Skip to main content
Key Specialties
Cardiology Diabetology Endocrinology Gastroenterology Geriatrics and Gerontology Gynecology and Obstetrics Hematology Infectious Disease Internal Medicine Nephrology Neurology Oncology Pediatrics Respiratory Medicine Rheumatology Surgery
Congress Coverage
2024 ACC Congress 2023 ESMO Congress 2023 EASD Congress 2023 ERS Congress 2023 ESC Congress
Clinical Collections
Advances in Alzheimer’s

At a glance: The STEP trials

A round-up of the STEP phase 3 clinical trials evaluating semaglutide for weight loss in people with overweight or obesity.
ADVANCED SEARCH
Log in
Top
Respiratory Research
Published in: Respiratory Research 1/2020

01-12-2020 | Severe Acute Respiratory Syndrome Coronavirus | Review

SARS coronavirus 2: from genome to infectome

Authors: Meghana Rastogi, Neha Pandey, Astha Shukla, Sunit K. Singh

Published in: Respiratory Research | Issue 1/2020

Login to get access

Abstract

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) belongs to the group of Betacoronaviruses. The SARS-CoV-2 is closely related to SARS-CoV-1 and probably originated either from bats or pangolins. SARS-CoV-2 is an etiological agent of COVID-19, causing mild to severe respiratory disease which escalates to acute respiratory distress syndrome (ARDS) or multi-organ failure. The virus was first reported from the animal market in Hunan, Hubei province of China in the month of December, 2019, and was rapidly transmitted from animal to human and human-to-human. The human-to-human transmission can occur directly or via droplets generated during coughing and sneezing. Globally, around 53.9 million cases of COVID-19 have been registered with 1.31 million confirmed deaths. The people > 60 years, persons suffering from comorbid conditions and immunocompromised individuals are more susceptible to COVID-19 infection. The virus primarily targets the upper and the lower respiratory tract and quickly disseminates to other organs. SARS-CoV-2 dysregulates immune signaling pathways which generate cytokine storm and leads to the acute respiratory distress syndrome and other multisystemic disorders.
Literature
1.
2.
3.
Zhong NS, Zheng BJ, Li YM, Poon, Xie ZH, Chan KH, Li PH, Tan SY, Chang Q, Xie JP, et al. Epidemiology and cause of severe acute respiratory syndrome (SARS) in Guangdong, People’s Republic of China, in February, 2003. Lancet. 2003;362:1353–8.PubMedPubMedCentralCrossRef
4.
Zaki AM, van Boheemen S, Bestebroer TM, Osterhaus AD, Fouchier RA. Isolation of a novel coronavirus from a man with pneumonia in Saudi Arabia. N Engl J Med. 2012;367:1814–20.PubMedCrossRef
5.
Hu B, Zeng LP, Yang XL, Ge XY, Zhang W, Li B, Xie JZ, Shen XR, Zhang YZ, Wang N, et al. Discovery of a rich gene pool of bat SARS-related coronaviruses provides new insights into the origin of SARS coronavirus. PLoS Pathog. 2017;13:e1006698.PubMedPubMedCentralCrossRef
6.
Lau SK, Li KS, Tsang AK, Lam CS, Ahmed S, Chen H, Chan KH, Woo PC, Yuen KY. Genetic characterization of Betacoronavirus lineage C viruses in bats reveals marked sequence divergence in the spike protein of pipistrellus bat coronavirus HKU5 in Japanese pipistrelle: implications for the origin of the novel Middle East respiratory syndrome coronavirus. J Virol. 2013;87:8638–50.PubMedPubMedCentralCrossRef
7.
8.
9.
Wu F, Zhao S, Yu B, Chen YM, Wang W, Song ZG, Hu Y, Tao ZW, Tian JH, Pei YY, et al. A new coronavirus associated with human respiratory disease in China. Nature. 2020;579:265–9.PubMedPubMedCentralCrossRef
10.
11.
12.
Zou X, Chen K, Zou J, Han P, Hao J, Han Z. Single-cell RNA-seq data analysis on the receptor ACE2 expression reveals the potential risk of different human organs vulnerable to 2019-nCoV infection. Front Med. 2020;14:185–92.PubMedCrossRef
13.
Xu Z, Shi L, Wang Y, Zhang J, Huang L, Zhang C, Liu S, Zhao P, Liu H, Zhu L, et al. Pathological findings of COVID-19 associated with acute respiratory distress syndrome. Lancet Respir Med. 2020;8:420–2.PubMedPubMedCentralCrossRef
14.
Li Q, Guan X, Wu P, Wang X, Zhou L, Tong Y, Ren R, Leung KSM, Lau EHY, Wong JY, et al. Early transmission dynamics in Wuhan, China, of novel coronavirus-infected pneumonia. N Engl J Med. 2020;382:1199–207.PubMedPubMedCentralCrossRef
15.
16.
Zhou P, Yang X-L, Wang X-G, Hu B, Zhang L, Zhang W, Si H-R, Zhu Y, Li B, Huang C-L, et al. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature. 2020;579:270–3.PubMedPubMedCentralCrossRef
17.
18.
Ren L, Wu C, Guo L, Yao J, Wang C, Xiao Y, Pisco AO, Wu Z, Lei X, Liu Y, et al. Single-cell transcriptional atlas of the Chinese horseshoe bat (Rhinolophus sinicus) provides insight into the cellular mechanisms which enable bats to be viral reservoirs. 2020:2020.2006.2030.175778.
