The B.1.427/1.429 (epsilon) SARS-CoV-2 variants are more virulent than ancestral B.1 (614G) in Syrian hamsters

Abstract

As novel SARS-CoV-2 variants continue to emerge, it is critical that their potential to cause severe disease and evade vaccine-induced immunity is rapidly assessed in humans and studied in animal models. In early January 2021, a novel SARS-CoV-2 variant designated B.1.429 comprising 2 lineages, B.1.427 and B.1.429, was originally detected in California (CA) and it was shown to have enhanced infectivity in vitro and decreased antibody neutralization by plasma from convalescent patients and vaccine recipients. Here we examine the virulence, transmissibility, and susceptibility to pre-existing immunity for B 1.427 and B 1.429 in the Syrian hamster model. We find that both variants exhibit enhanced virulence as measured by increased body weight loss compared to hamsters infected with ancestral B.1 (614G), with B.1.429 causing the most marked body weight loss among the 3 variants. Faster dissemination from airways to parenchyma and more severe lung pathology at both early and late stages were also observed with B.1.429 infections relative to B.1. (614G) and B.1.427 infections. In addition, subgenomic viral RNA (sgRNA) levels were highest in oral swabs of hamsters infected with B.1.429, however sgRNA levels in lungs were similar in all three variants. This demonstrates that B.1.429 replicates to higher levels than ancestral B.1 (614G) or B.1.427 in the oropharynx but not in the lungs. In multi-virus in-vivo competition experiments, we found that B.1. (614G), epsilon (B.1.427/B.1.429) and gamma (P.1) dramatically outcompete alpha (B.1.1.7), beta (B.1.351) and zeta (P.2) in the lungs. In the nasal cavity, B.1. (614G), gamma, and epsilon dominate, but the highly infectious alpha variant also maintains a moderate size niche. We did not observe significant differences in airborne transmission efficiency among the B.1.427, B.1.429 and ancestral B.1 (614G) and WA-1 variants in hamsters. These results demonstrate enhanced virulence and high relative oropharyngeal replication of the epsilon (B.1.427/B.1.429) variant in Syrian hamsters compared to an ancestral B.1 (614G) variant.

Fig 1. Change in body weight and lung histopathology scores in hamsters after intranasal inoculation with B.1 (614G), B.1.427 and B.1.429.

A) Change in body weight relative to the day of inoculation. Mean values of all groups were compared using a Kruskal-Wallis test, and a post-hoc Dunn multiple comparison test was used to compare the mean values of the 427 (N = 25) or 429 (N = 18) groups individually to the 614G (N = 22) group), each dot is the weight of a single animal. B) Total lung histopathology score (see Materials and Methods for explanation), each dot is the score of a single animal. C) Lung vascular histopathology score (see Materials and Methods for explanation), each dot is the score of a single animal. The top of the bars indicates mean values in B and C.

Fig 2. Lung histopathology in hamsters after intranasal inoculation with B.1.429 is more acute and prolonged than in hamsters inoculated with B.1 (614G) and B.1.427.

A, F, K) Sub-gross histology of normal lungs from uninfected hamsters. Top row: Sub-gross histology of B.1 (614G) infection after B) 2 days PI, C) 4 days PI, D) 6 days PI, E) 10 days PI. Middle row: Sub-gross histology of B.1.427 infection after G) 2 days PI, H) 4 days PI, I) 6 days PI, J) 10 days PI. Bottom row: Sub-gross histology of B.1.429 infection after L) 2 days PI, M) 4 days PI, N) 6 days PI, O) 10 days PI. Asterisks = foci of inflammation, necrosis and/or hemorrhage. Hematoxylin and eosin stain. Original magnification: 1x. Scale bars equal 1 mm.

Fig 3. The nature of lung histopathology in hamsters after intranasal inoculation with B.1 (614G), B.1.427 and B.1.429 is similar.

A, F, K) histology of normal lungs from uninfected hamsters. Top row: Histology of B.1 (614G) infection after B) 2 days PI, C) 4 days PI, D) 6 days PI, E) 10 days PI. Middle row: Histology of B.1.427 infection after G) 2 days PI, H) 4 days PI, I) 6 days PI, J) 10 days PI. Bottom row: Histology of B.1.429 infection after L) 2 days PI, M) 4 days PI, inset: and Perivascular cuffing with endothelium of a small vessel lifted off basal lamina by inflammatory infiltrate of lymphocytes and a few polymorphonuclear leukocytes (PMNs). N) 6 days PI, inset: multinucleate syncytial giant cell in bronchiolar epithelium. O) 10 days PI. Asterisks = mixed inflammatory infiltrate (lymphocytes, PMNs and macrophages); arrowheads = suppurative bronchiolitis with rupture of bronchiolar wall; arrows = endothelialitis; circles = foci of type II pneumocyte hyperplasia. Hematoxylin and eosin stain. Original magnification: 100x. Scale bars equal 50 um, Inset scale bars equal 20 um.

Fig 4. Distribution of SARS-CoV-2 RNA+ cells in lungs of hamsters after intranasal inoculation with B.1 (614G), B.1.427 and B.1.429 by in-situ hybridization (ISH).

