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Severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/human/CHN/SH-HG20230504-475/2023 ORF1ab polyprotein (ORF1ab), ORF1a polyprotein (ORF1ab), surface glycoprotein (S), ORF3a protein (ORF3a), envelope protein (E), membrane glycoprotein (M), ORF6 protein (ORF6), ORF7a protein (ORF7a), and ORF7b (ORF7b) genes, complete cds; ORF8 gene, complete sequence; and nucleocapsid phosphoprotein (N) and ORF10 protein (ORF10) genes, complete cds.

GenBase:
C_AA014163.1

LOCUS       C_AA014163             29677 bp    ss-RNA  linear   VRL 11-MAY-2023
DEFINITION  Severe acute respiratory syndrome coronavirus 2 isolate
            SARS-CoV-2/human/CHN/SH-HG20230504-475/2023 ORF1ab polyprotein
            (ORF1ab), ORF1a polyprotein (ORF1ab), surface glycoprotein (S),
            ORF3a protein (ORF3a), envelope protein (E), membrane glycoprotein
            (M), ORF6 protein (ORF6), ORF7a protein (ORF7a), and ORF7b (ORF7b)
            genes, complete cds; ORF8 gene, complete sequence; and nucleocapsid
            phosphoprotein (N) and ORF10 protein (ORF10) genes, complete cds.
ACCESSION   C_AA014163
VERSION     C_AA014163.1
KEYWORDS    .
SOURCE      Severe acute respiratory syndrome coronavirus 2
  ORGANISM  Severe acute respiratory syndrome coronavirus 2
            Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
            Nidovirales; Cornidovirineae; Coronaviridae; Orthocoronavirinae;
            Betacoronavirus; Sarbecovirus; Severe acute respiratory
            syndrome-related coronavirus.
REFERENCE   1  (bases 1 to 29677)
  AUTHORS   Zhang,W.
  TITLE     Direct Submission
  JOURNAL   Submitted (11-MAY-2023) Microbe lab, Shanghai Municipal Center for
            Disease Control & Prevention, west zhongshan road 1380, Shanghai
            200336, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method       :: Consensus sequence method v. 940-000133-00
            Sequencing Technology :: MGISEQ-200
            ##Genome-Assembly-Data-END##
            .
FEATURES             Location/Qualifiers
     source          1..29677
                     /organism="Severe acute respiratory syndrome coronavirus 2"
                     /mol_type="genomic RNA"
                     /isolate="SARS-CoV-2/human/CHN/SH-HG20230504-475/2023"
                     /isolation_source="Pharyngeal swab"
                     /host="Homo sapiens; Host_age: 39; Host_sex: Male"
                     /country="China:Shanghai"
                     /collection_date="2023-05-01"
                     /note="Passage_details/history: Original;
                     Additional_host_information: Patient infected while
                     traveling in unknown"
     gene            168..21448
                     /gene="ORF1ab"
     CDS             join(168..13361,13361..21448)
                     /gene="ORF1ab"
                     /ribosomal_slippage
                     /codon_start=1
                     /product="ORF1ab polyprotein"
                     /protein_id="C_AAB28850.1"
                     /translation="MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQH
                     LRDGTCGLVEVEKGVLPQLEQPYVFIKRSDARTAPHGHVMVELVAELEGIQYGRSGETL
                     GVLVPHVGEIPVAYRKVLLRKNGNKGAGGHRYGADLKSFDLGDELGTDPYEDFQENWNT
                     KHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLARAGKASCTLSEQLDFI
                     DTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSII
                     KTIQPRVEKKKLDXXXXXIRSVYPVASPNECNQMCLSTLMKCDHCGETSWQTGDFVKAT
                     CEFCGTENLTKECATTCGYLPQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRK
                     GGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHTGVVGEGSEGLNDNLLEILQKEK
                     VNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAK
                     KGAWNIGEQKSILSPLYAFASEAARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQY
                     SLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKF
                     KEGVEFLRDGWEIVKFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSII
                     IGGAKLKALNLGETFVTHSKGLYRKCVKSREETGLLMPLKAPKEIIFLEGETLPTEVLT
                     EEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYCALAPNMMVTNNT
                     FTLKGGAPTKVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSAYTVELGTEVNEF
                     ACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDED
                     EEEGDCEEEEFEPSTQYEYGTEDDYQGKPLEFGATSAALQPEEEQEEDWLDDDSQQTVG
                     QQDGSEDNQTTTIQTIVEVQPQLEMELTPVVQTIEVNSFSGYLKLTDNVYIKNADIVEE
                     AKKVKPTVVVNAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSG
                     HNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCV
                     DTVRTNVYLAVFDKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQR
                     KQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAP
                     YIVGDVVQEGVLTAVVIPTKKASGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAK
                     TVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTI
                     QRKYKGIKIQEGVVDYGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEE
                     AARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQS
                     TQLGIEFLKRGDKSVYYTSNPTTFHLDGEVITFDNLKTLLSLREVRTIKVFTTVDNINL
                     HTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRVEAFEYYHTT
                     DPSFLGRYMSALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQIELKFNPPALQD
                     AYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKRVLNVVCKTCG
                     QQQTTLKGVEAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYE
                     LKHSTFTCASEYTGNYQCGHYKHITSKETLYCIDGALLTKSSEYKGPITDVFYKENSYT
                     TTIKPVTYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPIDLVPNQPYPNASFDNFKFVCD
                     NIKFADDLNQLTGYKKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW
                     HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEV
                     VENPTIQKDVLECNVKTTEVVGDIILKPANNSLKITEEVGHTDLMAAYVDNSSLTIKKP
                     NELSRVLGLKTLATHGLAAVNSVPWDTIANYAKPFLNKVVSTTTNIVTRCLNRVCTNYM
                     PYFFTLLLQLCTFTRSTNSRIKASMPTTIAKNTVKSVGKFCLEASFNYLKSPNFSKLIN
                     IIIWFLLLSVCLGSLIYSTAALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCTGSIP
                     CSVCLSGLDSLDTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAI
                     MQLFFSYFAVHFISNSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCN
                     SSTCMMCYKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTF
                     ISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVN
                     LDNLRANNTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGD
                     SAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQGF
                     VDSDVETKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHIN
                     AQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA
                     LKGGKIVNNWLKQLIKVTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTR
                     DIASTDTCFANKHADFDTWFSQRGGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTT
                     NGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDT
                     NVLEGSVAYESLRPDTRYVLMDGSIIQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAG
                     VCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLFTNMFTPLIQPIGALDISASIVAGGIVA
                     IVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFIVLCLTPVYSFLPGVYSVIYLYLT
                     FYLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRVVFNGVSF
                     STFEEAALCTFLLNKEMYLKLRSDVLLPFTQYNRYLALYNKYKYFSGAMDTTSYREAAC
                     CHLAKALNDFSNSGSDVLYQPPQISITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTL
                     NGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCV
                     LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRHNFTIKGSFLNGSC
                     GSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNV
                     LAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLD
                     MCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLL
                     TILTSLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSL
                     ATVAYFNMVYMPASWVMRIMTWLDMVDTSLKLKDCVMYASAVVLLILMTARTVYDDGAR
                     RVWTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEY
                     CPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN
                     SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVES
                     SSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQ
                     AIASEFSSLPSYAAFATAQEAYEQAVANGDSEVVLKKLKKSLNVAKSEFDRDAAMQRKL
                     EKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLN
                     IIPLTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNS
                     PNLAWPLIVTALRANSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTIKGG
                     RFVLALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNL
                     NRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVK
                     MLCTHTGTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTT
                     CANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCGVSAARLTPC
                     GTGTSTDVVYRAFDIYNDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQ
                     HEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCD
                     TLKEILVTYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNA
                     GIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVD
                     TDLTKPYIKWDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLF
                     STVFPLTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAA
                     DPAMHAASGNLLLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSV
                     ELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVI
                     VNNLDKSAGFPFNKWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNR
                     ARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENP
                     HLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGS
                     SLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYEC
                     LYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQ
                     NNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIV
                     KTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVML
                     TNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHV
                     IPTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLY
                     KNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIA
                     TVREVLSDRELHLSWEFGKPRPPLNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVY
                     RGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQ
                     KVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVDALCEKALKYLPIDK
                     CSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVN
                     ARLCAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAE
                     IVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAW
                     RKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHSCNVNRFNVAI
                     TRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQA
                     PTHLSVDTKFKTEGLCVDVPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFITREEAIRH
                     VRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPP
                     PGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTSMKYFVK
                     IGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDL
                     YCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQHMVVK
                     AALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKF
                     TDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKSAF
                     VNLKQLPFFYYSDSPCESHGKQVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYL
                     DAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSII
                     NNTVYTKVDGVDVELFENKTTLPVNVAFELWAXXXXXXXXXXXXXXXXXVDIAANTVIW
                     DYKRDAPAHISTIGVCSMTDXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXLIGEAVKTQFNYYKKVDGVVQQLPETYFTQSRNLQEFK
                     PRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPF
                     ELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTI
                     DYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSAT
                     LPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTL
                     LVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYI
                     CGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYL
                     GKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMI
                     LSLLSKGRLIIRENNRVVISSDVLVNN"
     mat_peptide     168..707
                     /gene="ORF1ab"
                     /product="leader protein"
     mat_peptide     708..2621
                     /gene="ORF1ab"
                     /product="nsp2"
     mat_peptide     2622..8456
                     /gene="ORF1ab"
                     /product="nsp3"
     mat_peptide     8457..9956
                     /gene="ORF1ab"
                     /product="nsp4"
     mat_peptide     9957..10874
                     /gene="ORF1ab"
                     /product="3C-like proteinase"
     mat_peptide     10875..11735
                     /gene="ORF1ab"
                     /product="nsp6"
     mat_peptide     11736..11984
                     /gene="ORF1ab"
                     /product="nsp7"
     mat_peptide     11985..12578
                     /gene="ORF1ab"
                     /product="nsp8"
     mat_peptide     12579..12917
                     /gene="ORF1ab"
                     /product="nsp9"
     mat_peptide     12918..13334
                     /gene="ORF1ab"
                     /product="nsp10"