19.
20.
Dowd JB, Andriano L, Brazel DM, Rotondi V, Block P, Ding X, Liu Y, Mills MC. Demographic science aids in understanding the spread and fatality rates of COVID-19. Proc Natl Acad Sci USA. 2020;117:9696–8.PubMedCrossRefPubMedCentral
21.
Wu JT, Leung K, Bushman M, Kishore N, Niehus R, de Salazar PM, Cowling BJ, Lipsitch M, Leung GM. Estimating clinical severity of COVID-19 from the transmission dynamics in Wuhan, China. Nat Med. 2020;26:506–10.PubMedCrossRefPubMedCentral
22.
Onder G, Rezza G, Brusaferro S. Case-fatality rate and characteristics of patients dying in relation to COVID-19 in Italy. JAMA. 2020;323:1775–6.PubMed
23.
Venkatesan P. The changing demographics of COVID-19. Lancet Respir Med. 2020.
24.
25.
Sanyaolu A, Okorie C, Marinkovic A, Patidar R, Younis K, Desai P, Hosein Z, Padda I, Mangat J, Altaf M. Comorbidity and its impact on patients with COVID-19. SN Compr Clin Med. 2020:1–8.
26.
Ma C, Gu J, Hou P, Zhang L, Bai Y, Guo Z, Wu H, Zhang B, Li P, Zhao X. Incidence, clinical characteristics and prognostic factor of patients with COVID-19: a systematic review and meta-analysis. 2020:2020.2003.2017.20037572.
27.
Ghayda RA, Lee KH, Han YJ, Ryu S, Hong SH, Yoon S, Jeong GH, Lee J, Lee JY, Yang JW, et al. Estimation of global case fatality rate of coronavirus disease 2019 (COVID-19) using meta-analyses: comparison between calendar date and days since the outbreak of the first confirmed case. Int J Infect Dis. 2020;100:302–8.PubMedPubMedCentralCrossRef
28.
Zhang JJ, Dong X, Cao YY, Yuan YD, Yang YB, Yan YQ, Akdis CA, Gao YD. Clinical characteristics of 140 patients infected with SARS-CoV-2 in Wuhan, China. Allergy. 2020;75:1730–41.CrossRefPubMed
29.
Jin JM, Bai P, He W, Wu F, Liu XF, Han DM, Liu S, Yang JK. Gender differences in patients with COVID-19: focus on severity and mortality. Front Public Health. 2020;8:152.PubMedPubMedCentralCrossRef
30.
Richardson S, Hirsch JS, Narasimhan M, Crawford JM, McGinn T, Davidson KW, the Northwell C-RC, Barnaby DP, Becker LB, Chelico JD, et al. Presenting characteristics, comorbidities, and outcomes among 5700 patients hospitalized with COVID-19 in the New York City area. JAMA. 2020;323:2052–9.PubMedPubMedCentralCrossRef
31.
Sama IE, Ravera A, Santema BT, van Goor H, Ter Maaten JM, Cleland JGF, Rienstra M, Friedrich AW, Samani NJ, Ng LL, et al. Circulating plasma concentrations of angiotensin-converting enzyme 2 in men and women with heart failure and effects of renin-angiotensin-aldosterone inhibitors. Eur Heart J. 2020;41:1810–7.PubMedPubMedCentralCrossRef
32.
Griffith DM, Sharma G, Holliday CS, Enyia OK, Valliere M, Semlow AR, Stewart EC, Blumenthal RS. Men and COVID-19: a biopsychosocial approach to understanding sex differences in mortality and recommendations for practice and policy interventions. Prev Chronic Dis. 2020;17:E63.PubMedPubMedCentralCrossRef
33.
Bogoch II, Watts A, Thomas-Bachli A, Huber C, Kraemer MUG, Khan K. Pneumonia of unknown aetiology in Wuhan, China: potential for international spread via commercial air travel. J Travel Med. 2020;27:taa008.CrossRef
34.
Khan S, Siddique R, Shereen MA, Ali A, Liu J, Bai Q, Bashir N, Xue M. The emergence of a novel coronavirus (SARS-CoV-2), their biology and therapeutic options. J Clin Microbiol. 2020.
35.
Carlos WG, Dela Cruz CS, Cao B, Pasnick S, Jamil S. Novel Wuhan (2019-nCoV) coronavirus. Am J Respir Crit Care Med. 2020;201:P7–8.PubMedCrossRef
36.
37.
Holshue ML, DeBolt C, Lindquist S, Lofy KH, Wiesman J, Bruce H, Spitters C, Ericson K, Wilkerson S, Tural A, et al. First case of 2019 novel coronavirus in the United States. N Engl J Med. 2020;382:929–36.PubMedPubMedCentralCrossRef
38.
Schwartz DA. An analysis of 38 pregnant women with COVID-19, their newborn infants, and maternal-fetal transmission of SARS-CoV-2: maternal coronavirus infections and pregnancy outcomes. Arch Pathol Lab Med. 2020;144:799–805.CrossRefPubMed
39.
Wang L, Shi Y, Xiao T, Fu J, Feng X, Mu D, Feng Q, Hei M, Hu X, Li Z, et al. Chinese expert consensus on the perinatal and neonatal management for the prevention and control of the 2019 novel coronavirus infection (First edition). Ann Transl Med. 2020;8:47.PubMedPubMedCentralCrossRef
40.
41.
Ashour HM, Elkhatib WF, Rahman MM, Elshabrawy HA: Insights into the Recent, . Novel coronavirus (SARS-CoV-2) in light of past human coronavirus outbreaks. Pathogens. 2019;2020:9.
42.
