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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Molecular immune pathogenesis and diagnosis of COVID-19</title><author><name sortKey="Li, Xiaowei" sort="Li, Xiaowei" uniqKey="Li X" first="Xiaowei" last="Li">Xiaowei Li</name><affiliation><nlm:aff id="aff1">Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, China</nlm:aff></affiliation><affiliation><nlm:aff id="aff2">Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an, Shaanxi, 710061, China</nlm:aff></affiliation></author><author><name sortKey="Geng, Manman" sort="Geng, Manman" uniqKey="Geng M" first="Manman" last="Geng">Manman Geng</name><affiliation><nlm:aff id="aff1">Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, China</nlm:aff></affiliation><affiliation><nlm:aff id="aff2">Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an, Shaanxi, 710061, China</nlm:aff></affiliation></author><author><name sortKey="Peng, Yizhao" sort="Peng, Yizhao" uniqKey="Peng Y" first="Yizhao" last="Peng">Yizhao Peng</name><affiliation><nlm:aff id="aff1">Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, China</nlm:aff></affiliation><affiliation><nlm:aff id="aff2">Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an, Shaanxi, 710061, China</nlm:aff></affiliation></author><author><name sortKey="Meng, Liesu" sort="Meng, Liesu" uniqKey="Meng L" first="Liesu" last="Meng">Liesu Meng</name><affiliation><nlm:aff id="aff1">Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, China</nlm:aff></affiliation><affiliation><nlm:aff id="aff2">Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an, Shaanxi, 710061, China</nlm:aff></affiliation></author><author><name sortKey="Lu, Shemin" sort="Lu, Shemin" uniqKey="Lu S" first="Shemin" last="Lu">Shemin Lu</name><affiliation><nlm:aff id="aff1">Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, China</nlm:aff></affiliation><affiliation><nlm:aff id="aff2">Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an, Shaanxi, 710061, China</nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">32282863</idno><idno type="pmc">7104082</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7104082</idno><idno type="RBID">PMC:7104082</idno><idno type="doi">10.1016/j.jpha.2020.03.001</idno><date when="2020">2020</date><idno type="wicri:Area/Pmc/Corpus">001378</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">001378</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Molecular immune pathogenesis and diagnosis of COVID-19</title><author><name sortKey="Li, Xiaowei" sort="Li, Xiaowei" uniqKey="Li X" first="Xiaowei" last="Li">Xiaowei Li</name><affiliation><nlm:aff id="aff1">Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, China</nlm:aff></affiliation><affiliation><nlm:aff id="aff2">Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an, Shaanxi, 710061, China</nlm:aff></affiliation></author><author><name sortKey="Geng, Manman" sort="Geng, Manman" uniqKey="Geng M" first="Manman" last="Geng">Manman Geng</name><affiliation><nlm:aff id="aff1">Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, China</nlm:aff></affiliation><affiliation><nlm:aff id="aff2">Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an, Shaanxi, 710061, China</nlm:aff></affiliation></author><author><name sortKey="Peng, Yizhao" sort="Peng, Yizhao" uniqKey="Peng Y" first="Yizhao" last="Peng">Yizhao Peng</name><affiliation><nlm:aff id="aff1">Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, China</nlm:aff></affiliation><affiliation><nlm:aff id="aff2">Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an, Shaanxi, 710061, China</nlm:aff></affiliation></author><author><name sortKey="Meng, Liesu" sort="Meng, Liesu" uniqKey="Meng L" first="Liesu" last="Meng">Liesu Meng</name><affiliation><nlm:aff id="aff1">Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, China</nlm:aff></affiliation><affiliation><nlm:aff id="aff2">Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an, Shaanxi, 710061, China</nlm:aff></affiliation></author><author><name sortKey="Lu, Shemin" sort="Lu, Shemin" uniqKey="Lu S" first="Shemin" last="Lu">Shemin Lu</name><affiliation><nlm:aff id="aff1">Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, China</nlm:aff></affiliation><affiliation><nlm:aff id="aff2">Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an, Shaanxi, 710061, China</nlm:aff></affiliation></author></analytic><series><title level="j">Journal of Pharmaceutical Analysis</title><idno type="ISSN">2095-1779</idno><idno type="eISSN">2214-0883</idno><imprint><date when="2020">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Coronavirus disease 2019 (COVID-19) is a kind of viral pneumonia with an unusual outbreak in Wuhan, China, in December 2019, which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The emergence of SARS-CoV-2 has been marked as the third introduction of a highly pathogenic coronavirus into the human population after the severe acute respiratory syndrome coronavirus (SARS-CoV) and the Middle East respiratory syndrome coronavirus (MERS-CoV) in the twenty-first century. In this minireview, we provide a brief introduction of the general features of SARS-CoV-2 and discuss current knowledge of molecular immune pathogenesis, diagnosis and treatment of COVID-19 on the base of the present understanding of SARS-CoV and MERS-CoV infections, which may be helpful in offering novel insights and potential therapeutic targets for combating the SARS-CoV-2 infection.