The origins of SARS-CoV-2 remain a subject of intense debate, with the dominant zoonotic hypothesis facing increasing scrutiny. This study employs restriction site analysis, a forensic genomic approach, to determine whether SARS-CoV-2 exhibits patterns consistent with natural viral evolution or synthetic genome assembly. By analyzing the distribution of restriction sites for BsaI and BsmBI—enzymes frequently used in laboratory-based reverse genetics—this study identifies a highly atypical restriction site architecture in SARS-CoV-2. Unlike natural sarbecoviruses, which show randomly distributed restriction sites, SARS-CoV-2 exhibitssegregated site placement and a statistically improbable depletion of restriction sites, features strongly associated with laboratory-engineered viruses. The probability that such a pattern arose naturally is less than one in a billion, a finding that directly aligns with known synthetic virology techniques. Additionally, seven synonymous mutations separate SARS-CoV-2 from RaTG13 at restriction sites—an event so unlikely through natural evolution that it further supports the hypothesis of deliberate genome modification. Given that the Wuhan Institute of Virology (WIV) has previously published methods utilizing these restriction enzymes for synthetic virus assembly, this study underscores the need for greater transparency in pandemic origin research. Further supporting this, an analysis of international research collaborations in synthetic coronavirus studies highlights WIV’s central role in a network of institutions specializing in infectious clone development, including the University of North Carolina at Chapel Hill, the University of Texas Medical Branch, and the National Institutes of Health. These findings suggest that SARS-CoV-2’s genomic architecture is more consistent with an engineered virus than one shaped by natural selection, warranting further investigation into the laboratory-origin hypothesis.