Pathogenicity, transmissibility, and fitness of SARS-CoV-2 Omicron in Syrian hamsters

Yuan, Shuofeng; Ye, Zi‐Wei; Liang, Ronghui; Tang, Kaiming; Zhang, Anna Jinxia; Lü, Gang; Ong, Chon Phin; Poon, Vincent Kwok-Man; Chan, Chris; Mok, Bobo Wing-Yee; Qin, Zhenzhi; Xie, Yubin; Chu, Allen Wing-Ho; Chan, Wan-Mui; Ip, Jonathan Daniel; Sun, Haoran; Tsang, Jessica Oi-Ling; Yuen, Terrence Tsz‐Tai; Chik, Kenn Ka-Heng; Chan, Chris Chun-Yiu; Cai, Jian‐Piao; Luo, Cheng; Lu, Lu; Yip, Cyril Chik-Yan; Chu, Hin; To, Kelvin Kai-Wang; Chen, Honglin; Jin, Dong Yan; Yuen, Kwok Yung; Chan, Jasper Fuk‐Woo

doi:10.1126/science.abn8939

Cited by 160 publications

(124 citation statements)

References 46 publications

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“…This could further suggest that in these groups, a replication advantage was present for Omicron initially, which led to increased antibody affinity maturation towards this variant. Our findings align with observations from another study where the authors showed that the presence of neutralizing antibodies against Delta, but not Omicron, could prevent Delta from outcompeting Omicron in hamsters [ 47 ]. This suggests, that even in hamsters, where Delta is intrinsically more transmissible, immune pressure can provide a direct advantage for antigenically-different viruses.…”

Section: Discussionsupporting

confidence: 92%

Infection- or vaccine mediated immunity reduces SARS-CoV-2 transmission, but increases competitiveness of Omicron in hamsters

Port

Yinda

Riopelle

et al. 2022

Preprint

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Omicron has demonstrated a competitive advantage over Delta in vaccinated people. To understand this, we designed a transmission chain experiment using naive, intranasally (IN) or intramuscularly (IM) vaccinated, and previously infected (PI) hamsters. Vaccination and previous infection protected animals from disease and virus replication after Delta and Omicron dual challenge. A gradient in transmission blockage was observed: IM vaccination displayed moderate transmission blockage potential over three airborne chains (approx. 70%), whereas, IN vaccination and PI blocked airborne transmission in >90%. In naive hamsters, Delta completely outcompeted Omicron within and between hosts after dual infection in onward transmission. Although Delta also outcompeted Omicron in the vaccinated and PI transmission chains, an increase in Omicron competitiveness was observed in these groups. This correlated with the increase in the strength of the humoral response against Delta, with the strongest response seen in PI animals. These data highlight the continuous need to assess the emergence and spread of novel variants in populations with pre-existing immunity and address the additional evolutionary pressure this may exert on the virus.

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Section: Discussionsupporting

confidence: 92%

Infection- or vaccine mediated immunity reduces SARS-CoV-2 transmission, but increases competitiveness of Omicron in hamsters

Port

Yinda

Riopelle

et al. 2022

Preprint

View full text Add to dashboard Cite

show abstract

“…From the ML fitness model, we obtain a breakdown of intrinsic and antigenic selection components relevant for each clade shift. Intrinsic selection is strong and positive in all three major clade shifts, with average selection coefficients s 0 = 0.05 − 0.08, consistent with strong functional differences observed between the α, δ, and o variants 3,43 (Fig. 3b, Table S3).…”

Section: Impact Of Vaccination and Infection On Evolutionsupporting

confidence: 72%

Vaccination shapes evolutionary trajectories of SARS-CoV-2

Meijers

Ruchnewitz

Łuksza

et al. 2022

Preprint

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The large-scale evolution of the SARS-CoV-2 virus has been marked by rapid turnover of genetic clades. New variants show intrinsic changes, notably increased transmissibility, as well as antigenic changes that reduce the cross-immunity induced by previous infections or vaccinations. How this functional variation shapes the global evolutionary dynamics has remained unclear. Here we show that selection induced by vaccination impacts on the recent antigenic evolution of SARS-CoV-2; other relevant forces include intrinsic selection and antigenic selection induced by previous infections. We obtain these results from a fitness model with intrinsic and antigenic fitness components. To infer model parameters, we combine time-resolved sequence data, epidemiological records, and cross-neutralisation assays. This model accurately captures the large-scale evolutionary dynamics of SARS-CoV-2 in multiple geographical regions. In particular, it quantifies how recent vaccinations and infections affect the speed of frequency shifts between viral variants.Our results show that timely neutralisation data can be harvested to identify hotspots of antigenic selection and to predict the impact of vaccination on viral evolution.

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“…Nonetheless, many technical, scientific and policy challenges must be resolved to realise its full potential. For a robust quantification and interpretation of the data, a better understanding of the amount and the duration of virus shedding via faeces is needed, especially considering the influence of patient immune status and possibly altered variant-specific properties 82 . The timely transfer of insights gained from WBE into actionable results for public health will be key 83 .…”

Section: Discussionmentioning

confidence: 99%

Viral variant-resolved wastewater surveillance of SARS-CoV-2 at national scale

et al. 2022

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SARS-CoV-2 surveillance by wastewater-based epidemiology is poised to provide a complementary approach to sequencing individual cases. However, robust quantification of variants and de novo detection of emerging variants remains challenging for existing strategies. We deep sequenced 3,413 wastewater samples representing 94 municipal catchments, covering >59% of the population of Austria, from December 2020 to February 2022. Our system of variant quantification in sewage pipeline designed for robustness (termed VaQuERo) enabled us to deduce the spatiotemporal abundance of predefined variants from complex wastewater samples. These results were validated against epidemiological records of >311,000 individual cases. Furthermore, we describe elevated viral genetic diversity during the Delta variant period, provide a framework to predict emerging variants and measure the reproductive advantage of variants of concern by calculating variant-specific reproduction numbers from wastewater. Together, this study demonstrates the power of national-scale WBE to support public health and promises particular value for countries without extensive individual monitoring.

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Pathogenicity, transmissibility, and fitness of SARS-CoV-2 Omicron in Syrian hamsters

Cited by 160 publications

References 46 publications

Infection- or vaccine mediated immunity reduces SARS-CoV-2 transmission, but increases competitiveness of Omicron in hamsters

Infection- or vaccine mediated immunity reduces SARS-CoV-2 transmission, but increases competitiveness of Omicron in hamsters

Vaccination shapes evolutionary trajectories of SARS-CoV-2

Viral variant-resolved wastewater surveillance of SARS-CoV-2 at national scale

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