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Zhou, P" uniqKey="Zhou P">P. Zhou</name></author><author><name sortKey="Yang, X L" uniqKey="Yang X">X.L. Yang</name></author><author><name sortKey="Wang, X G" uniqKey="Wang X">X.G. 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<front><journal-meta><journal-id journal-id-type="nlm-ta">J Pharm Anal</journal-id><journal-id journal-id-type="iso-abbrev">J Pharm Anal</journal-id><journal-title-group><journal-title>Journal of Pharmaceutical Analysis</journal-title></journal-title-group><issn pub-type="ppub">2095-1779</issn><issn pub-type="epub">2214-0883</issn><publisher><publisher-name>Xi'an Jiaotong University</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">32282863</article-id><article-id pub-id-type="pmc">7104082</article-id><article-id pub-id-type="publisher-id">S2095-1779(20)30204-5</article-id><article-id pub-id-type="doi">10.1016/j.jpha.2020.03.001</article-id><article-categories><subj-group subj-group-type="heading"><subject>Article</subject></subj-group></article-categories><title-group><article-title>Molecular immune pathogenesis and diagnosis of COVID-19</article-title></title-group><contrib-group><contrib contrib-type="author" id="au1"><name><surname>Li</surname><given-names>Xiaowei</given-names></name><email>lixiaowei2017@stu.xjtu.edu.cn</email><xref rid="aff1" ref-type="aff">a</xref><xref rid="aff2" ref-type="aff">b</xref></contrib><contrib contrib-type="author" id="au2"><name><surname>Geng</surname><given-names>Manman</given-names></name><email>gengmanman@stu.xjtu.edu.cn</email><xref rid="aff1" ref-type="aff">a</xref><xref rid="aff2" ref-type="aff">b</xref></contrib><contrib contrib-type="author" id="au3"><name><surname>Peng</surname><given-names>Yizhao</given-names></name><email>pengyizhao@stu.xjtu.edu.cn</email><xref rid="aff1" ref-type="aff">a</xref><xref rid="aff2" ref-type="aff">b</xref></contrib><contrib contrib-type="author" id="au4"><name><surname>Meng</surname><given-names>Liesu</given-names></name><email>mengliesu@xjtu.edu.cn</email><xref rid="aff1" ref-type="aff">a</xref><xref rid="aff2" ref-type="aff">b</xref><xref rid="cor2" ref-type="corresp">∗∗</xref></contrib><contrib contrib-type="author" id="au5"><name><surname>Lu</surname><given-names>Shemin</given-names></name><email>lushemin@xjtu.edu.cn</email><xref rid="aff1" ref-type="aff">a</xref><xref rid="aff2" ref-type="aff">b</xref><xref rid="cor1" ref-type="corresp">∗</xref></contrib></contrib-group><aff id="aff1"><label>a</label>Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, China</aff><aff id="aff2"><label>b</label>Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an, Shaanxi, 710061, China</aff><author-notes><corresp id="cor1"><label>∗</label>Corresponding author. Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, China. <email>lushemin@xjtu.edu.cn</email></corresp><corresp id="cor2"><label>∗∗</label>Corresponding author. Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, China. <email>mengliesu@xjtu.edu.cn</email></corresp></author-notes><pub-date pub-type="pmc-release"><day>5</day><month>3</month><year>2020</year></pub-date><pmc-comment> PMC Release delay is 0 months and 0 days and was based on .</pmc-comment>
<pub-date pub-type="epub"><day>5</day><month>3</month><year>2020</year></pub-date><elocation-id></elocation-id><history><date date-type="received"><day>24</day><month>2</month><year>2020</year></date><date date-type="rev-recd"><day>1</day><month>3</month><year>2020</year></date><date date-type="accepted"><day>1</day><month>3</month><year>2020</year></date></history><permissions><copyright-statement>.</copyright-statement><copyright-year>2020</copyright-year><copyright-holder>Xi'an Jiaotong University</copyright-holder><license><license-p>Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.</license-p></license></permissions><abstract id="abs0010"><p>Coronavirus disease 2019 (COVID-19) is a kind of viral pneumonia with an unusual outbreak in Wuhan, China, in December 2019, which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The emergence of SARS-CoV-2 has been marked as the third introduction of a highly pathogenic coronavirus into the human population after the severe acute respiratory syndrome coronavirus (SARS-CoV) and the Middle East respiratory syndrome coronavirus (MERS-CoV) in the twenty-first century. In this minireview, we provide a brief introduction of the general features of SARS-CoV-2 and discuss current knowledge of molecular immune pathogenesis, diagnosis and treatment of COVID-19 on the base of the present understanding of SARS-CoV and MERS-CoV infections, which may be helpful in offering novel insights and potential therapeutic targets for combating the SARS-CoV-2 infection.</p></abstract><abstract abstract-type="graphical" id="abs0015"><title>Graphical abstract</title><p><fig id="undfig1" position="anchor"><alt-text id="alttext0010">Image 1</alt-text><graphic xlink:href="fx1_lrg"></graphic></fig></p></abstract><abstract abstract-type="author-highlights" id="abs0020"><title>Highlights</title><p><list list-type="simple" id="ulist0010"><list-item id="u0010"><label>•.</label><p id="p0010">The highly pathogenic SARS-CoV-2 appearing in December 2019 can cause COVID-19 and even death in infected persons.</p></list-item><list-item id="u0015"><label>•.