Sub-gross histology and magnified regions (inset) of ISH-labeled lung sections from hamsters infected with B.1 (614G) for A) 2 days PI, B) 4 days PI, C) 6 days PI and D) 10 days PI; or B.1.427 for E) 2 days PI, F) 4 days PI, G) 6 days PI and H) 10 days PI; or B.1.429 for I) 2 days PI, J) 4 days PI, K) 6 days PI and L) 10 days PI. Cells labeled by riboprobe in-situ hybridization stain red. Arrows = labeled bronchial/bronchiolar epithelial cells lining airways; asterisks = regions of lung parenchyma with labeled alveolar septal cells (type I/II pneumocytes and macrophages). Original magnification: 1x. Scale bars equal 1 mm. Inset scale bars equal 50 um.

Fig 5. Viral loads in hamsters after intranasal inoculation with B.1 (614G), B.1.427 or B.1.429.

A) sg RNA copies in oral swabs collected daily until day 4 or necropsy. Mean values of all groups were compared using a Kruskal-Wallis test, and a post-hoc Dunn multiple comparison test was used to compare the mean values of the B.1.427 (N = 16) or B.1.429 (N = 18) groups individually to the 614G group (N = 16). No significant differences between the groups were found using this approach. In addition, a Mann Whitney test was used to compare the daily mean sgRNA value of the B.1.429 and B.1.427 groups individually to the other 2 groups. Significant differences are noted by a line and numerical p value. B) sgRNA copies in upper respiratory tract (URT) washes collected at necropsy at 2, 4, 6 or days 10 PI. D) sgRNA copies in lungs collected at necropsy at 2, 4, 6 or days 10 PI. D) Infectious virus titers in lungs collected at necropsy at 2, 4, 6 or 10 days PI. The limit of quantitation for the PCR assay (125 copies per reaction) is indicated by the dotted line. Each dot is the sgRNA level or viral titer in a sample from one animal.

Fig 6. The proportion of each virus in hamsters after intranasal inoculation with a 1:1 or 9:1 mixed inoculum of B.1 (614G) and B.1.427; and sgRNA levels in hamsters inoculated with a mixed inoculum of 7 SARS-CoV-2 variants: B.1 (614G), B.1.427, B.1.427, P.1, P.2, B.1.1.7 and B.1.351.

A) proportion of the vRNA in URT washes collected at necropsy at 2 and 4 days PI that was B.1.427. B) proportion of the vRNA in lung collected at necropsy at 2 and 4 days PI that was B.1.427.

Fig 7. Relative levels of SARS-CoV-2 variants in hamsters after intranasal inoculation with a mixed inoculum of 7 SARS-CoV-2 variants: B.1 (614G), B.1.427, B.1.429, P.1, P.2, B.1.1.7 and B.1.351.

A) Proportion of each variant RNA in the total vRNA of each virus stock and the mixed inoculum. B) Frequency of each variant RNA in the total vRNA found in the URT washes of hamsters at day 2 PI. C) and day 4 PI. D) Frequency of each variant RNA in the total vRNA found in the lungs of hamsters at day 2 PI. E) and day 4 PI. In all panels, each dot represents the frequency of that variant in one sample. Each animal is denoted by a color.

Fig 8. Prior infection with B.1 (614G) protects the lungs of hamsters from subsequent challenge with B.1.427 or B.1.429.

A) sgRNA levels and infectious virus titer in lungs of hamsters infected with B.1 (614G) and necropsied at 2 days (N = 5) and 21 days PI (N = 5), and 5 hamsters that were challenged at day 21 PI with homologous B.1 (614G) and necropsied at day 23 PI. B) sgRNA levels and infectious virus titer in lungs of hamster infected with B.1.427 and necropsied at 2 days (N = 5) and 21 days PI (N = 5), and 5 hamsters that were challenged at day 21 PI with homologous B.1.427 and necropsied at day 23 PI. C) sgRNA levels and infectious virus titer in hamster infected with B.1 (614G) and necropsied at 2 days (N = 5) and 21 days PI (N = 5), and 5 hamsters that were challenged at day 21 PI with heterologous B.1.429. D) sgRNA levels and infectious virus titer in hamster infected with B.1 (614G) and necropsied at 2 days (N = 5) and 21 days PI (N = 5), and 5 hamsters that were challenged at day 21 PI with heterologous B.1.427. The limit of quantitation for the PCR assay (125 copies per reaction) is indicated by the dotted line.

Fig 9. Relative efficiency of B.1 (614G), B.1.427 and B.1.429 airborne hamster to hamster transmission.

Experiments were performed in a 1:1 ration in a airborne transmission setup. Nine or 10 independent 1:1 transmission animal pairs were performed for each of the investigated variants. A) sg RNA levels in oral swabs collected from donors 1 day after intranasal inoculation. Mean values from all groups were compared by fitting a mixed model, and a posthoc multiple comparison test was used to compare the mean values of the B.1.429 group to the other 3 groups individually. B) Percentage of sentinel animals (9 or 10) in each group that are infected each day based on detection of sgRNA in oral swabs collected at least daily after exposure. A quantitative limit of detection of 10 copies per reaction was applied to all samples (dotted line).