The proximal origin of SARS-CoV-2

The rapid spread of COVID-19, caused by SARS-CoV-2, necessitates understanding its origins. SARS-CoV-2 is the seventh known coronavirus to infect humans, with three causing severe disease (SARS-CoV, MERS-CoV, and SARS-CoV-2). This study uses comparative genomic analysis of SARS-CoV-2 and related coronaviruses to investigate its origins, addressing the crucial question of whether it emerged through natural processes or laboratory manipulation. The implications for future pandemic prevention are highlighted, emphasizing the importance of understanding the species jump mechanisms of zoonotic viruses.

The paper reviews existing knowledge on coronaviruses known to infect humans, distinguishing between those causing mild and severe symptoms. It draws upon previous research on the receptor-binding domain (RBD) of SARS-CoV-like viruses and its role in determining host range and the importance of polybasic cleavage sites in viral infectivity and host range. Prior studies on the insertion of furin cleavage sites in coronaviruses and avian influenza viruses are referenced to understand the potential implications of the polybasic cleavage site in SARS-CoV-2.

The study primarily relies on comparative genomic analysis of SARS-CoV-2 and related coronaviruses, including bat and pangolin coronaviruses. The authors compare the genome sequences, focusing on two key features: the receptor-binding domain (RBD) in the spike protein and the polybasic furin cleavage site. Phylogenetic analysis is implicitly used to determine relationships between viruses. Structural studies and biochemical experiments from other publications are cited to support the interpretation of genomic data and to understand the functional implications of the identified features. The authors also discuss various scenarios for the origin of SARS-CoV-2, including natural selection in an animal host before zoonotic transfer, natural selection in humans after zoonotic transfer, and the possibility of selection during passage in a laboratory setting. These scenarios are evaluated based on the genomic evidence and existing knowledge of coronavirus evolution.

The analysis reveals two significant genomic features of SARS-CoV-2: (1) an RBD optimized for binding to human ACE2 receptors, and (2) a functional polybasic (furin) cleavage site at the S1-S2 boundary. The RBD shows mutations compared to SARS-CoV that enhance binding to human ACE2, suggesting adaptation for human infection. The polybasic cleavage site is unique to SARS-CoV-2 among lineage B betacoronaviruses, potentially influencing viral infectivity and transmissibility. While the closest known relative of SARS-CoV-2 is a bat coronavirus (RaTG13), it differs significantly in the RBD. However, pangolin coronaviruses show strong similarity to SARS-CoV-2 in the RBD, but not in the polybasic cleavage site. The authors evaluate several hypotheses for SARS-CoV-2's origin: Natural selection in an animal host before zoonotic transfer, natural selection in humans after zoonotic transfer, and selection during passage in a lab are all considered. The analysis strongly argues against laboratory manipulation as the origin of SARS-CoV-2 due to the complexity of the RBD adaptations and the absence of genetic evidence supporting the use of established reverse-genetic systems. The high affinity binding of SARS-CoV-2 to human ACE2 is best explained by natural selection.

The findings strongly suggest a natural origin for SARS-CoV-2, with two plausible scenarios: pre-adaptation in an animal host with subsequent zoonotic transfer, or adaptation in humans following zoonotic transfer. The pangolin coronaviruses are significant because they possess an RBD nearly identical to SARS-CoV-2, suggesting that the RBD adaptation may have occurred in an intermediate animal host. The acquisition of the polybasic cleavage site remains unclear, with both scenarios being possible. The absence of a known progenitor virus and the complexity of the observed genomic features weigh against the laboratory origin hypothesis. The paper highlights the need for continued surveillance of animal coronaviruses to identify potential intermediate hosts and better understand the evolutionary pathways leading to pandemics. It emphasizes the importance of identifying related viral sequences from animal sources as the most definitive method for confirming viral origins.

The study concludes that SARS-CoV-2 is highly unlikely to have been a product of laboratory manipulation. Instead, natural selection, either in an animal host or within humans, is the most probable explanation for the emergence of SARS-CoV-2. Future research should focus on identifying intermediate animal hosts, sequencing viruses from very early cases, and continued surveillance for similar viruses to prevent future zoonotic events.

The study's limitations include the incomplete sampling of coronavirus diversity in animals, making it difficult to definitively identify the direct progenitor of SARS-CoV-2. While pangolin coronaviruses provide important insights into RBD evolution, the absence of a polybasic cleavage site in these viruses remains a gap in the understanding of SARS-CoV-2's origins. Further serological studies are needed to determine the extent of prior human exposure to SARS-CoV-2 to better understand the possibility of undetected transmission before the pandemic onset.