</label><p id="p0015">Coronavirus infections led to damage and infection of the lung, but imbalances and excessive immune responses may cause pneumonia.</p></list-item><list-item id="u0020"><label>•.</label><p id="p0020">RT-PCR and CT scans are the significant methods for the diagnosis of SARS-CoV-2 infection and drugs against SARS-CoV-2 are being developed.</p></list-item></list></p></abstract><kwd-group id="kwrds0010"><title>Keywords</title><kwd>Coronavirus</kwd><kwd>SARS-CoV-2</kwd><kwd>SARS-CoV</kwd><kwd>MERS-CoV</kwd><kwd>Pathogenesis</kwd></kwd-group></article-meta></front><body><sec id="sec1"><label>1</label><title>Introduction</title><p id="p0025">Novel coronavirus induced pneumonia, which was named as coronavirus disease 2019 (COVID-19) by the WHO on the February 11, 2020, has rapidly increased in epidemic scale since it first appeared in Wuhan, China, in December 2019 [<xref rid="bib1" ref-type="bibr">1</xref>]. On the same day, the international virus classification commission announced that the novel coronavirus was named as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). COVID-19 is not the first severe respiratory disease outbreak caused by the coronavirus. Just in the past two decades, coronaviruses have caused three epidemic diseases, namely, COVID-19, severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) [<xref rid="bib2" ref-type="bibr">2</xref>]. At present, the cases of COVID-19 have been found in many countries around the world [<xref rid="bib3" ref-type="bibr">3</xref>]. According to the latest data, up to the March 1, 2020, the number of confirmed cases in China reached 79,968, of which 2,873 were dead, and 41,681 were cured. In addition to China, the number of confirmed cases in other countries also reached 7,041, of which 105 were dead, and 459 were cured. On the 31st of January 2020, the World Health Organization (WHO) announced that COVID-19 was listed as the Public Health Emergency of International Concern (PHEIC), meaning that it may pose risks to multiple countries and requires a coordinated international response. The review tries to explain the molecular immune pathogenesis and diagnosis of COVID-19 and provide a reference for the prevention and drug development of SARS-CoV-2 infection, based on the recent research progress of SARS-CoV-2 and the knowledge from researches on SARS-CoV and MERS-CoV.</p></sec><sec id="sec2"><label>2</label><title>Virology of SARS-CoV-2</title><p id="p0030">Coronaviruses are enveloped viruses with a positive sense single-stranded RNA genome (26–32 kb) [<xref rid="bib4" ref-type="bibr">4</xref>]. Four coronavirus genera (α, β, γ, δ) have been identified so far, with human coronaviruses (HCoVs) detected in the α coronavirus (HCoV-229E and NL63) and β coronavirus (MERS-CoV, SARS-CoV, HCoV-OC43 and HCoV-HKU1) genera [<xref rid="bib5" ref-type="bibr">5</xref>]. In late December 2019, patients presenting with cough, fever, and dyspnea with acute respiratory distress syndrome (ARDS) due to an unidentified microbial infection were reported in Wuhan, China. Virus genome sequencing of five patients with pneumonia hospitalized from December 18 to December 29, 2019, revealed the presence of a previously unknown β-CoV strain in all of them [<xref rid="bib6" ref-type="bibr">6</xref>]. This isolated novel β-CoV shows 88% identity to the sequence of two bat-derived severe acute respiratory syndromes (SARS)-like coronaviruses, bat-SL-CoVZC45 and bat-SL-CoVZXC21, and about 50% identity to the sequence of MERS-CoV [<xref rid="bib6" ref-type="bibr">6</xref>]. The novel β-CoV was then named “SARS-CoV-2” by the International Virus Classification Commission. The phylogenetic tree of SARS-like coronaviruses complete genome sequences is clearly depicted in <xref rid="fig1" ref-type="fig">Fig. 1</xref>A.<fig id="fig1"><label>Fig. 1</label><caption><p>The phylogenetic tree of SARS-like coronaviruses complete genome sequences and genome of SARS-CoV, MERS-CoV and SARSCoV- 2.</p><p>(A) This phylogeny shows evolution of SARS-like β-coronaviruses including samples from human (n = 20), bat (n = 22), civet (n = 3) and pangolin (n = 6). The phylogenetic tree of complete genome sequences of coronaviruses was obtained and analyzed with Nextstrain (<ext-link ext-link-type="uri" xlink:href="https://github.com/blab/sars-like-cov" id="intref0020">https://github.com/blab/sars-like-cov</ext-link>). (B) Coronaviruses form enveloped and spherical particles of 100–160 nm in diameter. They contain a positivesense single stranded RNA (ssRNA) genome of 26–32 kb in size. In SARSCoV, MERS-CoV and SARS-CoV-2, the 5′-terminal two-thirds of the genome ORF1a/b encodes polyproteins, which form the viral replicase transcriptase complex. The other ORFs on the one-third of the genome encode four main structural proteins: spike (S), envelope (E), nucleocapsid (N) and membrane (M) proteins, as well as several accessory proteins.