Woo PCY, Lau SKP, Lam CSF, Lau CCY, Tsang AKL, Lau JHN, Bai R, Teng JLL, Tsang CCC, Wang M, et al. Discovery of seven novel Mammalian and avian coronaviruses in the genus deltacoronavirus supports bat coronaviruses as the gene source of alphacoronavirus and betacoronavirus and avian coronaviruses as the gene source of gammacoronavirus and deltacoronavirus. J Virol. 2012;86:3995–4008.PubMedPubMedCentralCrossRef
43.
Lu R, Zhao X, Li J, Niu P, Yang B, Wu H, Wang W, Song H, Huang B, Zhu N, et al. Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding. Lancet. 2020;395:565–74.PubMedPubMedCentralCrossRef
44.
45.
Rehman SU, Shafique L, Ihsan A, Liu Q. Evolutionary trajectory for the emergence of novel coronavirus SARS-CoV-2. Pathogens. 2020;9:240.PubMedCentralCrossRef
46.
Wan Y, Shang J, Graham R, Baric RS, Li F. Receptor recognition by the novel coronavirus from Wuhan: an analysis based on decade-long structural studies of SARS coronavirus. J Virol. 2020;94.
47.
Walls AC, Park Y-J, Tortorici MA, Wall A, McGuire AT, Veesler D. Structure, function, and antigenicity of the SARS-CoV-2 spike glycoprotein. Cell. 2020;181(281–292):e286.
48.
Andersen KG, Rambaut A, Lipkin WI, Holmes EC, Garry RF. The proximal origin of SARS-CoV-2. Nat Med. 2020;26:450–2.PubMedCrossRef
49.
Lam TT, Shum MH, Zhu HC, Tong YG, Ni XB, Liao YS, Wei W, Cheung WY, Li WJ, Li LF, et al. Identifying SARS-CoV-2 related coronaviruses in Malayan pangolins. Nature. 2020;583:282–5.PubMedCrossRef
50.
Xiao K, Zhai J, Feng Y, Zhou N, Zhang X, Zou JJ, Li N, Guo Y, Li X, Shen X, et al. Isolation of SARS-CoV-2-related coronavirus from Malayan pangolins. Nature. 2020;583:286–9.PubMedCrossRef
51.
Liu P, Chen W, Chen JP. Viral metagenomics revealed sendai virus and coronavirus infection of malayan pangolins (Manis javanica). Viruses. 2019;11:979.PubMedCentralCrossRef
52.
Shi J, Wen Z, Zhong G, Yang H, Wang C, Huang B, Liu R, He X, Shuai L, Sun Z, et al. Susceptibility of ferrets, cats, dogs, and other domesticated animals to SARS-coronavirus 2. Science. 2020;368:1016–20.PubMedPubMedCentralCrossRef
53.
Kim YI, Kim SG, Kim SM, Kim EH, Park SJ, Yu KM, Chang JH, Kim EJ, Lee S, Casel MAB, et al. Infection and rapid transmission of SARS-CoV-2 in Ferrets. Cell Host Microbe. 2020;27(704–709):e702.
54.
Richard M, Kok A, de Meulder D, Bestebroer TM, Lamers MM, Okba NMA, Fentener van Vlissingen M, Rockx B, Haagmans BL, Koopmans MPG, et al. SARS-CoV-2 is transmitted via contact and via the air between ferrets. Nat Commun. 2020;11:3496.PubMedPubMedCentralCrossRef
55.
Wu A, Peng Y, Huang B, Ding X, Wang X, Niu P, Meng J, Zhu Z, Zhang Z, Wang J, et al. Genome composition and divergence of the novel coronavirus (2019-nCoV) originating in China. Cell Host Microbe. 2020;27:325–8.PubMedPubMedCentralCrossRef
56.
Zhu N, Zhang D, Wang W, Li X, Yang B, Song J, Zhao X, Huang B, Shi W, Lu R, et al. A novel coronavirus from patients with pneumonia in China, 2019. N Engl J Med. 2020;382:727–33.PubMedPubMedCentralCrossRef
57.
Kim D, Lee J-Y, Yang J-S, Kim JW, Kim VN, Chang H. The architecture of SARS-CoV-2 transcriptome. Cell-Press. 2020:2020.2003.2012.988865.
58.
Chen N, Zhou M, Dong X, Qu J, Gong F, Han Y, Qiu Y, Wang J, Liu Y, Wei Y, et al. Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study. Lancet. 2020;395:507–13.PubMedPubMedCentralCrossRef
59.
Bárcena M, Oostergetel GT, Bartelink W, Faas FG, Verkleij A, Rottier PJ, Koster AJ, Bosch BJ. Cryo-electron tomography of mouse hepatitis virus: insights into the structure of the coronavirion. Proc Natl Acad Sci USA. 2009;106:582–7.PubMedCrossRefPubMedCentral
60.
Neuman BW, Adair BD, Yoshioka C, Quispe JD, Orca G, Kuhn P, Milligan RA, Yeager M, Buchmeier MJ. Supramolecular architecture of severe acute respiratory syndrome coronavirus revealed by electron cryomicroscopy. J Virol. 2006;80:7918–28.PubMedPubMedCentralCrossRef
61.
62.
De Maio F, Lo Cascio E, Babini G, Sali M, Della Longa S, Tilocca B, Roncada P, Arcovito A, Sanguinetti M, Scambia G, Urbani A. Improved binding of SARS-CoV-2 envelope protein to tight junction-associated PALS1 could play a key role in COVID-19 pathogenesis. Microbes Infect. 2020.
63.
64.
Atkins JF, Loughran G, Bhatt PR, Firth AE, Baranov PV. Ribosomal frameshifting and transcriptional slippage: from genetic steganography and cryptography to adventitious use. Nucleic Acids Res. 2016;44:7007–78.PubMedPubMedCentral
65.
Kelly JA, Dinman JD. Structural and functional conservation of the programmed -1 ribosomal frameshift signal of SARS-CoV-2. bioRxiv. 2020:2020.2003.2013.991083.
66.
67.
