac ttgaggccga tggcaagggc agtgtgaaag ttgacaaagt
     2341 gcaaagtgcc actgtgcaaa ccaacaatga actagctggt gccctacacc acctaaggtg
     2401 cgccagaatt agatactatg tcaagtgtgt ccaggaggcg ctgtattcca tcatccaaat
     2461 tgctggggct gcatttgtca ccacgcgcat cactaagcgc atgaacatac agaatctctg
     2521 gtccaggcca caggtggaag acacagaaga gacggctagc aaagatggtt gcccaaaacc
     2581 taaagatgat gaagagtttg tcgttgcatc cgacgacgtc aaaactgaag gcaagaaggg
     2641 gaaaaacaag actggccgtg gtaagaagca cacagccttc tcaagcaaag ggcttagtga
     2701 tgaggagtac gatgagtaca agagaatcag agaagaaagg aatggcaagt attccataga
     2761 ggagtacctt caggacaggg acaagtacta tgaggaggtg gccatcgcaa gggcaaccga
     2821 agaggacttc tgtgaagaag aagaggccaa aatccggcag agaatcttca gaccaacaag
     2881 gaaacaacgc aaagaggaga gggcttctct cggtttggtc acaggctctg aaattaggaa
     2941 gagaaaccca gaagacttca aacccaaggg gaaactgtgg gctgacgatg ataggagtgt
     3001 tgactacaat gagaaactca gctttgaagc cccaccaagc atctggtcac ggatagtcaa
     3061 ctttggttca ggttggggct tttgggtctc ccccagtctg tttataacct caacccatgt
     3121 cataccccaa gatgcaaaag agttctttgg agtccccatc aaacaaatcc agatacacaa
     3181 atcaggtgaa ttctgtcgat tgaggtttcc aaaaccaatc agaactgatg tgacgggcat
     3241 gattctagaa gaaggtgcgc ccgaaggaac cgtggccaca ctactcatca agagaccaac
     3301 tggagaactc atgcctttgg cagtaaggat gggaacccat gcaaccatga agattcaagg
     3361 gcgtacagtt gggggacaaa tgggcatgct cttgacagga tccaacgcca agagtatgga
     3421 cctaggcaca acaccaggtg actgcggctg tccctacatt tacaagagag ggaatgacta
     3481 cgtggtcata ggggtccaca cggccgctgc ccgtggagga aacactgtca tatgtgctac
     3541 ccaggggagt gaaggagagg ccacactcga aggtggtgac aataaaggaa catactgtgg
     3601 tgcaccaatc ttgggcccag ggagtgcccc gaaactcagc accaagacca agttttggag
     3661 atcatccacg acaccactcc cacctggcac ctatgaacca gcctacctcg gtggcaagga
     3721 ccccagagtc aaaggtggtc cctcgttgca acaagttatg agggaccagc taaagccatt
     3781 cacagaaccc agaggtaaac caccaagacc aagtgtgttg gaagctgcca agaaaaccat
     3841 tatcaatgtt cttgagcaaa caattgaccc accccaaaaa tggtcattcg cgcaagcttg
     3901 cgcgtccctc gacaaaacca cttccagcgg ttatccacac catgtgcgga agaacgactg
     3961 ttggaacggg gattccttca caggaaaatt ggcagaccag gcatccaagg ccaatctaat
     4021 gtttgaagag gggaagaaca tgactccagt ctacacaggt gcgcttaagg atgaactggt
     4081 aaagactgac aaaatttatg gtaagatcaa aaagaggctt ctgtggggct cagacctggc
     4141 gaccatgata cggtgcgccc gagcttttgg aggccttatg gatgaactca aggcacactg
     4201 tgtcaccctt cctgtcagag ttggcatgaa catgaatgag gatggcccca tcatctttga
     4261 gaaacactct agatatagat accactatga cgctgattat tcccggtggg actcaacaca
     4321 acaaagggat gtactggcag cagcccttga aatcatggtt aaattttctc cagaaccaca
     4381 cctagcccag gtagttgcag aagacctcct ttcccctagt gtaatggatg tgggtgactt
     4441 tcaaatatca ataaatgagg gactcccctc cggggtgcct tgcacctccc aatggaattc
     4501 cattgcccat tggcttctca ctctttgtgc actctctgaa gtcacggatt tgtcccctga
     4561 tattattcag gccaattccc ttttctcctt ctatggtgat gatgagattg tgagcacaga
     4621 cataaagttg gacccagaga agctgacggc aaagctcaag gagtacgggc taagaccaac
     4681 ccgccccgac aaaactgaag gaccccttgt catctctgaa gatctggatg gcctgacatt
     4741 cctgcggagg actgtgaccc gtgacatagc tggctggttt ggcaaattgg aacagagctc
     4801 aattctcagg caaatgtact ggaccaaggg tcccaaccat gaagatccat ctgaaacaat
     4861 gataccacac tcccaaagac ccatacaatt gatgtctctg ctgggcgagg ctgcactcca