</p></caption><alt-text id="alttext0020">Fig. 1</alt-text><graphic xlink:href="gr1_lrg"></graphic></fig></p><p id="p0035">The genome of SARS-CoV-2 is similar to typical CoVs and contains at least ten open reading frames (ORFs). The first ORFs (ORF1a/b), about two-thirds of viral RNA, are translated into two large polyproteins. In SARS-CoV and MERS-CoV, two polyproteins, pp1a and pp1ab, are processed into 16 non-structural proteins (nsp1-nsp16), which form the viral replicase transcriptase complex [<xref rid="bib7" ref-type="bibr">7</xref>]. Those nsps rearrange membranes originating from the rough endoplasmic reticulum (RER) into double-membrane vesicles where viral replication and transcription occur [<xref rid="bib8" ref-type="bibr">8</xref>,<xref rid="bib9" ref-type="bibr">9</xref>]. The other ORFs of SARS-CoV-2 on the one-third of the genome encode four main structural proteins: spike (S), envelope (E), nucleocapsid (N) and membrane (M) proteins, as well as several accessory proteins with unknown functions which do not participate in viral replication (<xref rid="fig1" ref-type="fig">Fig. 1</xref>B).</p><p id="p0040">Several of scientists in China have all discovered that SARS-CoV-2, just like SARS-CoV, requires the angiotensin-converting enzyme 2 (ACE2) [<xref rid="bib1" ref-type="bibr">1</xref>] as a receptor to enter cells [<xref rid="bib10" ref-type="bibr">10</xref>]. The binding of the virus with host cell receptors is a significant determinant for the pathogenesis of infection. SARS-CoV most likely originated in bats [<xref rid="bib11" ref-type="bibr">11</xref>]and adapted to non-bat ACE2 variants as it crossed species to infect humans [<xref rid="bib12" ref-type="bibr">12</xref>]. Dipeptidyl peptidase 4 (DPP4, also known as CD26) was identified as a functional receptor for MERS-CoV, because the receptor-binding S1 domain of the MERS-CoV spike protein was copurified with DPP4 specifically from lysates of susceptible Huh-7 cells [<xref rid="bib13" ref-type="bibr">13</xref>]. MERS-CoV can bind DPP4 from multiple species, which promotes the transmission to humans and other species, and infection of cells from a large number of species [<xref rid="bib14" ref-type="bibr">14</xref>]. A better understanding of the relative effects of receptor binding and protease action will help predict whether specific zoonotic coronaviruses infect humans and the possibility of adaptation.</p></sec><sec id="sec3"><label>3</label><title>Pathogenesis of COVID-19</title><p id="p0045">Patients with COVID-19 show clinical manifestations include fever, nonproductive cough, dyspnea, myalgia, fatigue, normal or decreased leukocyte counts, and radiographic evidence of pneumonia [<xref rid="bib15" ref-type="bibr">15</xref>], which are similar to the symptoms of SARS-CoV and MERS-CoV infections [<xref rid="bib16" ref-type="bibr">16</xref>]. Hence, although the pathogenesis of COVID-19 is poorly understood, the similar mechanisms of SARS-CoV and MERS-CoV still can give us a lot of information on the pathogenesis of SARS-CoV-2 infection to facilitate our recognition of COVID-19.</p><sec id="sec3.1"><label>3.1</label><title>Coronavirus entry and replication</title><p id="p0050">Coronavirus S protein has been reported as a significant determinant of virus entry into host cells [<xref rid="bib2" ref-type="bibr">2</xref>]. The envelope spike glycoprotein binds to its cellular receptor, ACE2 for SARS-CoV [<xref rid="bib10" ref-type="bibr">10</xref>] and SARS-CoV-2 [<xref rid="bib17" ref-type="bibr">17</xref>], CD209L(a C-type lectin, also called L-SIGN) for SARS-CoV [<xref rid="bib18" ref-type="bibr">18</xref>], DPP4 for MERS-CoV [<xref rid="bib13" ref-type="bibr">13</xref>]. The entry of SARS-CoV into cells was initially identified to be accomplished by direct membrane fusion between the virus and plasma membrane [<xref rid="bib19" ref-type="bibr">19</xref>]. Belouzard et al. [<xref rid="bib20" ref-type="bibr">20</xref>] found that a critical proteolytic cleavage event occurred at SARS-CoV S protein at position (S2′) mediated the membrane fusion and viral infectivity. MERS-CoV also has evolved an abnormal two-step furin activation for membrane fusion [<xref rid="bib21" ref-type="bibr">21</xref>]. Besides membrane fusion, the clathrin-dependent and -independent endocytosis mediated SARS-CoV entry too [<xref rid="bib22" ref-type="bibr">22</xref>,<xref rid="bib23" ref-type="bibr">23</xref>]. After the virus enters the cells, the viral RNA genome is released into the cytoplasm and is translated into two polyproteins and structural proteins, after which the viral genome begins to replicate [<xref rid="bib5" ref-type="bibr">5</xref>]. The newly formed envelope glycoproteins are inserted into the membrane of the endoplasmic reticulum or Golgi, and the nucleocapsid is formed by the combination of genomic RNA and nucleocapsid protein. Then, viral particles germinate into the endoplasmic reticulum-Golgi intermediate compartment (ERGIC). At last, the vesicles containing the virus particles then fuse with the plasma membrane to release the virus [<xref rid="bib2" ref-type="bibr">2</xref>].