     mat_peptide     join(13335..13361,13361..16129)
                     /gene="ORF1ab"
                     /product="RNA-dependent RNA polymerase"
     mat_peptide     16130..17932
                     /gene="ORF1ab"
                     /product="helicase"
     mat_peptide     17933..19513
                     /gene="ORF1ab"
                     /product="3'-to-5' exonuclease"
     mat_peptide     19514..20551
                     /gene="ORF1ab"
                     /product="endoRNAse"
     mat_peptide     20552..21445
                     /gene="ORF1ab"
                     /product="2'-O-ribose methyltransferase"
     CDS             168..13376
                     /gene="ORF1ab"
                     /codon_start=1
                     /product="ORF1a polyprotein"
                     /protein_id="C_AAB28853.1"
                     /translation="MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQH
                     LRDGTCGLVEVEKGVLPQLEQPYVFIKRSDARTAPHGHVMVELVAELEGIQYGRSGETL
                     GVLVPHVGEIPVAYRKVLLRKNGNKGAGGHRYGADLKSFDLGDELGTDPYEDFQENWNT
                     KHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLARAGKASCTLSEQLDFI
                     DTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSII
                     KTIQPRVEKKKLDXXXXXIRSVYPVASPNECNQMCLSTLMKCDHCGETSWQTGDFVKAT
                     CEFCGTENLTKECATTCGYLPQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRK
                     GGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHTGVVGEGSEGLNDNLLEILQKEK
                     VNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAK
                     KGAWNIGEQKSILSPLYAFASEAARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQY
                     SLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKF
                     KEGVEFLRDGWEIVKFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSII
                     IGGAKLKALNLGETFVTHSKGLYRKCVKSREETGLLMPLKAPKEIIFLEGETLPTEVLT
                     EEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYCALAPNMMVTNNT
                     FTLKGGAPTKVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSAYTVELGTEVNEF
                     ACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDED
                     EEEGDCEEEEFEPSTQYEYGTEDDYQGKPLEFGATSAALQPEEEQEEDWLDDDSQQTVG
                     QQDGSEDNQTTTIQTIVEVQPQLEMELTPVVQTIEVNSFSGYLKLTDNVYIKNADIVEE
                     AKKVKPTVVVNAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSG
                     HNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCV
                     DTVRTNVYLAVFDKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQR
                     KQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAP
                     YIVGDVVQEGVLTAVVIPTKKASGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAK
                     TVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTI
                     QRKYKGIKIQEGVVDYGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEE
                     AARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQS
                     TQLGIEFLKRGDKSVYYTSNPTTFHLDGEVITFDNLKTLLSLREVRTIKVFTTVDNINL
                     HTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRVEAFEYYHTT
                     DPSFLGRYMSALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQIELKFNPPALQD
                     AYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKRVLNVVCKTCG
                     QQQTTLKGVEAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYE
                     LKHSTFTCASEYTGNYQCGHYKHITSKETLYCIDGALLTKSSEYKGPITDVFYKENSYT
                     TTIKPVTYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPIDLVPNQPYPNASFDNFKFVCD
                     NIKFADDLNQLTGYKKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW
                     HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEV
                     VENPTIQKDVLECNVKTTEVVGDIILKPANNSLKITEEVGHTDLMAAYVDNSSLTIKKP
                     NELSRVLGLKTLATHGLAAVNSVPWDTIANYAKPFLNKVVSTTTNIVTRCLNRVCTNYM
                     PYFFTLLLQLCTFTRSTNSRIKASMPTTIAKNTVKSVGKFCLEASFNYLKSPNFSKLIN
                     IIIWFLLLSVCLGSLIYSTAALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCTGSIP
                     CSVCLSGLDSLDTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAI
                     MQLFFSYFAVHFISNSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCN
                     SSTCMMCYKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTF
                     ISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVN
                     LDNLRANNTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGD
                     SAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQGF
                     VDSDVETKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHIN
                     AQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA
                     LKGGKIVNNWLKQLIKVTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTR
                     DIASTDTCFANKHADFDTWFSQRGGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTT
                     NGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDT
                     NVLEGSVAYESLRPDTRYVLMDGSIIQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAG
                     VCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLFTNMFTPLIQPIGALDISASIVAGGIVA
                     IVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFIVLCLTPVYSFLPGVYSVIYLYLT
                     FYLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRVVFNGVSF
                     STFEEAALCTFLLNKEMYLKLRSDVLLPFTQYNRYLALYNKYKYFSGAMDTTSYREAAC
                     CHLAKALNDFSNSGSDVLYQPPQISITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTL
                     NGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCV
                     LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRHNFTIKGSFLNGSC
                     GSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNV
                     LAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLD
                     MCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLL
                     TILTSLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSL
                     ATVAYFNMVYMPASWVMRIMTWLDMVDTSLKLKDCVMYASAVVLLILMTARTVYDDGAR
                     RVWTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEY
                     CPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN
                     SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVES
                     SSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQ
                     AIASEFSSLPSYAAFATAQEAYEQAVANGDSEVVLKKLKKSLNVAKSEFDRDAAMQRKL
                     EKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLN
                     IIPLTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNS
                     PNLAWPLIVTALRANSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTIKGG
                     RFVLALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNL
                     NRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVK
                     MLCTHTGTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTT
                     CANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNGFAV"
     mat_peptide     168..707
                     /gene="ORF1ab"
                     /product="leader protein"
     mat_peptide     708..2621
                     /gene="ORF1ab"
                     /product="nsp2"
     mat_peptide     2622..8456
                     /gene="ORF1ab"
                     /product="nsp3"
     mat_peptide     8457..9956
                     /gene="ORF1ab"
                     /product="nsp4"
     mat_peptide     9957..10874
                     /gene="ORF1ab"
                     /product="3C-like proteinase"
     mat_peptide     10875..11735
                     /gene="ORF1ab"
                     /product="nsp6"
     mat_peptide     11736..11984
                     /gene="ORF1ab"
                     /product="nsp7"
     mat_peptide     11985..12578
                     /gene="ORF1ab"
                     /product="nsp8"
     mat_peptide     12579..12917
                     /gene="ORF1ab"
                     /product="nsp9"
     mat_peptide     12918..13334
                     /gene="ORF1ab"
                     /product="nsp10"
     mat_peptide     13335..13373
                     /gene="ORF1ab"
                     /product="nsp11"
     stem_loop       13369..13396
                     /gene="ORF1ab"
                     /note="Coronavirus frameshifting stimulation element
                     stem-loop 1"
     stem_loop       13381..13435
                     /gene="ORF1ab"
                     /note="Coronavirus frameshifting stimulation element
                     stem-loop 2"
     gene            21456..25265
                     /gene="S"
     CDS             21456..25265
                     /gene="S"
                     /codon_start=1
                     /product="surface glycoprotein"
                     /protein_id="C_AAB28854.1"
                     /translation="MFVFLVLLPLVSSQCVNLITRTQSYTNSFTRGVYYPDKVFRSSVL
                     HSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPALPFNDGVYFASTEKSNIIRGWIFG
                     TTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYQKNNKSWMESEFRVYSSANNCT
                     FEYVSQPFLMDLEGKEGNFKNLREFVFKNIDGYFKIYSKHTPINLERDLPQGFSALEPL
                     VDLPIGINITRFQTLLALHRSYLTPVDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTI
                     TDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFHEVFNA
                     TTFASVYAWNRKRISNCVADYSVIYNFAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIR
                     GNEVSQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKPSGNYNYLYRLFRKSKLK
                     PFERDISTEIYQAGNKPCNGVAGPNCYSPLQSYGFRPTYGVGHQPYRVVVLSFELLHAP
                     ATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQ
                     TLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTG
                     SNVFQTRAGCLIGAEYVNNSYECDIPIGAGICASYQTQTKSHRRARSVASQSIIAYTMS
                     LGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYG
                     SFCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPSKRS
                     FIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTS
                     ALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKI
                     QDSLSSTASALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDILSRLDKVEAEVQI
                     DRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSF
                     PQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYE
                     PQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDIS
                     GINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPWYIWLGFIAGLIAIVM
                     VTIMLCCMTSCCSCLKGCCSCGSCCKFDEDDSEPVLKGVKLHYT"
     gene            25274..26101
                     /gene="ORF3a"
     CDS             25274..26101
                     /gene="ORF3a"
                     /codon_start=1
                     /product="ORF3a protein"
                     /protein_id="C_AAB28855.1"
                     /translation="MDLFMRIFTIGTVTLKQGEIKDATPSDFVRATATIPIQASLPFGW
                     LIVGVALLAVFQSASKIITLKKRWQLALSKGVHFVCNLLLLFVTVYSHLLLVAAGFEAP
                     FLYLYALVYFLQSINFVRIIMRLWLCWKCRSKNPLLYDANYFLCWHTNCYDYCIPYNSV
                     TSSIVITSGDGTTSPISEHDYQIGGYTEKWESGVKDCVVLHSYFTSDYYQLYSTQLSTD
                     IGVEHVTFFIYNKIVDEPEEHVQIHTIDGSSGVVNPVMEPIYDEPTTTTSVPL"
     gene            26126..26353
                     /gene="E"
     CDS             26126..26353
                     /gene="E"
                     /codon_start=1
                     /product="envelope protein"
                     /protein_id="C_AAB28856.1"
                     /translation="MYSFVSEEIGALIVNSVLLFLAFVVFLLVTLAILTALRLCAYCCN
                     IVNVSLVKPSFYVYSRVKNLNSSRVPDLLV"
     gene            26404..27072
                     /gene="M"
     CDS             26404..27072
                     /gene="M"
                     /codon_start=1
                     /product="membrane glycoprotein"
                     /protein_id="C_AAB28857.1"
                     /translation="MADSNGTITVEELKKLLEEWNLVIGFLFLTWICLLQFAYANRNRF
                     LYIIKLIFLWLLWPVTLTCFVLAAVYRINWITGGIAIAMACLVGLMWLSYFIASFRLFA
                     RTRSMWSFNPETNILLNVPLHGTILTRPLLESELVIGAVILRGHLRIAGHHLGRCDIKD
                     LPKEITVATSRTLSYYKLGASQRVAGDSGFAAYSRYRIGNYKLNTDHSSSSDNIALLVQ
                     "
     gene            27083..27268
                     /gene="ORF6"
     CDS             27083..27268
                     /gene="ORF6"
                     /codon_start=1
                     /product="ORF6 protein"
                     /protein_id="C_AAB28858.1"
                     /translation="MFHLVDFQVTIAEILLIIMRTFKVSIWNLDYIINLIIKNLSKSLT
                     ENKYSQLDEEQPMEIL"
     gene            27275..27640
                     /gene="ORF7a"
     CDS             27275..27640
                     /gene="ORF7a"
                     /codon_start=1
                     /product="ORF7a protein"
                     /protein_id="C_AAB28859.1"
                     /translation="MKIILFLALITLATCELYHYQECVRGTTVLLKEPCSSGTYEGNSP
                     FHPLADNKFALTCFSTQFAFACPDGVKHVYQLRARSVSPKLFIRQEEVQELYSPIFLIV
                     AAIVFITLCFTLKRKTE"
     gene            27637..27768
                     /gene="ORF7b"
     CDS             27637..27768
                     /gene="ORF7b"
                     /codon_start=1
                     /product="ORF7b"
                     /protein_id="C_AAB28860.1"
                     /translation="MIELSLIDFYLCFLAFLLFLVLIMLIIFWFSLELQDHNETCHA"
     gene            27775..28140
                     /gene="ORF8"
     misc_feature    27775..28140
                     /gene="ORF8"
                     /note="similar to ORF8 protein"
     gene            28155..29405
                     /gene="N"
     CDS             28155..29405
                     /gene="N"
                     /codon_start=1
                     /product="nucleocapsid phosphoprotein"
                     /protein_id="C_AAB28851.1"
                     /translation="MSDNGPQNQRNALRITFGGPSDSTGSNQNGGARSKQRRPQGLPNN
