Rapid assessment of SARS-CoV-2-evolved variants using virus-like particles

• Published in: Science (American Association for the Advancement of Science) 2021-12, Vol.374 (6575), p.1626-1632
• Main Authors: Syed, Abdullah M, Taha, Taha Y, Tabata, Takako, Chen, Irene P, Ciling, Alison, Khalid, Mir M, Sreekumar, Bharath, Chen, Pei-Yi, Hayashi, Jennifer M, Soczek, Katarzyna M, Ott, Melanie, Doudna, Jennifer A
• Format: Article
• Language: English
• Subjects: Animals; Artificial Virus-Like Particles; Assembly; Assessments; Biological effects; Biology; Biosafety; Cell Line; Coronavirus Envelope Proteins - genetics; Coronavirus Envelope Proteins - metabolism; Coronavirus Nucleocapsid Proteins - genetics; Coronavirus Nucleocapsid Proteins - metabolism; Coronaviruses; COVID-19; Evolution, Molecular; Gene expression; Genetics; Genome, Viral; Humans; Life cycles; Methionine; Mutation; Nucleocapsids; Packaging; Phosphoproteins - genetics; Phosphoproteins - metabolism; Plasmids; Producer cells; Proteins; Respiratory diseases; RNA, Messenger - genetics; SARS-CoV-2 - genetics; SARS-CoV-2 - physiology; Science & Technology - Other Topics; Severe acute respiratory syndrome coronavirus 2; Spike Glycoprotein, Coronavirus - genetics; Spike Glycoprotein, Coronavirus - metabolism; Structural proteins; Viral diseases; Viral Genome Packaging; Viral Matrix Proteins - genetics; Viral Matrix Proteins - metabolism; Virus Internalization; Virus-like particles; Viruses
• ISSN: 0036-8075; 1095-9203
• DOI: 10.1126/science.abl6184

Efforts to determine why new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants demonstrate improved fitness have been limited to analyzing mutations in the spike (S) protein with the use of S-pseudotyped particles. In this study, we show that SARS-CoV-2 virus-like particles (SC2-VLPs) can package and deliver exogenous transcripts, enabling analysis of mutations within all structural proteins and at multiple steps in the viral life cycle. In SC2-VLPs, four nucleocapsid (N) mutations found universally in more-transmissible variants independently increased messenger RNA delivery and expression ~10-fold, and in a reverse genetics model, the serine-202→arginine (S202R) and arginine-203→methionine (R203M) mutations each produced >50 times as much virus. SC2-VLPs provide a platform for rapid testing of viral variants outside of a biosafety level 3 setting and demonstrate N mutations and particle assembly to be mechanisms that could explain the increased spread of variants, including B.1.617.2 (Delta, which contains the R203M mutation).