Chen YW, Yiu C-PB, Wong K-Y. Prediction of the SARS-CoV-2 (2019-nCoV) 3C-like protease (3CL (pro)) structure: virtual screening reveals velpatasvir, ledipasvir, and other drug repurposing candidates. F1000Research. 2020;9:129.PubMedPubMedCentralCrossRef
68.
Gao Y, Yan L, Huang Y, Liu F, Zhao Y, Cao L, Wang T, Sun Q, Ming Z, Zhang L, et al. Structure of RNA-dependent RNA polymerase from 2019-nCoV, a major antiviral drug target. bioRxiv. 2020:2020.2003.2016.993386.
69.
Smith EC, Blanc H, Surdel MC, Vignuzzi M, Denison MR. Coronaviruses lacking exoribonuclease activity are susceptible to lethal mutagenesis: evidence for proofreading and potential therapeutics. PLoS Pathog. 2013;9:e1003565.PubMedPubMedCentralCrossRef
70.
Sawicki SG, Sawicki DL, Siddell SG. A contemporary view of coronavirus transcription. J Virol. 2007;81:20.PubMedCrossRef
71.
Yeager CL, Ashmun RA, Williams RK, Cardellichio CB, Shapiro LH, Look AT, Holmes KV. Human aminopeptidase N is a receptor for human coronavirus 229E. Nature. 1992;357:420–2.PubMedPubMedCentralCrossRef
72.
Raj VS, Mou H, Smits SL, Dekkers DH, Müller MA, Dijkman R, Muth D, Demmers JA, Zaki A, Fouchier RA, et al. Dipeptidyl peptidase 4 is a functional receptor for the emerging human coronavirus-EMC. Nature. 2013;495:251–4.PubMedPubMedCentralCrossRef
73.
Li W, Moore MJ, Vasilieva N, Sui J, Wong SK, Berne MA, Somasundaran M, Sullivan JL, Luzuriaga K, Greenough TC, et al. Angiotensin-converting enzyme 2 is a functional receptor for the SARS coronavirus. Nature. 2003;426:450–4.PubMedPubMedCentralCrossRef
74.
Li F, Li W, Farzan M, Harrison SC. Structure of SARS coronavirus spike receptor-binding domain complexed with receptor. Science. 2005;309:1864–8.PubMedCrossRef
75.
Burkard C, Verheije MH, Wicht O, van Kasteren SI, van Kuppeveld FJ, Haagmans BL, Pelkmans L, Rottier PJM, Bosch BJ, de Haan CAM. Coronavirus cell entry occurs through the endo-/lysosomal pathway in a proteolysis-dependent manner. PLoS Pathog. 2014;10:e1004502.PubMedPubMedCentralCrossRef
76.
Millet JK, Whittaker GR. Host cell proteases: critical determinants of coronavirus tropism and pathogenesis. Virus Res. 2015;202:120–34.PubMedCrossRef
77.
78.
Lu G, Hu Y, Wang Q, Qi J, Gao F, Li Y, Zhang Y, Zhang W, Yuan Y, Bao J, et al. Molecular basis of binding between novel human coronavirus MERS-CoV and its receptor CD26. Nature. 2013;500:227–31.PubMedPubMedCentralCrossRef
79.
Madu IG, Roth SL, Belouzard S, Whittaker GR. Characterization of a highly conserved domain within the severe acute respiratory syndrome coronavirus spike protein S2 domain with characteristics of a viral fusion peptide. J Virol. 2009;83:7411–21.PubMedPubMedCentralCrossRef
80.
Glowacka I, Bertram S, Muller MA, Allen P, Soilleux E, Pfefferle S, Steffen I, Tsegaye TS, He Y, Gnirss K, et al. Evidence that TMPRSS2 activates the severe acute respiratory syndrome coronavirus spike protein for membrane fusion and reduces viral control by the humoral immune response. J Virol. 2011;85:4122–34.PubMedPubMedCentralCrossRef
81.
Hoffmann M, Kleine-Weber H, Schroeder S, Krüger N, Herrler T, Erichsen S, Schiergens TS, Herrler G, Wu N-H, Nitsche A, et al. SARS-CoV-2 cell entry depends on ACE2 and TMPRSS2 and is blocked by a clinically proven protease inhibitor. Cell. 2020;181:271-280.e278.PubMedPubMedCentralCrossRef
82.
Elbe S, Buckland-Merrett G. Data, disease and diplomacy: GISAID's innovative contribution to global health. In: Global challenges (Hoboken, NJ), vol. 1. pp. 33–46; 2017:33–46.
83.
Huang C, Wang Y, Li X, Ren L, Zhao J, Hu Y, Zhang L, Fan G, Xu J, Gu X, et al. Clinical features of patients infected with 2019 novel coronavirus in Wuhan. China. Lancet. 2020;395:497–506.PubMedPubMedCentralCrossRef
84.
Wang D, Hu B, Hu C, Zhu F, Liu X, Zhang J, Wang B, Xiang H, Cheng Z, Xiong Y, et al. Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China. JAMA. 2020.
85.
Li J, Guo M, Tian X, Liu C, Wang X, Yang X, Wu P, Xiao Z, Qu Y, Yin Y, et al. Virus-host interactome and proteomic survey of PMBCs from COVID-19 patients reveal potential virulence factors influencing SARS-CoV-2 pathogenesis. bioRxiv. 2020:2020.2003.2031.019216.
86.
Chu H, Zhou J, Wong BH-Y, Li C, Chan JF-W, Cheng Z-S, Yang D, Wang D, Lee AC-Y, Li C, et al. Middle East respiratory syndrome coronavirus efficiently infects human primary T lymphocytes and activates the extrinsic and intrinsic apoptosis pathways. J Infect Dis. 2015;213:904–14.PubMedCrossRef
87.
Wang X, Xu W, Hu G, Xia S, Sun Z, Liu Z, Xie Y, Zhang R, Jiang S, Lu L. SARS-CoV-2 infects T lymphocytes through its spike protein-mediated membrane fusion. Cell Mol Immunol. 2020.
88.
