Induction of significant neutralizing antibodies against SARS-CoV-2 by a highly attenuated pangolin coronavirus variant with a 104nt deletion at the 3'-UTR

ABSTRACT

SARS-CoV-2 related coronaviruses (SARS-CoV-2r) from Guangdong and Guangxi pangolins have been implicated in the emergence of SARS-CoV-2 and future pandemics. We previously reported the culture of a SARS-CoV-2r GX_P2V from Guangxi pangolins. Here we report the GX_P2V isolate rapidly adapted to Vero cells by acquiring two genomic mutations: an alanine to valine substitution in the nucleoprotein and a 104-nucleotide deletion in the hypervariable region (HVR) of the 3′-terminus untranslated region (3′-UTR). We further report the characterization of the GX_P2V variant (renamed GX_P2V(short_3UTR)) in in vitro and in vivo infection models. In cultured Vero, BGM and Calu-3 cells, GX_P2V(short_3UTR) had similar robust replication kinetics, and consistently produced minimum cell damage. GX_P2V(short_3UTR) infected golden hamsters and BALB/c mice but was highly attenuated. Golden hamsters infected intranasally had a short duration of productive infection in pulmonary, not extrapulmonary, tissues. These productive infections induced neutralizing antibodies against pseudoviruses of GX_P2V and SARS-CoV-2. Collectively, our data show that the GX_P2V(short_3UTR) is highly attenuated in in vitro and in vivo infection models. Attenuation of the variant is likely partially due to the 104-nt deletion in the HVR in the 3′-UTR. This study furthers our understanding of pangolin coronaviruses pathogenesis and provides novel insights for the design of live attenuated vaccines against SARS-CoV-2.

KEYWORDS:

• Coronavirus
• SARS-CoV-2
• pangolin coronavirus
• neutralizing antibody
• live attenuated vaccine

Acknowledgements

We thank Harlan D. Caldwell for critical review of the manuscript. The funding sources had no role in the study design, data collection, analysis, interpretation, or writing of the report.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Additional information

Funding

This research was supported by NSFC-MFST projects (China–Mongolia) [grant numbers 32161143027 and 31961143024], Inner Mongolia Key Research and Development Program [grant number 2019ZD006], Funds for First-class Discipline Construction [grant numbers XK1805 and XK1803-06], National Key Research and Development Program of China [grant numbers 2018YFA0903000, 2020YFC2005405, 2020YFA0712100, 2020YFC0840805, 19SWAQ06, 20SWAQX27 and 20SWAQK22], Fundamental Research Funds for Central Universities [grant numbers BUCTRC201917 and BUCTZY2022], Military Biosecurity Research Program [grant number BWS21J025].