</p></sec><sec id="sec3.2"><label>3.2</label><title>Antigen presentation in coronavirus infection</title><p id="p0055">While the virus enters the cells, its antigen will be presented to the antigen presentation cells(APC), which is a central part of the body's anti-viral immunity. Antigenic peptides are presented by major histocompatibility complex (MHC; or human leukocyte antigen (HLA) in humans) and then recognized by virus-specific cytotoxic T lymphocytes (CTLs). Hence, the understanding of antigen presentation of SARS-CoV-2 will help our comprehension of COVID-19 pathogenesis. Unfortunately, there is still lack of any report about it, and we can only get some information from previous researches on SARS-CoV and MERS-CoV. The antigen presentation of SARS-CoV mainly depends on MHC I molecules [<xref rid="bib24" ref-type="bibr">24</xref>], but MHC II also contributes to its presentation. Previous research shows numerous HLA polymorphisms correlate to the susceptibility of SARS-CoV, such as HLA-B*4601, HLA-B*0703, HLA-DR B1*1202 [<xref rid="bib25" ref-type="bibr">25</xref>] and HLA-Cw*0801 [<xref rid="bib26" ref-type="bibr">26</xref>], whereas the HLA-DR0301, HLA-Cw1502 and HLA-A*0201 alleles are related to the protection from SARS infection [<xref rid="bib27" ref-type="bibr">27</xref>]. In MERS-CoV infection, MHC II molecules, such as HLA-DRB1*11:01 and HLA-DQB1*02:0, are associated with the susceptibility to MERS-CoV infection [<xref rid="bib28" ref-type="bibr">28</xref>]. Besides, gene polymorphisms of MBL (mannose-binding lectin) associated with antigen presentation are related to the risk of SARS-CoV infection [<xref rid="bib29" ref-type="bibr">29</xref>]. These researches will provide valuable clues for the prevention, treatment, and mechanism of COVID-19.</p></sec><sec id="sec3.3"><label>3.3</label><title>Humoral and cellular immunity</title><p id="p0060">Antigen presentation subsequently stimulates the body's humoral and cellular immunity, which are mediated by virus-specific B and T cells. Similar to common acute viral infections, the antibody profile against SARS-CoV virus has a typical pattern of IgM and IgG production. The SARS-specific IgM antibodies disappeared at the end of week 12, while the IgG antibody can last for a long time, which indicates IgG antibody may mainly play a protective roles [<xref rid="bib30" ref-type="bibr">30</xref>], and the SARS-specific IgG antibodies primarily are S-specific and N-specific antibodies [<xref rid="bib2" ref-type="bibr">2</xref>]. Comparing to humoral responses, there are more researches on the cellular immunity of coronavirus. The latest report shows the number of CD4<sup>+</sup> and CD8<sup>+</sup> T cells in the peripheral blood of SARS-CoV-2-infected patients significantly is reduced, whereas its status is excessive activation, as evidenced by high proportions of HLA-DR (CD4 3.47%) and CD38 (CD8 39.4%) double-positive fractions [<xref rid="bib31" ref-type="bibr">31</xref>]. Similarly, the acute phase response in patients with SARS-CoV is associated with severe decrease of CD4<sup>+</sup> T and CD8<sup>+</sup> T cells. Even if there is no antigen, CD4<sup>+</sup> and CD8<sup>+</sup> memory T cells can persist for four years in a part of SARS-CoV recovered individuals and can perform T cell proliferation, DTH response and production of IFN-γ [<xref rid="bib32" ref-type="bibr">32</xref>]. Six years after SARS-CoV infection, specific T-cell memory responses to the SARS-CoV S peptide library could still be identified in 14 of 23 recovered SARS patients [<xref rid="bib33" ref-type="bibr">33</xref>]. The specific CD8<sup>+</sup> T cells also show a similar effect on MERS-CoV clearance in mice [<xref rid="bib34" ref-type="bibr">34</xref>]. These findings may provide valuable information for the rational design of vaccines against SARS-CoV-2.</p></sec><sec id="sec3.4"><label>3.4</label><title>Cytokine storm in COVID-19</title><p id="p0065">The report in <italic>Lancet</italic> shows ARDS is the main death cause of COVID-19. Of the 41 SARS-CoV-2-infected patients admitted in the early stages of the outbreak, six died from ARDS [<xref rid="bib15" ref-type="bibr">15</xref>]. ARDS is the common immunopathological event for SARS-CoV-2, SARS-CoV and MERS-CoV infections [<xref rid="bib31" ref-type="bibr">31</xref>]. One of the main mechanisms for ARDS is the cytokine storm, the deadly uncontrolled systemic inflammatory response resulting from the release of large amounts of pro-inflammatory cytokines (IFN-α, IFN-γ, IL-1β, IL-6, IL-12, IL-18, IL-33, TNF-α, TGFβ, etc.) and chemokines (CCL2, CCL3, CCL5, CXCL8, CXCL9, CXCL10, etc.) by immune effector cells in SARS-CoV infection [<xref rid="bib15" ref-type="bibr">15</xref>,<xref rid="bib35" ref-type="bibr">[35]</xref>, <xref rid="bib36" ref-type="bibr">[36]</xref>, <xref rid="bib37" ref-type="bibr">[37]</xref>]. Similar to those with SARS-CoV, individuals with severe MERS-CoV infection show elevated levels of IL-6, IFN-α, and CCL5, CXCL8, CXCL-10 in serum compared to those with the mild-moderate disease [<xref rid="bib38" ref-type="bibr">38</xref>]. The cytokine storm will trigger a violent attack by the immune system to the body, cause ARDS and multiple organ failure, and finally lead to death in severe cases of SARS-CoV-2 infection, just like what occurs in SARS-CoV and MERS-CoV infection [<xref rid="bib31" ref-type="bibr">31</xref>].