Wrapp D, Wang N, Corbett KS, Goldsmith JA, Hsieh CL, Abiona O, Graham BS, McLellan JS. Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation. Science. 2020;367:1260–3.PubMedPubMedCentralCrossRef
89.
90.
Peng Y, Mentzer AJ, Liu G, Yao X, Yin Z, Dong D, Dejnirattisai W, Rostron T, Supasa P, Liu C, et al. Broad and strong memory CD4(+) and CD8(+) T cells induced by SARS-CoV-2 in UK convalescent individuals following COVID-19. Nat Immunol. 2020;21:1336–45.PubMedCrossRefPubMedCentral
91.
Mathew D, Giles JR, Baxter AE, Greenplate AR, Wu JE, Alanio C, Oldridge DA, Kuri-Cervantes L, Pampena MB, D'Andrea K, et al. Deep immune profiling of COVID-19 patients reveals patient heterogeneity and distinct immunotypes with implications for therapeutic interventions. bioRxiv. 2020.
92.
Grifoni A, Weiskopf D, Ramirez SI, Mateus J, Dan JM, Moderbacher CR, Rawlings SA, Sutherland A, Premkumar L, Jadi RS, et al. Targets of T cell responses to SARS-CoV-2 coronavirus in humans with COVID-19 disease and unexposed individuals. Cell. 2020;181:1489-1501.e1415.PubMedPubMedCentralCrossRef
93.
Dumonde DC, Wolstencroft RA, Panayi GS, Matthew M, Morley J, Howson WT. “Lymphokines”: non-antibody mediators of cellular immunity generated by lymphocyte activation. Nature. 1969;224:38–42.PubMedCrossRef
94.
Kopecky-Bromberg SA, Martínez-Sobrido L, Frieman M, Baric RA, Palese P. Severe acute respiratory syndrome coronavirus open reading frame (ORF) 3b, ORF 6, and nucleocapsid proteins function as interferon antagonists. J Virol. 2007;81:548–57.PubMedCrossRef
95.
Channappanavar R, Fehr AR, Vijay R, Mack M, Zhao J, Meyerholz DK, Perlman S. Dysregulated type I interferon and inflammatory monocyte-macrophage responses cause lethal pneumonia in SARS-CoV-infected mice. Cell Host Microbe. 2016;19:181–93.PubMedPubMedCentralCrossRef
96.
Lokugamage KG, Hage A, Schindewolf C, Rajsbaum R, Menachery VD. SARS-CoV-2 is sensitive to type I interferon pretreatment. bioRxiv. 2020:2020.2003.2007.982264.
97.
Yang X, Yu Y, Xu J, Shu H, Xia J, Liu H, Wu Y, Zhang L, Yu Z, Fang M, et al. Clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia in Wuhan, China: a single-centered, retrospective, observational study. Lancet Respir Med. 2020;8:475–81.PubMedPubMedCentralCrossRef
98.
Wu Z, McGoogan JM. Characteristics of and important lessons from the coronavirus disease 2019 (COVID-19) outbreak in China: summary of a report of 72 314 cases from the Chinese Center for Disease Control and Prevention. JAMA. 2020;323:1239–42.PubMedCrossRef
99.
100.
Leino A, Lukkarinen M, Turunen R, Vuorinen T, Söderlund-Venermo M, Vahlberg T, Camargo CA Jr, Bochkov YA, Gern JE, Jartti T. Pulmonary function and bronchial reactivity 4 years after the first virus-induced wheezing. Allergy. 2019;74:518–26.PubMedCrossRef
101.
Badawi A, Ryoo SG. Prevalence of comorbidities in the Middle East respiratory syndrome coronavirus (MERS-CoV): a systematic review and meta-analysis. Int J Infect Dis. 2016;49:129–33.PubMedPubMedCentralCrossRef
102.
Lessler J, Reich NG, Brookmeyer R, Perl TM, Nelson KE, Cummings DAT. Incubation periods of acute respiratory viral infections: a systematic review. Lancet Infect Dis. 2009;9:291–300.PubMedPubMedCentralCrossRef
103.
104.
105.
Rodriguez-Morales AJ, Cardona-Ospina JA, Gutiérrez-Ocampo E, Villamizar-Peña R, Holguin-Rivera Y, Escalera-Antezana JP, Alvarado-Arnez LE, Bonilla-Aldana DK, Franco-Paredes C, Henao-Martinez AF, et al. Clinical, laboratory and imaging features of COVID-19: a systematic review and meta-analysis. Travel Med Infect Dis. 2020:101623.
106.
Méndez R, Menéndez R, Amara-Elori I, Feced L, Piró A, Ramírez P, Sempere A, Ortega A, Bermejo-Martín JF, Torres A. Lymphopenic community-acquired pneumonia is associated with a dysregulated immune response and increased severity and mortality. J Infect. 2019;78:423–31.PubMedCrossRef
107.
Liu J, Li S, Liu J, Liang B, Wang X, Wang H, Li W, Tong Q, Yi J, Zhao L, et al. Longitudinal characteristics of lymphocyte responses and cytokine profiles in the peripheral blood of SARS-CoV-2 infected patients. medRxiv. 2020:2020.2002.2016.20023671.
108.
Osborn M. Autopsy practice relating to possible cases of COVID-19 (2019-nCov, novel coronavirus from China 2019/2020). Pathologists TRCo ed.; 2020.
109.
Hanley B, Lucas SB, Youd E, Swift B, Osborn M. Autopsy in suspected COVID-19 cases. J Clin Pathol. 2020;73:239–42.PubMedCrossRef
110.
Ng DL, Al Hosani F, Keating MK, Gerber SI, Jones TL, Metcalfe MG, Tong S, Tao Y, Alami NN, Haynes LM, et al. Clinicopathologic, immunohistochemical, and ultrastructural findings of a fatal case of middle east respiratory syndrome coronavirus infection in the United Arab Emirates, April 2014. Am J Pathol. 2016;186:652–8.PubMedCrossRef
