Live attenuated virus vaccine protects against SARS-CoV-2 variants of concern B.1.1.7 (Alpha) and B.1.351 (Beta)

Abstract

Vaccines are instrumental and indispensable in the fight against the COVID-19 pandemic. Several recent SARS-CoV-2 variants are more transmissible and evade infection- or vaccine-induced protection. We constructed live attenuated vaccine candidates by large-scale recoding of the SARS-CoV-2 genome and showed that the lead candidate, designated sCPD9, protects Syrian hamsters from a challenge with ancestral virus. Here, we assessed immunogenicity and protective efficacy of sCPD9 in the Roborovski dwarf hamster, a nontransgenic rodent species that is highly susceptible to SARS-CoV-2 and severe COVID-19–like disease. We show that a single intranasal vaccination with sCPD9 elicited strong cross-neutralizing antibody responses against four current SARS-CoV-2 variants of concern, B.1.1.7 (Alpha), B.1.351 (Beta), B.1.1.28.1 (Gamma), and B.1.617.2 (Delta). The sCPD9 vaccine offered complete protection from COVID-19–like disease caused by the ancestral SARS-CoV-2 variant B.1 and the two variants of concern B.1.1.7 and B.1.351.

Fig. 1.. Live attenuated virus vaccine candidate sCPD9s is strongly attenuated and protects Roborovski dwarf hamsters from challenge with B.1, B.1.1.7, and B.1.351 viruses.

(A) Schematic representation of the genome of the live attenuated virus sCPD9. The SARS-CoV-2 genome is a single-stranded, positive-sense mRNA molecule of approximately 30,000 nucleotides (nt), which encodes 11 canonical open reading frames (ORFs; blue arrows). After infection, ORF 1a/1ab is directly translated and cleaved into 15 proteins that constitute the replication-transcription complex. The genome of the sCPD9 vaccine candidate contains a 1,146-nt-long, recoded, codon pair–deoptimized sequence (red segment of the ORF 1ab). The recoded sequence is located near the 3′ end of ORF 1ab and encodes the nonstructural proteins endoribonuclease and 2′O-ribose methyltransferase (2′-O-MT). Nsp, nonstructural protein; 3CL-Pro, 3C-like proteinase; RdRp, RNA-dependent RNA polymerase; ExoN, 3′-to-5′ exoribonuclease; NendoU, endoribonuclease. (B) Body weight change of Roborovski dwarf hamsters after vaccination. The thick black lines show median, and the thin lines show the quartiles. (C) Viral load in the upper (oropharyngeal swab) and lower (lungs) respiratory tract and the number of infectious virus particles detected in 50 mg of lung tissue (lung titers) on day 3 after vaccination. (D) Body weight change of Roborovski dwarf hamsters after challenge with pathogenic B.1, B.1.1.7, or B.1.351 viruses. (E and F) Viral load in the upper (E) and lower (F) respiratory tracts of animals on days 2, 3, 5, and 5 after challenge. (G) Number of infectious virus particles detected in 50 mg of lung tissue on days 2, 3, and 5 after challenge. (B) and (C) were adapted from (21).

Fig. 2.. Pulmonary histopathology of mock/sCPD9-vaccinated and challenged Roborovski dwarf hamsters on days 2 (left column), 3 (middle column), or 5 (right column) after challenge.

(A to T) Representative photomicrographs of hematoxylin and eosin (H&E)–stained, formalin-fixed, and paraffin-embedded lung tissue of infected hamsters. sCPD9-vaccinated hamsters were challenged with B.1, B.1.1.7, or B.1.351 virus on day 21 after vaccination. The lungs of sCPD9-vaccinated hamsters that were challenge-infected with three different SARS-CoV-2 variants showed very similar pulmonary morphology. Bronchioles had regular, columnar bronchiolar epithelium on days 2 and 3 after challenge (A, C, F, H, K, and M). Alveoli on days 3 (B, G, and L) and 5 after challenge (D, E, I, J, N, and O) showed mild to moderate infiltration by macrophages and few neutrophils with scattered mild alveolar edema (asterisk). In contrast, mock-vaccinated hamsters challenge-infected with the ancestral SARS-CoV-2 variant B.1 displayed typical lesions of COVID-19 at all times tested (P to T). After 2 days, the bronchiolar epithelium was flattened due to necrosis of bronchiolar epithelial cells and necrotic cellular debris, and degenerate neutrophils and macrophages were present in the bronchiolar lumen (hash) (P). In the course of disease, there was moderate to severe bronchiointerstitial pneumonia with necrosis of alveolar epithelial cells and massive infiltration by macrophages and neutrophils in the alveolar septa and alveolar spaces (Q). Similarly, bronchiolar epithelium was infiltrated by an increasing number of neutrophils (arrow) intraluminal cellular debris was accumulating (hash) (R). On day 5 after challenge, lungs showed predominantly interstitial pneumonia with remnants of alveolar edema fluid (asterisk) (S), neutrophils (T, arrow), and an increasing number of macrophages with prominently foamy cytoplasm (T, arrowhead). Scale bars, 50 μm (A, B, D, F, G, I, K, L, N, P, Q, and S) and 20 μm (C, E, H, J, M, O, R, and T).

Fig. 3.. Sensitivity of SARS-CoV-2 variants B.1, B.1.1.7 (Alpha), B.1.351 (Beta), B.1.128.1 (Gamma), and B.1.617.2 (Delta) to neutralization by antibodies in sera of sCPD9-vaccinated Roborovski dwarf hamsters.

(A) Neutralizing antibody titers of hamster sera collected on days 2 and 3 after challenge. Geometric mean and SD of the respective group titers are shown. The Kruskal-Wallis test with Dunn’s post hoc test showed that hamster sera neutralized the virus variants B.1.351, B.1.128.1, and B.1.617.2 significantly less efficiently than variants B.1 or B.1.1.7 (*P = 0.0264, **P = 0.0012, *** P < 0.001, and ****P < 0.0001). (B) Titers of neutralizing antibodies are plotted as a function of challenge virus. (C) Ratios of serum neutralization titers against different virus variants. The ratios show to which extent each hamster serum neutralizes different virus variants. The ratios of the neutralization titers of individual sera, the geometric mean, and the SD are shown. The geometric mean is also displayed as a number in the upper part of the diagram.