</p></sec><sec id="sec3.5"><label>3.5</label><title>Coronavirus immune evasion</title><p id="p0070">To better survive in host cells, SARS-CoV and MERS-CoV use multiple strategies to avoid immune responses. The evolutionarily conserved microbial structures called pathogen-associated molecular patterns (PAMPs) can be recognized by pattern recognition receptors (PRRs). However, SARS-CoV and MERS-CoV can induce the production of double-membrane vesicles that lack PRRs and then replicate in these vesicles, thereby avoiding the host detection of their dsRNA [<xref rid="bib39" ref-type="bibr">39</xref>]. IFN-I(IFN-α and IFN-β) has a protective effect on SARS-CoV and MERS-CoV infection, but the IFN-I pathway is inhibited in infected mice [<xref rid="bib40" ref-type="bibr">40</xref>,<xref rid="bib41" ref-type="bibr">41</xref>]. Accessory protein 4a of MERS-CoV may block the induction of IFN at the level of MDA5 activation through direct interaction with double-stranded RNA [<xref rid="bib42" ref-type="bibr">42</xref>]. Besides, ORF4a, ORF4b, ORF5, and membrane proteins of MERS-CoV inhibit nuclear transport of IFN regulatory factor 3 (IRF3) and activation of IFN β promoter [<xref rid="bib43" ref-type="bibr">43</xref>]. The antigen presentation can also be affected by the coronavirus. For example, gene expression related to antigen presentation is down-regulated after MERS-CoV infection [<xref rid="bib44" ref-type="bibr">44</xref>]. Therefore, destroying the immune evasion of SARS-CoV-2 is imperative in its treatment and specific drug development.</p></sec></sec><sec id="sec4"><label>4</label><title>Diagnosis of COVID-19</title><p id="p0075">Clinical diagnosis of COVID-19 is mainly based on epidemiological history, clinical manifestations and some auxiliary examinations, such as nucleic acid detection, CT scan, immune identification technology (Point-of-care Testing (POCT) of IgM/IgG, enzyme-linked immunosorbent assay (ELISA)) and blood culture. However, the clinical symptoms and signs of patients infected with SARS-CoV-2 are highly atypical, including respiratory symptoms, cough, fever, dyspnea, and viral pneumonia. Therefore, auxiliary examinations are necessary for the diagnosis of COVID-19, just as the epidemiological history.</p><sec id="sec4.1"><label>4.1</label><title>Nucleic acid detection technology</title><p id="p0080">The two commonly used nucleic acid detection technologies for SARS-CoV-2 are real-time quantitative polymerase chain reaction (RT-qPCR) and high-throughput sequencing. The authoritative identification method for SARS-CoV-2 is virus blood culture and high-throughput sequencing of the whole genome [<xref rid="bib1" ref-type="bibr">1</xref>]. However, the application of high-throughput sequencing technology in clinical diagnosis is limited because of its equipment dependency and high cost. So RT-qPCR is the most common, effective and straightforward method for detecting pathogenic viruses in respiratory secretions and blood [<xref rid="bib45" ref-type="bibr">45</xref>].</p><p id="p0085">After the outbreak of SARS-CoV-2 in China, many companies soon launched RT-qPCR test kits for clinical diagnosis. The Chinese Center for Disease Control and Prevention (China CDC) recommends the use of specific primers and probes in the ORF1ab and N gene regions for SARS-CoV-2 detection by RT-qPCR. The patient is defined as having a laboratory-confirmed infection when both targets are positive (<ext-link ext-link-type="uri" xlink:href="http://ivdc.chinacdc.cn/kyjz/202001/t20200121_211337.html" id="intref0010">http://ivdc.chinacdc.cn/kyjz/202001/t20200121_211337.html</ext-link>). Chu et al. [<xref rid="bib46" ref-type="bibr">46</xref>] described two 1-step RT-qPCR assays (TaqMan-based fluorescence signal) to detect two different regions (ORF1b and N) of the viral genome separately. The negative control samples were all confirmed as negative ones, while samples from two SARS-CoV-2 infected patients were confirmed as positive ones in respiratory specimens by this method. Another study showed that the positive rate of SARS-CoV-2 was 91.7% (11/12) in the patients’ self-collected saliva by using RT-qPCR (non-probes SYBR based fluorescence signal), which suggests that saliva is a promising non-invasive specimen for the diagnosis, monitoring, and infection control of patients with SARS-CoV-2 infection [<xref rid="bib47" ref-type="bibr">47</xref>]. RT-qPCR detection also showed high sensitivity and specificity for SARS-CoV and MERS-CoV infection [<xref rid="bib48" ref-type="bibr">48</xref>]. However, five patients with negative results of RT-qPCR for SARS-CoV-2 may present with positive chest CT findings, and repeated swab tests (RT-qPCR) eventually confirmed that all patients were infected by SARS-CoV-2 [<xref rid="bib49" ref-type="bibr">49</xref>]. The detection of SARS-CoV using RT-qPCR can only achieve a sensitivity of 50%–79%, depending on the protocol used the sample type and number of clinical specimens collected [<xref rid="bib50" ref-type="bibr">50</xref>]. Thus, it is essential to improve the detection rate of RT-qPCR for SARS-CoV-2 infection. Besides, RT-qPCR has some other shortcomings, including certain biological safety hazards brought by the retention and operation of patient samples, cumbersome nucleic acid detection operations, and long waiting time for results.