111.
Cheema M, Aghazadeh H, Nazarali S, Ting A, Hodges J, McFarlane A, Kanji JN, Zelyas N, Damji KF, Solarte C. Keratoconjunctivitis as the initial medical presentation of the novel coronavirus disease 2019 (COVID-19). Can J Ophthalmol. 2020;55:e125–9.PubMedPubMedCentralCrossRef
112.
113.
Chu DKW, Pan Y, Cheng SMS, Hui KPY, Krishnan P, Liu Y, Ng DYM, Wan CKC, Yang P, Wang Q, et al. Molecular diagnosis of a novel coronavirus (2019-nCoV) causing an outbreak of pneumonia. Clin Chem. 2020;66:549–55.PubMedCrossRefPubMedCentral
114.
115.
Rothe C, Schunk M, Sothmann P, Bretzel G, Froeschl G, Wallrauch C, Zimmer T, Thiel V, Janke C, Guggemos W, et al. Transmission of 2019-nCoV infection from an asymptomatic contact in Germany. N Engl J Med. 2020;382:970–1.PubMedPubMedCentralCrossRef
116.
Yu P, Zhu J, Zhang Z, Han Y, Huang L. A familial cluster of infection associated with the 2019 novel coronavirus indicating potential person-to-person transmission during the incubation period. J Infect Dis. 2020;221:1757–61.PubMedCrossRef
117.
Walsh EE, Frenck RW, Jr., Falsey AR, Kitchin N, Absalon J, Gurtman A, Lockhart S, Neuzil K, Mulligan MJ, Bailey R, et al. Safety and immunogenicity of two RNA-based Covid-19 vaccine candidates. N Engl J Med. 2020.
118.
Anderson EJ, Rouphael NG, Widge AT, Jackson LA, Roberts PC, Makhene M, Chappell JD, Denison MR, Stevens LJ, Pruijssers AJ, et al. Safety and immunogenicity of SARS-CoV-2 mRNA-1273 vaccine in older adults. N Engl J Med. 2020.
119.
Folegatti PM, Ewer KJ, Aley PK, Angus B, Becker S, Belij-Rammerstorfer S, Bellamy D, Bibi S, Bittaye M, Clutterbuck EA, et al. Safety and immunogenicity of the ChAdOx1 nCoV-19 vaccine against SARS-CoV-2: a preliminary report of a phase 1/2, single-blind, randomised controlled trial. Lancet. 2020;396:467–78.PubMedPubMedCentralCrossRef
120.
Logunov DY, Dolzhikova IV, Zubkova OV, Tukhvatullin AI, Shcheblyakov DV, Dzharullaeva AS, Grousova DM, Erokhova AS, Kovyrshina AV, Botikov AG, et al. Safety and immunogenicity of an rAd26 and rAd5 vector-based heterologous prime-boost COVID-19 vaccine in two formulations: two open, non-randomised phase 1/2 studies from Russia. Lancet. 2020;396:887–97.PubMedPubMedCentralCrossRef
121.
122.
123.
Caly L, Druce JD, Catton MG, Jans DA, Wagstaff KM. The FDA-approved drug ivermectin inhibits the replication of SARS-CoV-2 in vitro. Antivir Res. 2020;178:104787.PubMedCrossRef
124.
Wang M, Cao R, Zhang L, Yang X, Liu J, Xu M, Shi Z, Hu Z, Zhong W, Xiao G. Remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-nCoV) in vitro. Cell Res. 2020;30:269–71.PubMedPubMedCentralCrossRef
125.
Warren TK, Jordan R, Lo MK, Ray AS, Mackman RL, Soloveva V, Siegel D, Perron M, Bannister R, Hui HC, et al. Therapeutic efficacy of the small molecule GS-5734 against Ebola virus in rhesus monkeys. Nature. 2016;531:381–5.PubMedPubMedCentralCrossRef
126.
127.
128.
Vincent MJ, Bergeron E, Benjannet S, Erickson BR, Rollin PE, Ksiazek TG, Seidah NG, Nichol ST. Chloroquine is a potent inhibitor of SARS coronavirus infection and spread. Virol J. 2005;2:69–69.PubMedPubMedCentralCrossRef
129.
Oestereich L, Lüdtke A, Wurr S, Rieger T, Muñoz-Fontela C, Günther S. Successful treatment of advanced Ebola virus infection with T-705 (favipiravir) in a small animal model. Antivir Res. 2014;105:17–21.PubMedCrossRef
130.
Duan K, Liu B, Li C, Zhang H, Yu T, Qu J, Zhou M, Chen L, Meng S, Hu Y, et al: Effectiveness of convalescent plasma therapy in severe COVID-19 patients. Proc Natl Acad Sci. 2020:202004168.
131.
Luo P, Liu Y, Qiu L, Liu X, Liu D, Li J. Tocilizumab treatment in COVID-19: a single center experience. J Med Virol. 2020;92:814–8.PubMedCrossRef
132.
Dong S, Sun J, Mao Z, Wang L, Lu Y-L, Li J. A guideline for homology modeling of the proteins from newly discovered betacoronavirus, 2019 novel coronavirus (2019-nCoV). J Med Virol. n/a.
133.
Schubert K, Karousis ED, Jomaa A, Scaiola A, Echeverria B, Gurzeler LA, Leibundgut M, Thiel V, Muhlemann O, Ban N. SARS-CoV-2 Nsp1 binds the ribosomal mRNA channel to inhibit translation. Nat Struct Mol Biol. 2020;27:959–66.PubMedCrossRef
134.
Angeletti S, Benvenuto D, Bianchi M, Giovanetti M, Pascarella S, Ciccozzi M. COVID-2019: The role of the nsp2 and nsp3 in its pathogenesis. J Med Virol. 2020;92:584–8.PubMedCrossRef
135.
Lei J, Kusov Y, Hilgenfeld R. Nsp3 of coronaviruses: structures and functions of a large multi-domain protein. Antivir Res. 2018;149:58–74.PubMedCrossRef
136.
Beachboard DC, Anderson-Daniels JM, Denison MR. Mutations across murine hepatitis virus nsp4 alter virus fitness and membrane modifications. J Virol. 2015;89:2080–9.PubMedCrossRef
