An early warning system for emerging SARS-CoV-2 variants

Subissi, Lorenzo; Gottberg, Anne von; Thukral, Lipi; Worp, Nathalie; Munnink, Bas B. Oude; Rathore, Surabhi; Abu‐Raddad, Laith J.; Aguilera, Ximena; Alm, Erik; Archer, Brett N.; Cohen, Homa Attar; Barakat, Amal; Barclay, William; Bhiman, Jinal N.; Caly, Leon; Chand, Meera; Chen, Mark; Cullinane, Ann; Oliveira, Túlio de; Drosten, Christian; Druce, Julian; Effler, Paul V.; Masry, Ihab El; Faye, Adama; Gaseitsiwe, Simani; Ghedin, Elodie; Grant, Rebecca; Haagmans, Bart L.; Herring, Belinda L.; Iyer, Shilpa S.; Kassamali, Zyleen; Kakkar, Manish; Kondor, Rebecca; Leite, Juliana Almeida; Leo, Yee Sin; Leung, Gabriel M.; Marklewitz, Marco; Moyo, Sikhulile; Méndez‐Rico, Jairo; Melhem, Nada M.; Munster, Vincent J.; Nahapetyan, Karen; Oh, Djin-Ye; Pavlin, Boris I; Peacock, Thomas P.; Peiris, Malik; Peng, Zhibin; Poon, Leo L. M.; Rambaut, Andrew; Sacks, Jilian A.; Shen, Yinzhong; Siqueira, Marilda Mendonça; Tessema, Sofonias K.; Volz, Erik; Thiel, Volker; Werf, Sylvie van der; Briand, Sylvie; Perkins, Mark D.; Kerkhove, Maria D. Van; Koopmans, Marion; Agrawal, Anurag

doi:10.1038/s41591-022-01836-w

Cited by 67 publications

(36 citation statements)

References 54 publications

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“…The future of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic is uncertain, but it hinges on virus evolution and the level and duration of immune protection of natural infection against reinfection. 1–3 While current coronavirus disease 2019 (COVID-19) vaccines had a critical role in reducing COVID-19 hospitalizations and deaths, their rapidly waning immune protection, particularly against the Omicron (B.1.1.529) variant, 4–8 limits their role in shaping the future of SARS-CoV-2 epidemiology compared to other vaccines, such as vaccinia, which eradicated smallpox. 9…”

Section: Introductionmentioning

confidence: 99%

Duration of immune protection of SARS-CoV-2 natural infection against reinfection in Qatar

Chemaitelly

Nagelkerke

Ayoub

et al. 2022

Preprint

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BACKGROUND: The future of the SARS-CoV-2 pandemic hinges on virus evolution and duration of immune protection of natural infection against reinfection. We investigated duration of protection afforded by natural infection, the effect of viral immune evasion on duration of protection, and protection against severe reinfection, in Qatar, between February 28, 2020 and June 5, 2022. METHODS: Three national, matched, retrospective cohort studies were conducted to compare incidence of SARS-CoV-2 infection and COVID-19 severity among unvaccinated persons with a documented SARS-CoV-2 primary infection, to incidence among those infection-naive and unvaccinated. Associations were estimated using Cox proportional-hazard regression models. RESULTS: Effectiveness of pre-Omicron primary infection against pre-Omicron reinfection was 85.5% (95% CI: 84.8-86.2%). Effectiveness peaked at 90.5% (95% CI: 88.4-92.3%) in the 7th month after the primary infection, but waned to ~70% by the 16th month. Extrapolating this waning trend using a Gompertz curve suggested an effectiveness of 50% in the 22nd month and <10% by the 32nd month. Effectiveness of pre-Omicron primary infection against Omicron reinfection was 38.1% (95% CI: 36.3-39.8%) and declined with time since primary infection. A Gompertz curve suggested an effectiveness of <10% by the 15th month. Effectiveness of primary infection against severe, critical, or fatal COVID-19 reinfection was 97.3% (95% CI: 94.9-98.6%), irrespective of the variant of primary infection or reinfection, and with no evidence for waning. Similar results were found in sub-group analyses for those ≥50 years of age. CONCLUSIONS: Protection of natural infection against reinfection wanes and may diminish within a few years. Viral immune evasion accelerates this waning. Protection against severe reinfection remains very strong, with no evidence for waning, irrespective of variant, for over 14 months after primary infection.

