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Front. Med.    2024, Vol. 18 Issue (1) : 1-18    https://doi.org/10.1007/s11684-024-1066-6
Emergence of SARS and COVID-19 and preparedness for the next emerging disease X
Ben Hu1, Hua Guo1, Haorui Si1,2, Zhengli Shi1()
1. CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
2. University of Chinese Academy of Sciences, Beijing 100049, China
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Abstract

Severe acute respiratory syndrome (SARS) and coronavirus disease 2019 (COVID-19) are two human coronavirus diseases emerging in this century, posing tremendous threats to public health and causing great loss to lives and economy. In this review, we retrospect the studies tracing the molecular evolution of SARS-CoV, and we sort out current research findings about the potential ancestor of SARS-CoV-2. Updated knowledge about SARS-CoV-2-like viruses found in wildlife, the animal susceptibility to SARS-CoV-2, as well as the interspecies transmission risk of SARS-related coronaviruses (SARSr-CoVs) are gathered here. Finally, we discuss the strategies of how to be prepared against future outbreaks of emerging or re-emerging coronaviruses.
Keywords SARS      COVID-19      coronavirus     
Corresponding Author(s): Zhengli Shi   
About author:

Li Liu and Yanqing Liu contributed equally to this work.
Just Accepted Date: 26 February 2024   Online First Date: 27 March 2024    Issue Date: 22 April 2024
 Cite this article:   
Ben Hu,Hua Guo,Haorui Si, et al. Emergence of SARS and COVID-19 and preparedness for the next emerging disease X[J]. Front. Med., 2024, 18(1): 1-18.
 URL:  
https://academic.hep.com.cn/fmd/EN/10.1007/s11684-024-1066-6
https://academic.hep.com.cn/fmd/EN/Y2024/V18/I1/1
Fig.1  Phylogenetic analysis of the full-length RdRp gene sequences of SARSr-CoVs. The trees were constructed by the Maximum-likelihood method using the Jukes-Cantor model with bootstrap values determined by 1000 replicates. The scale bars represent 0.05 substitutions per nucleotide position. Ra, Rhinolophus affinis; Rs or Rst, Rhinolophus stheno; Rsh, Rhinolophus shameli; Rp, Rhinolophus pusilus; Rac, Rhinolophus acuminatus; Rm, Rhinolophus malayanus; Rc, Rhinolophus cornutus. The percentage numbers in the parentheses refer to the complete genome sequence identity of each SARS-CoV-2-like coronavirus to SARS-CoV-2.
Fig.2  Possible transmission chains of SARS-CoV and SARS-CoV-2. SARS-CoV likely first spilled over from its bat reservoir to palm civet or other game animals, and was then transmitted to humans in the wet markets from this intermediate host. The spillover of the SARS-CoV-2 ancestral virus likely occurred from bats or pangolins, but the direct transmission of SARS-CoV-2 to humans could be from some unidentified intermediate hosts. SARS-CoV-2 may have gone through adaptive evolution in the intermediate hosts and/or in humans for a period prior to the outbreak. It cannot be ruled out that the outbreak was caused by contaminated cold-chain food products and the spreading was facilitated in the market.
PrimatesChiropteraPholidotaRodentiaPerissodactylaLagomorphaCarnivoraArtiodactylaGaliformes
HumanMonkeyBatPangolinHamsterRatMouseHorseRabbitFerretCivetRaccoon dogCatDogFoxMinkBovinePigGoatChick
Clade 1 (without deletion)SARS-CoV-2****************NN**********************N
BANAL-236****–––––––––––––––––––
Pangolin-CoV-GD************–********–N********–**Y**N
RaTG13****–****–N****–***–
Pangolin-CoV-GX***********–******–N********–**Y**N
SARS-CoV*************NN****************–******N
WIV1**Y***––N–––*–––––––––
Clade 1 (one deletion)Rc-o0319N–*–––––––––––––––––
BtKY72N–*N––N–––––––––––––
RaTG15N–**––––––––––––––––
RmYN04*–––––––––––––––––––
Clade 2 (two deletions)RmYN02N–NN––N–––––––––––––
RacCS203N–N–––––––––––––––––
Rp3NNNN––N–––––––––––––
Tab.1  Susceptibility of different animal species to SARSr-CoVs
Fig.3  Alignment of the receptor binding motif (RBM) in SARSr-CoVs. (A) Schematic diagram of the spike protein of SARS-CoV-2. The residue numbers of each region correspond to their positions in the S protein. (B) Maximum-likelihood phylogeny of sarbecovirus RBDs, constructed from RBD amino acid sequences. The scale bars represent 0.1 substitutions per amino acid position, bootstrap values determined by 1000 replicates. (C) RBM sequences of SARS-CoV, SARS-CoV-2, and representative SARSr-CoVs from different clades were aligned. The clade 1 is in pink and clade 2 is in light blue. The six key residues that contact ACE2 directly are highlighted in green. The red boxes represent deletions in the RBM. CP, cytoplasmic domain; FP, fusion peptide; HR1, heptad repeat 1; HR2, heptad repeat 2; NTD, N-terminal domain; SP, signal peptide; TM, transmembrane domain.
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