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