</p></sec><sec id="sec4.2"><label>4.2</label><title>CT scans and other diagnostic methods</title><p id="p0090">For the diagnosis of COVID-19, although RT-qPCR is specific, its false-negative rate cannot be ignored because of the severe consequences of missed diagnosis. So many clinicians proposed CT scans should be one necessary auxiliary diagnostic method because it is more sensitive. For individuals with a high clinical suspicion of SARS-CoV-2 infection with negative RT-qPCR screening, a combination of repeated RT-qPCR tests and chest CT scan may be helpful. Especially the high-resolution CT (HRCT) for the chest is essential for early diagnosis and evaluation of disease severity of patients with SARS-CoV-2 [<xref rid="bib51" ref-type="bibr">51</xref>]. Several studies have analyzed chest CT images of patients infected with SARS-CoV-2 [<xref rid="bib52" ref-type="bibr">52</xref>,<xref rid="bib53" ref-type="bibr">53</xref>]. The typical CT images show bilateral pulmonary parenchymal ground-glass and consolidative pulmonary opacities, sometimes with a rounded morphology and a peripheral lung distribution. Lung involvement with a peripheral predominance was also seen in patients with SARS-CoV and MERS-CoV infections, and the chest CT showed that disease progressed with ground-glass opacities and consolidation, which is similar to that of SARS-CoV-2 infection [<xref rid="bib54" ref-type="bibr">54</xref>,<xref rid="bib55" ref-type="bibr">55</xref>]. According to those findings, CT scans have a great clinical diagnostic value for COVID-19, especially in the high prevalence area of SARS-CoV-2 infection. However, CT scans also have some shortcomings, such as indistinguishability from other viral pneumonia and the hysteresis of abnormal CT imaging.</p><p id="p0095">Given the shortcomings of the currently used nucleic acid detection and CT scans for the diagnosis of COVID-19, clinical laboratories should apply some immunological detection kits that target viral antigens or antibodies as soon as possible. Currently, POCT of IgM/IgG and ELISA kits for SARS-CoV-2 have been developed and pre-tested by some companies and have shown higher detection rates than nucleic acid detection, but there is still no product or published article. The sensitivity of SARS-CoV N-based IgG ELISA (94.7%) is significantly higher than that of SARS-CoV S-based IgG ELISA (58.9%) [<xref rid="bib48" ref-type="bibr">48</xref>], but the sensitivity of SARS-CoV-2 IgG/IgM remains to be studied. Hence, developing other sensitive and specific auxiliary methods is necessary and urgent for the diagnosis of COVID-19.</p></sec></sec><sec id="sec5"><label>5</label><title>Current treatment strategies for COVID-19</title><p id="p0100">Just like SARS-CoV and MERS-CoV [<xref rid="bib2" ref-type="bibr">2</xref>,<xref rid="bib56" ref-type="bibr">56</xref>], there is currently no clinically proven specific antiviral agent available for SARS-CoV-2 infection. The supportive treatment, including oxygen therapy, conservation fluid management, and the use of broad-spectrum antibiotics to cover secondary bacterial infection, remains to be the most important management strategy [<xref rid="bib15" ref-type="bibr">15</xref>]. According to the research on molecular mechanisms of coronavirus infection [<xref rid="bib57" ref-type="bibr">57</xref>] and the genomic organization of SARS-CoV-2 [<xref rid="bib6" ref-type="bibr">6</xref>], there are several potential therapeutic targets to repurpose the existing antiviral agents or develop effective interventions against this novel coronavirus.</p><sec id="sec5.1"><label>5.1</label><title>Virally targeted inhibitors</title><p id="p0105">Remdesivir, an adenosine analogue that can target the RNA-dependent RNA polymerase and block viral RNA synthesis, which has been a promising antiviral drug against a wide array of RNA viruses (including SARS/MERS-CoV 5) infections in cultured cells [<xref rid="bib58" ref-type="bibr">58</xref>], mice [<xref rid="bib59" ref-type="bibr">59</xref>] and nonhuman primate models [<xref rid="bib60" ref-type="bibr">60</xref>,<xref rid="bib61" ref-type="bibr">61</xref>]. The Washington Department of Health administrated remdesivir intravenously firstly and found that remdesivir might have potential protection from SARS-CoV-2 infection [<xref rid="bib62" ref-type="bibr">62</xref>]. Then remdesivir and chloroquine have been demonstrated to inhibit SARS-CoV-2 effectively in vitro [<xref rid="bib63" ref-type="bibr">63</xref>]. Hence, other nucleoside analogues, such as favipiravir, ribavirin and galidesivir [<xref rid="bib56" ref-type="bibr">56</xref>,<xref rid="bib64" ref-type="bibr">64</xref>] may be potentially clinically applicable against SARS-CoV-2. Chymotrypsin-like (3C-like protease, 3CLpro) and papain-like protease (PLP) are non-structural proteins, which have an essential function for coronaviral replication and can inhibit the host innate immune responses [<xref rid="bib65" ref-type="bibr">65</xref>]. So 3CLpro inhibitors, such as cinanserin [<xref rid="bib66" ref-type="bibr">66</xref>] and flavonoids [<xref rid="bib67" ref-type="bibr">67</xref>], and PLP inhibitors, such as diarylheptanoids [<xref rid="bib68" ref-type="bibr">68</xref>], are other attractive choices to fight against SARS-CoV-2. ACE2 mediates SARS-CoV-2 entry into the cell as a functional receptor of coronaviruses. So blocking the binding of S protein with ACE2 is also a meaningful strategy against SARS-CoV-2 infection [<xref rid="bib10" ref-type="bibr">10</xref>].</p></sec><sec id="sec5.2"><label>5.2</label><title>Antibody and plasma therapy</title><p id="p0110">It has also been reported that there are many convalescent patients donating plasma against SARS-CoV-2, just as SARS-CoV [<xref rid="bib69" ref-type="bibr">69</xref>] and MERS-CoV [<xref rid="bib70" ref-type="bibr">70</xref>] trials. It has preliminary acquired favorable results in acute, severe SARS-CoV-2 patients. Moreover, the generation of recombinant human monoclonal antibody (mAb) is a fairly straightforward path to neutralize SARS-CoV. CR3022, a SARS coronavirus-specific human monoclonal antibody, can bind potently with the receptor-binding domain(RBD) of SARS-CoV-2 and has the potential to be developed as candidate therapeutics of SARS-CoV-2 infections [<xref rid="bib71" ref-type="bibr">71</xref>]. Other monoclonal antibodies neutralizing SARS-CoV, such as m396, CR3014, could be an alternative for the treatment of SARS-CoV-2 [<xref rid="bib72" ref-type="bibr">72</xref>].