137.
Manolaridis I, Wojdyla JA, Panjikar S, Snijder EJ, Gorbalenya AE, Berglind H, Nordlund P, Coutard B, Tucker PA. Structure of the C-terminal domain of nsp4 from feline coronavirus. Acta Crystallogr D Biol Crystallogr. 2009;65:839–46.PubMedCrossRef
138.
Zhu X, Fang L, Wang D, Yang Y, Chen J, Ye X, Foda MF, Xiao S. Porcine deltacoronavirus nsp5 inhibits interferon-β production through the cleavage of NEMO. Virology. 2017;502:33–8.PubMedCrossRef
139.
Angelini MM, Akhlaghpour M, Neuman BW, Buchmeier MJ. Severe acute respiratory syndrome coronavirus nonstructural proteins 3, 4, and 6 induce double-membrane vesicles. mBio. 2013;4.
140.
141.
Krichel B, Falke S, Hilgenfeld R, Redecke L, Uetrecht C. Processing of the SARS-CoV pp1a/ab nsp7-10 region. Biochem J. 2020;477:1009–19.PubMedCrossRef
142.
143.
144.
Ong E, Wong MU, Huffman A, He Y. COVID-19 coronavirus vaccine design using reverse vaccinology and machine learning. bioRxiv. 2020:2020.2003.2020.000141.
145.
Mutlu O, Ugurel OM, Sariyer E, Ata O, Inci TG, Ugurel E, Kocer S, Turgut-Balik D. Targeting SARS-CoV-2 Nsp12/Nsp8 interaction interface with approved and investigational drugs: an in silico structure-based approach. J Biomol Struct Dyn. 2020:1–13.
146.
Peng Q, Peng R, Yuan B, Zhao J, Wang M, Wang X, Wang Q, Sun Y, Fan Z, Qi J, et al. Structural and biochemical characterization of the nsp12-nsp7-nsp8 core polymerase complex from SARS-CoV-2. Cell Rep. 2020;31:107774.PubMedPubMedCentralCrossRef
147.
Jang K-J, Jeong S, Kang DY, Sp N, Yang YM, Kim D-E. A high ATP concentration enhances the cooperative translocation of the SARS coronavirus helicase nsP13 in the unwinding of duplex RNA. Sci Rep. 2020;10:4481.PubMedPubMedCentralCrossRef
148.
Yuen CK, Lam JY, Wong WM, Mak LF, Wang X, Chu H, Cai JP, Jin DY, To KK, Chan JF, et al. SARS-CoV-2 nsp13, nsp14, nsp15 and orf6 function as potent interferon antagonists. Emerg Microbes Infect. 2020;9:1418–28.PubMedPubMedCentralCrossRef
149.
Shu T, Huang M, Wu D, Ren Y, Zhang X, Han Y, Mu J, Wang R, Qiu Y, Zhang DY, Zhou X. SARS-coronavirus-2 Nsp13 possesses NTPase and RNA helicase activities that can be inhibited by bismuth salts. Virol Sin. 2020;35:321–9.PubMedCrossRefPubMedCentral
150.
Ogando NS, Zevenhoven-Dobbe JC, van der Meer Y, Bredenbeek PJ, Posthuma CC, Snijder EJ. The enzymatic activity of the nsp14 exoribonuclease is critical for replication of MERS-CoV and SARS-CoV-2. J Virol. 2020;94.
151.
Kim Y, Jedrzejczak R, Maltseva NI, Wilamowski M, Endres M, Godzik A, Michalska K, Joachimiak A. Crystal structure of Nsp15 endoribonuclease NendoU from SARS-CoV-2. Protein Sci. 2020;29:1596–605.PubMedCrossRefPubMedCentral
152.
Zhang L, Li L, Yan L, Ming Z, Jia Z, Lou Z, Rao Z. Structural and biochemical characterization of endoribonuclease Nsp15 encoded by Middle East respiratory syndrome coronavirus. J Virol. 2018;92.
153.
Wang Y, Sun Y, Wu A, Xu S, Pan R, Zeng C, Jin X, Ge X, Shi Z, Ahola T, et al. Coronavirus nsp10/nsp16 methyltransferase can be targeted by nsp10-derived peptide in vitro and in vivo to reduce replication and pathogenesis. J Virol. 2015;89:8416–27.PubMedPubMedCentralCrossRef
154.
155.
156.
157.
158.
159.
160.
161.
162.
163.
164.
165.
166.
167.
168.
169.
WHO. Draft landscape of COVID-19 candidate vaccines. Geneva: WHO; 2020.
170.
171.
172.
173.
Gautret P, Lagier JC, Parola P, Hoang VT, Meddeb L, Mailhe M, Doudier B, Courjon J, Giordanengo V, Vieira VE, et al. Hydroxychloroquine and azithromycin as a treatment of COVID-19: results of an open-label non-randomized clinical trial. Int J Antimicrob Agents. 2020:105949.
174.
Gao J, Tian Z, Yang X. Breakthrough: chloroquine phosphate has shown apparent efficacy in treatment of COVID-19 associated pneumonia in clinical studies. Biosci Trends. 2020;14:72–3.PubMedCrossRef
175.
Cai Q, Yang M, Liu D, Chen J, Shu D, Xia J, Liao X, Gu Y, Cai Q, Yang Y, et al. Experimental treatment with favipiravir for COVID-19: an open-label control study. Engineering. 2020.
176.
177.
178.
179.
180.
181.
Chen P, Nirula A, Heller B, Gottlieb RL, Boscia J, Morris J, Huhn G, Cardona J, Mocherla B, Stosor V, et al. SARS-CoV-2 neutralizing antibody LY-CoV555 in outpatients with Covid-19. N Engl J Med. 2020.
182.
183.
184.
Metadata
Title
SARS coronavirus 2: from genome to infectome
Authors
Meghana Rastogi
Neha Pandey
Astha Shukla
Sunit K. Singh
Publication date
01-12-2020
Publisher
BioMed Central
Published in
Respiratory Research / Issue 1/2020
Electronic ISSN: 1465-993X
DOI
https://doi.org/10.1186/s12931-020-01581-z

