Risk period for transmission of SARS-CoV-2 and seasonal influenza: a rapid review

Infection Control and Hospital Epidemiology, Journal Year: 2025, Volume and Issue: unknown, P. 1 - 9

Published: Feb. 24, 2025

Abstract Background: Restricting infectious healthcare workers (HCWs) from the workplace is an important infection prevention strategy. The duration of viral shedding or symptoms are often used as proxies for period in adults but may not accurately estimate it. Objective: To determine risk transmission among previously healthy infected with SARS-CoV-2 omicron variant (omicron) influenza A (influenza) by examining and symptoms, day symptom onset secondary cases pairs. Design: Rapid review Methods: This rapid adhered to PRISMA-ScR; five databases were searched. cumulative daily proportion participants outcome interest was calculated each study summarized. Results: Forty-three studies included. Shedding resolved ≥ 70% end nine post omicron, seven influenza; 90% participants, 10 influenza. Two suggested continues > 24 hours post-fever resolution both viruses. Symptom occurred 80% post-primary case six Conclusions: Omicron consistent previous recommendations exclude HCWs work days; follows a similar trend. Earlier most pathogens indicates that, despite persistent shedding, occurs earlier; serial interval might better approximate infectiousness.

Language: Английский

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SARS-CoV-2 cellular coinfection is limited by superinfection exclusion

Journal of Virology, Journal Year: 2025, Volume and Issue: unknown

Published: March 21, 2025

ABSTRACT The coinfection of individual cells is a requirement for exchange between two or more virus genomes, which major mechanism driving evolution. Coinfection restricted by known as superinfection exclusion (SIE), prohibits the infection previously infected cell related after period time. SIE regulates many different viruses, but its relevance to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was unknown. In this study, we investigated using pair SARS-CoV-2 variant viruses encoding distinct fluorescent reporter proteins. We show first time that limited temporally SIE. defined kinetics onset in system, showing potential starts diminish within hour primary and then falls exponentially events increased. asked how these would affect with during spreading infection. used plaque assays model localized spread observed tissue showed restrict coinfection—and therefore sites possible genetic exchange—to small interface viral infections. This indicates SIE, reducing likelihood cells, likely reduces opportunities strains an underappreciated factor shaping IMPORTANCE Since emerged 2019, it has continued evolve, occasionally generating variants concern. One ways can evolve through recombination, where information swapped genomes. Recombination requires cells; therefore, factors impacting are influence phenomenon whereby becomes increasingly resistant subsequent Here report activated following Furthermore, prevents at boundary expanding areas infection, scenario most lead recombination lineages. Our work suggests genomes shapes

Language: Английский

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In depth sequencing of a serially sampled household cohort reveals the within-host dynamics of Omicron SARS-CoV-2 and rare selection of novel spike variants

PLoS Pathogens, Journal Year: 2025, Volume and Issue: 21(4), P. e1013134 - e1013134

Published: April 28, 2025

SARS-CoV-2 has undergone repeated and rapid evolution to circumvent host immunity. However, outside of prolonged infections in immunocompromised hosts, within-host positive selection rarely been detected. Here we combine daily longitudinal sampling individuals with replicate sequencing increase the accuracy lower threshold for variant calling. We sequenced 577 specimens from 105 a household cohort during BA.1/BA.2 period. Individuals exhibited extremely low viral diversity, estimated evolutionary rate. Within-host dynamics were dominated by genetic drift purifying selection. Positive was rare but highly concentrated spike. A Wright Fisher Approximate Bayesian Computational model identified at 14 loci 7 spike, including S:448 S:339. This detectable immune-mediated is unusual acute respiratory may be caused relatively narrow antibody repertoire early Omicron phase pandemic.

Language: Английский

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Airborne Transmission of SARS-CoV-2: The Contrast between Indoors and Outdoors

Fluids, Journal Year: 2024, Volume and Issue: 9(3), P. 54 - 54

Published: Feb. 22, 2024

COVID-19 is an airborne disease, with the vast majority of infections occurring indoors. In comparison, little transmission occurs outdoors. Here, we investigate pathways that differentiate indoors from outdoors and conclude profound differences exist, which help to explain why SARS-CoV-2 much more prevalent Near- far-field are discussed along factors affect infection risk, aerosol concentration, air entrainment, thermal plumes, occupancy duration all identified as being influential. particular, present fundamental equations underpin Wells–Riley model show mathematical relationship between inhaled virus particles quanta infection. A simple also presented for assessing risk in spaces incomplete mixing. Transmission assessed terms concentration using 1D equations, followed by a description plume–ceiling interactions. With respect this, new experimental results Schlieren visualisation computational fluid dynamics (CFD) based on Eulerian–Lagrangian approach. Pathways discussed, key contribution exhalation plumes evaluated, presence near-field/far-field feedback loop postulated, absent

