Nature Reviews Microbiology, Journal Year: 2024, Volume and Issue: unknown
Published: Nov. 25, 2024
Language: Английский
Nature Medicine, Journal Year: 2023, Volume and Issue: 29(2), P. 348 - 357
Published: Jan. 18, 2023
The SARS-CoV-2 Omicron variant has demonstrated enhanced transmissibility and escape of vaccine-derived immunity. Although first-generation vaccines remain effective against severe disease death, robust evidence on vaccine effectiveness (VE) all infections, irrespective symptoms, remains sparse. We used a community-wide serosurvey with 5,310 subjects to estimate how vaccination histories modulated risk infection in infection-naive Hong Kong during large wave BA.2 epidemic January-July 2022. estimated that infected 45% (41-48%) the local population. Three four doses BNT162b2 or CoronaVac were 7 days after (VE 48% (95% credible interval 34-64%) 69% (46-98%) for three BNT162b2, respectively; VE 30% (1-66%) 56% (6-97%) CoronaVac, respectively). At 100 immunization, waned 26% (7-41%) 35% (10-71%) 6% (0-29%) 11% (0-54%) CoronaVac. rapid waning conferred by an increasingly complex viral evolutionary landscape highlight necessity rapidly deploying updated followed vigilant monitoring VE.
Language: Английский
Citations
156
Virus Evolution, Journal Year: 2023, Volume and Issue: 9(2)
Published: July 1, 2023
Knowledge of the fitness effects mutations to SARS-CoV-2 can inform assessment new variants, design therapeutics resistant escape, and understanding functions viral proteins. However, experimentally measuring is challenging: we lack tractable lab assays for many proteins, comprehensive deep mutational scanning has been applied only two Here, develop an approach that leverages millions publicly available sequences estimate mutations. We first calculate how independent occurrences each mutation are expected be observed along phylogeny in absence selection. then compare these observations actual effect mutation. These estimates correlate well with measurements. For most genes, synonymous nearly neutral, stop-codon deleterious, amino acid have a range effects. some accessory proteins under little no provide interactive visualizations all (https://jbloomlab.github.io/SARS2-mut-fitness/). The framework describe applicable any virus which number sufficiently large neutral observed.
Language: Английский
Citations
73
Emerging infectious diseases, Journal Year: 2024, Volume and Issue: 30(2)
Published: Jan. 12, 2024
Abstract To support the ongoing management of viral respiratory diseases while transitioning out acute phase COVID-19 pandemic, many countries are moving toward an integrated model surveillance for SARS-CoV-2, influenza virus, and other pathogens. Although approaches catalyzed by pandemic provide novel epidemiologic insight, continuing them as implemented during is unlikely to be feasible nonemergency surveillance, have already been scaled back. Furthermore, given anticipated cocirculation SARS-CoV-2 activities in place before require review adjustment ensure their value public health. In this report, we highlight key challenges development models surveillance. We discuss relative strengths limitations different practices studies well contribution assessment, forecasting, health decision-making.
Language: Английский
Citations
19
Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)
Published: Nov. 20, 2023
Our ability to forecast epidemics far into the future is constrained by many complexities of disease systems. Realistic longer-term projections may, however, be possible under well-defined scenarios that specify state critical epidemic drivers. Since December 2020, U.S. COVID-19 Scenario Modeling Hub (SMH) has convened multiple modeling teams make months ahead SARS-CoV-2 burden, totaling nearly 1.8 million national and state-level projections. Here, we find SMH performance varied widely as a function both scenario validity model calibration. We show remained close reality for 22 weeks on average before arrival unanticipated variants invalidated key assumptions. An ensemble participating models preserved variation between (using linear opinion pool method) was consistently more reliable than any single in periods valid assumptions, while projection interval coverage near target levels. were used guide pandemic response, illustrating value collaborative hubs
Language: Английский
Citations
32
bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown
Published: Jan. 31, 2023
Knowledge of the fitness effects mutations to SARS-CoV-2 can inform assessment new variants, design therapeutics resistant escape, and understanding functions viral proteins. However, experimentally measuring is challenging: we lack tractable lab assays for many proteins, comprehensive deep mutational scanning has been applied only two Here develop an approach that leverages millions publicly available sequences estimate mutations. We first calculate how independent occurrences each mutation are expected be observed along phylogeny in absence selection. then compare these observations actual effect mutation. These estimates correlate well with measurements. For most genes, synonymous nearly neutral, stop-codon deleterious, amino-acid have a range effects. some accessory proteins under little no provide interactive visualizations all (https://jbloomlab.github.io/SARS2-mut-fitness/). The framework describe applicable any virus which number sufficiently large neutral observed.
Language: Английский
Citations
31
Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)
Published: March 14, 2023
Abstract Expansion of the SARS-CoV-2 BA.4 and BA.5 Omicron subvariants in populations with prevalent immunity from prior infection vaccination, associated burden severe COVID-19, has raised concerns about epidemiologic characteristics these lineages including their association immune escape or clinical outcomes. Here we show that BA.4/BA.5 cases a large US healthcare system had at least 55% (95% confidence interval: 43–69%) higher adjusted odds documented than time-matched BA.2 cases, as well 15% (9–21%) 38% (27–49%) having received 3 ≥4 COVID-19 vaccine doses, respectively. However, after adjusting for differences among each lineage, was not differential risk emergency department presentation, hospital admission, intensive care unit admission following an initial outpatient diagnosis. This finding held sensitivity analyses correcting potential exposure misclassification resulting unascertained infections. Our results demonstrate reduced severity (BA.1 BA.2) lineages, relative to Delta variant, persisted BA.4/BA.5, despite increased breakthrough previously vaccinated infected individuals.
Language: Английский
Citations
31
Nature Medicine, Journal Year: 2024, Volume and Issue: 30(10), P. 2805 - 2812
Published: July 26, 2024
Language: Английский
Citations
11
Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)
Published: May 7, 2024
Abstract Little is known about SARS-CoV-2 infection risk in African countries with high levels of infection-driven immunity and low vaccine coverage. We conducted a prospective cohort study 349 participants from 52 households The Gambia between March 2021 June 2022, routine weekly RT-PCR 6-monthly serology. Attack rates 45% 57% were seen during Delta Omicron BA.1 waves respectively. Eighty-four percent RT-PCR-positive infections asymptomatic. Children under 5-years had lower incidence than 18-49-year-olds. One prior reduced the wave only, ≥2 required to reduce early lineage viruses. In an population coverage, we find attack waves, proportion asymptomatic young children remaining relatively protected infection.
Language: Английский
Citations
5
Scientific Reports, Journal Year: 2025, Volume and Issue: 15(1)
Published: Feb. 14, 2025
Language: Английский
Citations
0
Virology, Journal Year: 2025, Volume and Issue: 605, P. 110467 - 110467
Published: Feb. 25, 2025
Language: Английский
Citations
0