Other articles of this Issue 1/2020

Respiratory Research 1/2020 Go to the issue

Review

Assessment of comorbidities and prognosis in patients with COPD diagnosed with the fixed ratio and the lower limit of normal: a systematic review and meta-analysis

Research

An authoritative algorithm most appropriate for the prediction of pulmonary embolism in patients with AECOPD

Research

Thymosin β10 promotes tumor-associated macrophages M2 conversion and proliferation via the PI3K/Akt pathway in lung adenocarcinoma

Research

Prevalence and distribution patterns of allergens among children with asthma and asthma-like symptoms in Shanghai, China

Correction

Correction to: The ‘can do, do do’ concept in COPD; quadrant interpretation, affiliation and tracking longitudinal changes

Research

Patient and site characteristics associated with pirfenidone and nintedanib use in the United States; an analysis of idiopathic pulmonary fibrosis patients enrolled in the Pulmonary Fibrosis Foundation Patient Registry
Obesity Clinical Trial Summary

At a glance: The STEP trials

Read more

A round-up of the STEP phase 3 clinical trials evaluating semaglutide for weight loss in people with overweight or obesity.

Developed by: Springer Medicine

Highlights from the ACC 2024 Congress

Year in Review: Pediatric cardiology

Pediatric Cardiology Video

Watch Dr. Anne Marie Valente present the last year's highlights in pediatric and congenital heart disease in the official ACC.24 Year in Review session.

Year in Review: Pulmonary vascular disease

Cardiopulmonary Comorbidity Video

The last year's highlights in pulmonary vascular disease are presented by Dr. Jane Leopold in this official video from ACC.24.

Year in Review: Valvular heart disease

Valvular Heart Disease Video

Watch Prof. William Zoghbi present the last year's highlights in valvular heart disease from the official ACC.24 Year in Review session.

Year in Review: Heart failure and cardiomyopathies

Heart Failure Video

Watch this official video from ACC.24. Dr. Biykem Bozkurt discusses last year's major advances in heart failure and cardiomyopathies.

ACC 2024 Congress Coverage

Year in Review: Heart failure and cardiomyopathies

Heart Failure Video

Watch this official video from ACC.24. Dr. Biykem Bozkurt discusses last year's major advances in heart failure and cardiomyopathies.

Watch now

Semaglutide benefits people with type 2 diabetes and obesity-related heart failure

16-04-2024 Type 2 Diabetes News

Incentivised to exercise

11-04-2024 Lifestyle Modifications News

New intervention for STEMI-related cardiogenic shock

10-04-2024 Myocardial Infarction News

» View more highlights on the ACC 2024 congress hub page

Image Credits