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Section: Introductionmentioning

confidence: 99%

Duration of immune protection of SARS-CoV-2 natural infection against reinfection in Qatar

Chemaitelly

Nagelkerke

Ayoub

et al. 2022

Preprint

Self Cite

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“…Several vaccines have already been approved, but worldwide vaccination coverage is still insufficient. In addition, current vaccines are suboptimal in preventing transmission, and novel variants of the virus with reduced susceptibility to the vaccines continue to emerge ( Subissi et al., 2022 ). Antivirals are a critical addition to the vaccination campaigns, to increase the resilience to SARS-CoV-2 infection, particularly in at-risk populations.…”

Section: Introductionmentioning

confidence: 99%

Carbohydrate-binding protein from stinging nettle as fusion inhibitor for SARS-CoV-2 variants of concern

Vanhulle

D’huys²,

Provinciael³

et al. 2022

Front. Cell. Infect. Microbiol.

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Urtica dioica agglutinin (UDA) is a carbohydrate-binding small monomeric protein isolated from stinging nettle rhizomes. It inhibits replication of a broad range of viruses, including coronaviruses, in multiple cell types, with appealing selectivity. In this work, we investigated the potential of UDA as a broad-spectrum antiviral agent against SARS-CoV-2. UDA potently blocks transduction of pseudotyped SARS-CoV-2 in A549.ACE2+-TMPRSS2 cells, with IC50 values ranging from 0.32 to 1.22 µM. Furthermore, UDA prevents viral replication of the early Wuhan-Hu-1 strain in Vero E6 cells (IC50 = 225 nM), but also the replication of SARS-CoV-2 variants of concern, including Alpha, Beta and Gamma (IC50 ranging from 115 to 171 nM). In addition, UDA exerts antiviral activity against the latest circulating Delta and Omicron variant in U87.ACE2+ cells (IC50 values are 1.6 and 0.9 µM, respectively). Importantly, when tested in Air-Liquid Interface (ALI) primary lung epithelial cell cultures, UDA preserves antiviral activity against SARS-CoV-2 (20A.EU2 variant) in the nanomolar range. Surface plasmon resonance (SPR) studies demonstrated a concentration-dependent binding of UDA to the viral spike protein of SARS-CoV-2, suggesting interference of UDA with cell attachment or subsequent virus entry. Moreover, in additional mechanistic studies with cell-cell fusion assays, UDA inhibited SARS-CoV-2 spike protein-mediated membrane fusion. Finally, pseudotyped SARS-CoV-2 mutants with N-glycosylation deletions in the S2 subunit of the spike protein remained sensitive to the antiviral activity of UDA. In conclusion, our data establish UDA as a potent fusion inhibitor for the current variants of SARS-CoV-2.

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“…We have provided robust evidence that epidemic intelligence at country level is not enough, alone, to contrast the pandemic of respiratory pathogens such as SARS-CoV-2, in the absence of well-coordinated genomic surveillance – especially in low-income and middle-income countries currently lacking and adequate response capacity [45] – and global projections of variant’s pandemic potential. Our approach is inherently integrated and scalable, adding to ongoing modeling efforts and pan-viral analyses [46, 47, 48, 49, 22] and responding to global calls for coordinated action [45, 50, 51]. The data-driven approach provides a vital step in the path towards pandemic intelligence – where the interconnected and interdependent nature of human activities [21, 18, 52] is naturally accounted for at a global level – as well a means of enhancing global preparedness against future emerging variants.…”

Section: Discussionmentioning

confidence: 99%

Enhancing global preparedness during an ongoing pandemic from partial and noisy data

Klamser

d’Andrea

Lauro

et al. 2022

Preprint

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As the coronavirus disease 2019 (COVID-19) spread globally, emerging variants such as B.1.1.529 quickly became dominant worldwide. Sustained community transmission favors the proliferation of mutated sub-lineages with pandemic potential, due to cross-national mobility flows, which are responsible for consecutive cases surge worldwide. We show that, in the early stages of an emerging variant, integrating data from national genomic surveillance and global human mobility with large-scale epidemic modeling allows to quantify its pandemic potential, providing quantifiable indicators for pro-active policy interventions. We validate our framework on worldwide spreading variants and gain insights about the pandemic potential of BA.5 and BA.2.75 sub-lineages. Country-level epidemic intelligence is not enough to contrast the pandemic of respiratory pathogens such as SARS-CoV-2 and a scalable integrated approach, i.e. pandemic intelligence, is required to enhance global preparedness.

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An early warning system for emerging SARS-CoV-2 variants

Abstract: Global sequencing and surveillance capacity for SARS-CoV-2 must be strengthened and combined with multidisciplinary studies of infectivity, virulence and immune escape, in order to track the unpredictable evolution of the ongoing COVID-19 pandemic.

Cited by 67 publications

References 54 publications

Duration of immune protection of SARS-CoV-2 natural infection against reinfection in Qatar

Duration of immune protection of SARS-CoV-2 natural infection against reinfection in Qatar

Carbohydrate-binding protein from stinging nettle as fusion inhibitor for SARS-CoV-2 variants of concern

Enhancing global preparedness during an ongoing pandemic from partial and noisy data

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