     4921 tggcccggca ttctatagca aaattagcaa gttagttatt gcagagttga aggaaggtgg
     4981 catggatttt tacgtgccca gacaagagcc aatgttcaga tggatgagat tctcagatct
     5041 gagcacgtgg gagggcgatc gcaatctggc tcccagtttt gtgaatgaag atggcgtcga
     5101 atgacgccaa cccatctgat gggtccacag ccaacctcgt cccagaggtc aacaatgagg
     5161 ttatggcttt ggagcccgtt gtaggcgccg ctattgcggc acctgtggcg ggccaacaaa
     5221 atttaattga cccctggatt agaaataatt ttgtacaagc ccctggtgga gagttcacag
     5281 tgtcccccag aaacgctcca ggtgaaatac tatggagcgc gcctttgggc cccgatttga
     5341 acccttatct ttctcatttg gccagaatgt acaatggtta tgcaggtggc tttgaggtgc
     5401 aggtaatcct tgcggggaac gcgttcaccg ccgggaaaat catatttgca gcagtcccac
     5461 caaatttccc aactgaaggc ttgagcccca gccaggttac catgtttccc catgtaatag
     5521 tagatgttag gcaactagaa cctgtgttga tccctttacc tgatgtcagg aataatttct
     5581 atcattataa tcaatcaaat gattctacca ttaaattgat agcaatgctg tatacaccac
     5641 ttagggcaaa taatgctggg gatgatgtct tcacggtctc ttgtcgggtc cttacgaggc
     5701 catcccctga ttttgatttt atatttctgg taccaccaac agttgagtca agaactaaac
     5761 cttttactgt cccaatctta accgttgagg aaatgaccaa ttcaagattc cccattccct
     5821 tggagaagct gtatacgggt cccagcactg cttttgttgt tcagccacaa aatggtagat
     5881 gcacgactga tggcgtgctc ttgggcacta cccagctgtc tgctgtcaac atctgtacct
     5941 ttagaggaga tctcacccac attgcaggca ctcgccaatt cacaatgcat ttggcctctc
     6001 cgaactggaa caactatgat ccaacagaag aaatcccagc ccccctggga accccagatt
     6061 tcgtggggaa gattcaaggc atgctcaccc aaaccacaaa aggagatggc tcgacccgcg
     6121 gccacaaagc catagtgtcc actggggctg ccgactttgc cccaaaatca ggcaacattc
     6181 gattcggcac tgacacagaa gatgatctcc aatctggcac aaacacgaaa ttcaccccaa
     6241 ttggcgtcgt ccaagatggt gaaaaccccc actttagtga accccaacaa tgggtgctcc
     6301 caagttacac aggtagaact ggacataatg tgcatttggc ccctgctgtt gcccccactt
     6361 acccgggtga gcaactcctt ttcttcaggt ccaccatgcc cggatgcagc gggtacccca
     6421 acttggacat agactgcttg ctcccccagg aatgggtgca gcacttctac caagaagcag
     6481 ctccagcaca atctgatgtg gctttgctaa gatttgtgaa tccagacaca ggtagggttt
     6541 tgtttgagtg caagcttcat aaatcaggat atgttacagt agctcatact ggtcctcatg
     6601 atctagctat cccccccaat ggttatttta gatttgattc ctgggtcaac cagttttaca
     6661 cacttgcccc catgggaaat ggaacggggc gcagacgtgt attataatgg ctggagcttt
     6721 ctttgctgga ttggcatctg atgtccttgg ttctggactt ggttccttga ttaatgctgg
     6781 ggctggagct atcaatcaaa aagttgaatt tgaaaataat agaaaattgc aacaagctgc
     6841 tttccaattt agtagtaatc tgcaacaagc ttcctttcaa catgacaagg agatgctcca
     6901 agcacaaatt gaggccactc aaaaattgca acaaggtatg atgaaggtta agcaggcgat
     6961 gcttctagaa ggtggattct ctgaaacaga tgcagctcgt ggggcaatta acgcccccat
     7021 gacaaaggcc ttggattgga gtggaacaag atactgggca cctgatgcta gggttacaac
     7081 atataatgca ggccgctttt ccacccctca accttcgggg gcattgccag gaaggactaa
     7141 tctcagggct actctcccca ctcggggttc ttctagtgtt acttctgctt cttctgctac
     7201 ttctgtgtat tcaaataaaa ctgtctcaac gaggcttggt tcttcagcag gttctggcac
     7261 cagcgcctca agcaccccgt taactacaag gaccaggagc tgggttgagg atcaaaacag
     7321 aaacttgtca cccttcatga gtggggctct caacacatca ttcgtcaccc caccatctag
     7381 cagatcctcc agtcaaggca cagtctcaac cgtgcctaaa gaaattttgg actcctggac
     7441 tggcgctttc aacacgcgca ggcagcctct cttcgctcat gtccgtaggc gaggggagtc
     7501 acgggtgtaa tgtgaaaaga caaaattgat tatctatcct ttctttattg tctttt
//