PT  - JOURNAL ARTICLE
AU  - Abdullah M. Syed
AU  - Taha Y. Taha
AU  - Mir M. Khalid
AU  - Takako Tabata
AU  - Irene P. Chen
AU  - Bharath Sreekumar
AU  - Pei-Yi Chen
AU  - Jennifer M. Hayashi
AU  - Katarzyna M. Soczek
AU  - Melanie Ott
AU  - Jennifer A. Doudna
TI  - Rapid assessment of SARS-CoV-2 evolved variants using virus-like particles
AID  - 10.1101/2021.08.05.455082
DP  - 2021 Jan 01
TA  - bioRxiv
PG  - 2021.08.05.455082
4099  - http://biorxiv.org/content/early/2021/08/05/2021.08.05.455082.short
4100  - http://biorxiv.org/content/early/2021/08/05/2021.08.05.455082.full
AB  - Newly evolved SARS-CoV-2 variants are driving ongoing outbreaks of COVID-19 around the world. Efforts to determine why these viral variants have improved fitness are limited to mutations in the viral spike (S) protein and viral entry steps using non-SARS-CoV-2 viral particles engineered to display S. Here we show that SARS-CoV-2 virus-like particles can package and deliver exogenous transcripts, enabling analysis of mutations within all structural proteins and rapid dissection of multiple steps in the viral life cycle. Identification of an RNA packaging sequence was critical for engineered transcripts to assemble together with SARS-CoV-2 structural proteins S, nucleocapsid (N), membrane (M) and envelope (E) into non-replicative SARS-CoV-2 virus-like particles (SC2-VLPs) that deliver these transcripts to ACE2- and TMPRSS2-expressing cells. Using SC2-VLPs, we tested the effect of 30 individual mutations within the S and N proteins on particle assembly and entry. While S mutations unexpectedly did not affect these steps, SC2-VLPs bearing any one of four N mutations found universally in more-transmissible viral variants (P199L, S202R, R203M and R203K) showed increased particle production and up to 10-fold more reporter transcript expression in receiver cells. Our study provides a platform for rapid testing of viral variants outside a biosafety level 3 setting and identifies viral N mutations and viral particle assembly as mechanisms to explain the increased spread of current viral variants, including Delta (N:R203M).One-Sentence Summary R203M substitution within SARS-CoV-2 N, found in delta variant, improves RNA packaging into virus-like particles by 10-fold.Competing Interest StatementThe authors have declared no competing interest.