                     TASWFTALTQHGKEDLKFPRGQGVPINTNSSPDDQIGYYRRATRRIRGGDGKMKDLSPR
                     WYFYYLGTGPEAGLPYGANKDGIIWVATEGALNTPKDHIGTRNPANNAAIVLQLPQGTT
                     LPKGFYAEGSRGGSQASSRSSSRSRNSSRNSTPGSSKRTSPARMAGNGGDAALALLLLD
                     RLNQLESKMSGKGQQQQGQTVTKKSAAEASKKPRQKRTATKAYNVTQAFGRRGPEQTQG
                     NFGDQELIRQGTDYKHWPQIAQFAPSASAFFGMSRIGMEVTPSGTWLTYTGAIKLDDKD
                     PNFKDQVILLNKHIDAYKTFPPTEPKKDKKKKADETQALPQRQKKQQTVTLLPAADLDD
                     FSKQLQQSMSRADSTQA"
     gene            29430..29546
                     /gene="ORF10"
     CDS             29430..29546
                     /gene="ORF10"
                     /codon_start=1
                     /product="ORF10 protein"
                     /protein_id="C_AAB28852.1"
                     /translation="MGYINVFAFPFTIYSLLLCRMNSRNYIAQVDVVNFNLT"
     stem_loop       29481..29516
                     /gene="ORF10"
                     /note="Coronavirus 3' UTR pseudoknot stem-loop 1"
     stem_loop       29501..29529
                     /gene="ORF10"
                     /note="Coronavirus 3' UTR pseudoknot stem-loop 2"
     stem_loop       29600..29614
                     /note="Coronavirus 3' stem-loop II-like motif (s2m)"
ORIGIN
        1 tcggctgcat gcttagtgca ctcacgcagt ataattaata actaattact gtcgttgaca
       61 ggacacgagt aactcgtcta tcttctgcag gctgcttacg gtttcgtccg tgttgcagcc
      121 gatcatcagc acatctaggt tttgtccggg tgtgaccgaa aggtaagatg gagagccttg
      181 tccctggttt caacgagaaa acacacgtcc aactcagttt gcctgtttta caggttcgcg
      241 acgtgctcgt acgtggcttt ggagactccg tggaggaggt cttatcagag gcacgtcaac
      301 atcttagaga tggcacttgt ggcttagtag aagttgaaaa aggcgttttg cctcaacttg
      361 aacagcccta tgtgttcatc aaacgttcgg atgctcgaac tgcacctcat ggtcatgtta
      421 tggttgagct ggtagcagaa ctcgaaggca ttcagtacgg tcgtagtggt gagacacttg
      481 gtgtccttgt ccctcatgtg ggcgaaatac cagtggctta ccgcaaggtt cttcttcgta
      541 agaacggtaa taaaggagct ggtggccata ggtacggcgc cgatctaaag tcatttgact
      601 taggcgacga gcttggcact gatccttatg aagattttca agaaaactgg aacactaaac
      661 atagcagtgg tgttacccgt gaactcatgc gtgagcttaa cggaggggca tacactcgct
      721 atgtcgataa caacttctgt ggccctgatg gctaccctct tgagtgcatt aaagaccttc
      781 tagcacgtgc tggtaaagct tcatgcactt tgtccgaaca actggacttt attgacacta
      841 agaggggtgt atactgctgc cgtgaacatg agcatgaaat tgcttggtac acggaacgtt
      901 ctgaaaagag ctatgaattg cagacacctt ttgaaattaa attggcaaag aaatttgaca
      961 ccttcaatgg ggaatgtcca aattttgtat ttcccttaaa ttccataatc aagactattc
     1021 aaccaagggt tgaaaagaaa aagcttgatg nnnnnnnnnn nngaattcga tctgtctatc
     1081 cagttgcgtc accaaatgaa tgcaaccaaa tgtgcctttc aactctcatg aagtgtgatc
     1141 attgtggtga aacttcatgg cagacgggcg attttgttaa agccacttgc gaattttgtg
     1201 gcactgagaa tttgactaaa gaatgtgcca ctacttgtgg ttacttaccc caaaatgctg
     1261 ttgttaaaat ttattgtcca gcatgtcaca attcagaagt aggacctgag catagtcttg
     1321 ccgaatacca taatgaatct ggcttgaaaa ccattcttcg taagggtggt cgcactattg
     1381 cctttggagg ctgtgtgttc tcttatgttg gttgccataa caagtgtgcc tattgggttc
     1441 cacgtgctag cgctaacata ggttgtaacc atacaggtgt tgttggagaa ggttccgaag
     1501 gtcttaatga caaccttctt gaaatactcc aaaaagagaa agtcaacatc aatattgttg
     1561 gtgactttaa acttaatgaa gagatcgcca ttattttggc atctttttct gcttccacaa
     1621 gtgcttttgt ggaaactgtg aaaggtttgg attataaagc attcaaacaa attgttgaat
     1681 cctgtggtaa ttttaaagtt acaaaaggaa aagctaaaaa aggtgcctgg aatattggtg
     1741 aacagaaatc aatactgagt cctctttatg catttgcatc agaggctgct cgtgttgtac
     1801 gatcaatttt ctcccgcact cttgaaactg ctcaaaattc tgtgcgtgtt ttacagaagg
     1861 ccgctataac aatactagat ggaatttcac agtattcact gagactcatt gatgctatga
     1921 tgttcacatc tgatttggct actaacaatc tagttgtaat ggcctacatt acaggtggtg
     1981 ttgttcagtt gacttcgcag tggctaacta acatctttgg cactgtttat gaaaaactca
     2041 aacccgtcct tgattggctt gaagagaagt ttaaggaagg tgtagagttt cttagagacg
     2101 gttgggaaat tgttaaattt atctcaacct gtgcttgtga aattgtcggt ggacaaattg
     2161 tcacctgtgc aaaggaaatt aaggagagtg ttcagacatt ctttaagctt gtaaataaat
     2221 ttttggcttt gtgtgctgac tctatcatta ttggtggagc taaacttaaa gccttgaatt
     2281 taggtgaaac atttgtcacg cactcaaagg gattgtacag aaagtgtgtt aaatccagag
     2341 aagaaactgg cctactcatg cctctaaaag ccccaaaaga aattatcttc ttagagggag
     2401 aaacacttcc cacagaagtg ttaacagagg aagttgtctt gaaaactggt gatttacaac
     2461 cattagaaca acctactagt gaagctgttg aagctccatt ggttggtaca ccagtttgta
     2521 ttaacgggct tatgttgctc gaaatcaaag acacagaaaa gtactgtgcc cttgcaccta
     2581 atatgatggt aacaaacaat accttcacac tcaaaggcgg tgcaccaaca aaggttactt
     2641 ttggtgatga cactgtgata gaagtgcaag gttacaagag tgtgaatatc acttttgaac
     2701 ttgatgaaag gattgataaa gtacttaatg agaagtgctc tgcctataca gttgaactcg
数据集编号
序列分析