Language: Английский

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SARS-CoV-2 shedding and evolution in immunocompromised hosts during the Omicron period: a multicenter prospective analysis

medRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Aug. 24, 2023

ABSTRACT Background Prolonged SARS-CoV-2 infections in immunocompromised hosts may predict or source the emergence of highly mutated variants. The types immunosuppression placing patients at highest risk for prolonged infection and associated intrahost viral evolution remain unclear. Methods Adults aged ≥18 years were enrolled 5 hospitals followed from 4/11/2022 – 2/1/2023. Eligible SARS-CoV-2-positive previous 14 days had a moderate severely immunocompromising condition treatment. Nasal specimens tested by rRT-PCR every 2–4 weeks until negative consecutive specimens. Positive underwent culture whole genome sequencing. A Cox proportional hazards model was used to assess factors with duration infection. Results We 150 with: B cell malignancy anti-B therapy (n=18), solid organ hematopoietic stem transplant (SOT/HSCT) (n=59), AIDS (n=5), non-B (n=23), autoimmune/autoinflammatory conditions (n=45). Thirty-eight (25%) rRT-PCR-positive 12 (8%) culture-positive ≥21 after initial detection illness onset. Patients dysfunction longer rRT-PCR- positivity compared those (aHR 0.32, 95% CI 0.15-0.64). Consensus (>50% frequency) spike mutations identified individuals who >56 days; 61% receptor-binding domain (RBD). Mutations shared multiple rare (<5%) global circulation. Conclusions In this cohort, replication-competent Omicron uncommon. Within-host evolutionary rates similar across patients, but lasting accumulated mutations, which distinct seen globally.

Language: Английский

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Revealing SARS-CoV-2 Mpro Mutation Cold and Hot Spots: Dynamic Residue Network Analysis Meets Machine Learning

Computational and Structural Biotechnology Journal, Journal Year: 2024, Volume and Issue: 23, P. 3800 - 3816

Published: Oct. 23, 2024

Language: Английский

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Transmission Bottleneck Size Estimation from De Novo Viral Genetic Variation

Molecular Biology and Evolution, Journal Year: 2023, Volume and Issue: 41(1)

Published: Dec. 30, 2023

Abstract Sequencing of viral infections has become increasingly common over the last decade. Deep sequencing data in particular have proven useful characterizing roles that genetic drift and natural selection play shaping within-host populations. They also been used to estimate transmission bottleneck sizes from identified donor–recipient pairs. These quantify number particles establish lineages recipient host are important due their impact on evolution. Current approaches for estimating exclusively consider subset sites observed as polymorphic donor individual. However, these potential substantially underestimate true sizes. Here, we present a new statistical approach instead using patterns variation arise de novo within Specifically, our makes use clonal variants pair, defined monomorphic both but carry different alleles. We first test simulated dataset then apply it influenza A virus sequence SARS-CoV-2 Our results confirm existence extremely tight bottlenecks 2 respiratory viruses.

Language: Английский

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Airborne Transmission of SARS-CoV-2: The Contrast between Indoors and Outdoors

Published: Jan. 11, 2024

Covid-19 is an airborne disease, with the vast majority of infections occurring indoors. By comparison, little transmission occurs outdoors. Here, we investigate pathways that differentiate indoors from outdoors, and conclude profound differences exist, which help to explain why SARS-CoV-2 much more prevalent Near far-field are discussed along factors affect infection risk, aerosol concentration, air entrainment, thermal plumes, occupancy duration all identified as being influential. In particular, present fundamental equations underpin Wells-Riley model, show mathematical relationship between inhaled virus particles quanta infection. A simple model also presented for assessing risk in spaces incomplete mixing. Transmission assessed terms concentration using 1D equations, followed by a description plume-ceiling interactions. With respect this, new experimental results Schlieren-visualisation Computational Fluid Dynamics (CFD) based on Eulerian-Lagrangian approach. Pathways discussed, key contribution exhalation plumes evaluated, presence near-field/far-field feedback loop postulated, absent

Language: Английский

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Within-host evolution of SARS-CoV-2: how often are de novo mutations transmitted from symptomatic infections?

Virus Evolution, Journal Year: 2024, Volume and Issue: 10(1)

Published: Jan. 1, 2024

Despite a relatively low mutation rate, the large number of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections has allowed for substantial genetic change, leading to multitude emerging variants. Using recently determined rate (per site replication), as well within-host parameter estimates symptomatic SARS-CoV-2 infection, we apply stochastic transmission-bottleneck model describe survival probability

Language: Английский

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A Simulation Framework for Modeling the Within-Patient Evolutionary Dynamics of SARS-CoV-2

Genome Biology and Evolution, Journal Year: 2023, Volume and Issue: 15(11)

Published: Nov. 1, 2023

Abstract The global impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to considerable interest in detecting novel beneficial mutations and other genomic changes that may signal the development variants concern (VOCs). ability accurately detect these within individual patient samples is important enabling early detection VOCs. Such scans for rarely acting positive selection are best performed via comparison empirical data with simulated wherein commonly evolutionary factors, including mutation recombination, reproductive infection dynamics, purifying background selection, can be carefully accounted parameterized. Although there been work quantify factors SARS-CoV-2, they have yet integrated into a baseline model describing intrahost dynamics. To construct such model, we develop simulation framework enables one establish expectations underlying levels patterns patient-level variation. By varying eight key parameters, evaluated 12,096 different model–parameter combinations compared them existing data. Of these, 592 models (∼5%) were plausible based on resulting mean expected number segregating variants. These shared several commonalities shedding light SARS-CoV-2 dynamics: bottlenecks, low skew, distribution fitness effects skewed toward strongly deleterious mutations. We also describe areas uncertainty highlight additional sequence help further refine model. This study lays groundwork improved analysis future within-patient

Language: Английский

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