</p></sec><sec id="sec5.3"><label>5.3</label><title>Vaccines</title><p id="p0115">Effective SARS-CoV-2 vaccines are essential for reducing disease severity, viral shedding and transmission, thus helping to control the coronavirus outbreaks. There are several vaccination strategies against SARS-CoV, MERS-CoV tested in animals, including a live-attenuated virus, viral vectors, inactivated virus, subunit vaccines, recombinant DNA, and proteins vaccines [<xref rid="bib73" ref-type="bibr">73</xref>]. These studies are in progress, but it requires months to years to develop the vaccines for SARS-CoV-2.</p><p id="p0120">Currently, there may be many promising targets for SARS-CoV-2, but more laboratory and clinical evidence still should be explored. The WHO is working with Chinese scientists to launch more than 80 clinical trials on potential treatments for SARS-CoV-2. Traditional Chinese medicine seems to have some effect in the supportive treatments. Some new pharmaceutical drugs, including HIV drugs and stem cells, were testified in those clinical trials.</p></sec></sec><sec id="sec6"><label>6</label><title>Conclusion</title><p id="p0125">In conclusion, the occurrence and development of SARS-CoV-2 depend on the interaction between the virus and the individual's immune system. Viral factors include virus type, mutation, viral load, viral titer, and viability of the virus in vitro. The individual's immune system factors include genetics (such as HLA genes), age, gender, nutritional status, neuroendocrine-immune regulation, and physical status. These factors all contribute to whether an individual is infected with the virus, the duration and severity of the disease, and the reinfection. In the early stages of the epidemic, accurate diagnosis helps control the spread of the disease. It is imperative to develop new, safe, accurate, fast and simple new technologies for detecting SARS-CoV-2. Of course, physicians will intentionally intervene in the two factors to make them develop into a direction beneficial to human health, which can help patients recover as soon as possible. However, it must not be considered that medical intervention can achieve a 100% curative effect.</p></sec><sec sec-type="COI-statement"><title>Declaration of competing interest</title><p id="p0130">The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.</p></sec></body><back><ref-list id="cebib0010"><title>References</title><ref id="bib1"><label>1</label><element-citation publication-type="journal" id="sref1"><person-group person-group-type="author"><name><surname>Zhou</surname><given-names>P.</given-names></name><name><surname>Yang</surname><given-names>X.L.</given-names></name><name><surname>Wang</surname><given-names>X.G.</given-names></name></person-group><article-title>A pneumonia outbreak associated with a new coronavirus of probable bat origin</article-title><source>Nature</source><year>2020</year></element-citation></ref><ref id="bib2"><label>2</label><element-citation publication-type="journal" id="sref2"><person-group person-group-type="author"><name><surname>de Wit</surname><given-names>E.</given-names></name><name><surname>van Doremalen</surname><given-names>N.</given-names></name><name><surname>Falzarano</surname><given-names>D.</given-names></name></person-group><article-title>SARS and MERS: recent insights into emerging coronaviruses</article-title><source>Nat. 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Microbiol.</source><volume>11</volume><year>2013</year><fpage>836</fpage><lpage>848</lpage><pub-id pub-id-type="pmid">24217413</pub-id></element-citation></ref></ref-list><sec id="appsec1" sec-type="supplementary-material"><label>Appendix A</label><title>Supplementary data</title><p id="p0140">The following is the Supplementary data to this article:<supplementary-material content-type="local-data" id="mmc1"><caption><title>Multimedia component 1</title></caption><media xlink:href="mmc1.xml"><alt-text>Multimedia component 1</alt-text></media></supplementary-material></p></sec><ack id="ack0010"><title>Acknowledgments</title><p>This work was supported by the <funding-source id="gs1">National Natural Science Foundation of China</funding-source> (project No.81970029) and <funding-source id="gs2">Fundamental Research Funds for the Central Universities of China</funding-source> (The Emergency Projects on COVID-19). We sincerely thank the individuals who contributed to this work including Xudong Yang, Wenhua Zhu, Jing Xu, Fumeng Huang, Muhammad Saadiq Khan, Jiajun Ren, Xipeng Wang.</p></ack><fn-group><fn id="appsec2" fn-type="supplementary-material"><label>Appendix A</label><p id="p0145">Supplementary data to this article can be found online at <ext-link ext-link-type="uri" xlink:href="https://doi.org/10.1016/j.jpha.2020.03.001" id="intref0015">https://doi.org/10.1016/j.jpha.2020.03.001</ext-link>.</p></fn></fn-group></back></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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