Modelling COVID-19 mutant dynamics: understanding the interplay between viral evolution and disease transmission dynamics DOI Creative Commons
Fernando Saldaña, Nico Stollenwerk, Maíra Aguiar

et al.

medRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: June 4, 2024

Abstract Understanding virus mutations is critical for shaping public health interventions. These lead to complex multi-strain dynamics often underrepresented in models. Aiming understand the factors influencing variants’ fitness and evolution, we explore several scenarios of spreading gain qualitative insight into dictating which variants ultimately predominate at population level. To this end, propose a two-strain stochastic model that accounts asymptomatic transmission, mutations, possibility disease import. We find with milder symptoms are likely spread faster than those severe symptoms. This because can prompt affected individuals seek medical help earlier, potentially leading quicker identification isolation cases. However, or cases may more widely, making it harder control spread. Therefore, increased transmissibility still result higher hospitalizations fatalities due widespread infection. The proposed highlights interplay between viral evolution transmission dynamics. Offering nuanced view variant spread, provides foundation further investigation mitigating strategies

Language: Английский

Rapid review and meta-analysis of serial intervals for SARS-CoV-2 Delta and Omicron variants DOI Creative Commons
Zachary J. Madewell, Yang Yang, Ira M. Longini

et al.

BMC Infectious Diseases, Journal Year: 2023, Volume and Issue: 23(1)

Published: June 26, 2023

The serial interval is the period of time between symptom onset in primary case and secondary case. Understanding important for determining transmission dynamics infectious diseases like COVID-19, including reproduction number attack rates, which could influence control measures. Early meta-analyses COVID-19 reported intervals 5.2 days (95% CI: 4.9-5.5) original wild-type variant 4.87-5.47) Alpha variant. has been shown to decrease over course an epidemic other respiratory diseases, may be due accumulating viral mutations implementation more effective nonpharmaceutical interventions. We therefore aggregated literature estimate Delta Omicron variants.

Language: Английский

Citations

38
Estimating the reproduction number and transmission heterogeneity from the size distribution of clusters of identical pathogen sequences DOI Creative Commons
Cécile Tran Kiem, Trevor Bedford

Proceedings of the National Academy of Sciences, Journal Year: 2024, Volume and Issue: 121(15)

Published: April 3, 2024

Quantifying transmission intensity and heterogeneity is crucial to ascertain the threat posed by infectious diseases inform design of interventions. Methods that jointly estimate reproduction number R dispersion parameter k have however mainly remained limited analysis epidemiological clusters or contact tracing data, whose collection often proves difficult. Here, we show identical sequences are imprinted pathogen offspring distribution, derive an analytical formula for distribution size these clusters. We develop evaluate inference framework from sequences. then illustrate its application across a range situations. Finally, hypothesis testing relying on determine whether given genetic subpopulation associated with increased reduced transmissibility. Our work provides tools without building phylogenetic tree, thus making it easily scalable large genome datasets.

Language: Английский

Citations

13
Using big sequencing data to identify chronic SARS-Coronavirus-2 infections DOI Creative Commons
Sheri Harari, Danielle Miller,

Shay Fleishon

et al.

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

Published: July 17, 2023

Abstract The evolution of SARS-Coronavirus-2 (SARS-CoV-2) has been characterized by the periodic emergence highly divergent variants, many which may have arisen during chronic infections immunocompromised individuals. Here, we harness a global phylogeny ∼11.7 million SARS-CoV-2 genomes and search for clades composed sequences with identical metadata (location, age, sex) spanning more than 21 days. We postulate that such represent repeated sampling from same chronically infected individual. A set 271 chronic-like was inferred, displayed signatures an elevated rate adaptive evolution, in line validated infections. More 70% mutations present currently circulating variants are found BA.1 predate months, demonstrating predictive nature clades. find probability observing is approximately 10-20 higher transmission chains. next employ language models to most use them infer hundreds additional absence phylogenetic information. Our proposed approach presents innovative method mining extensive sequencing data providing valuable insights into future evolutionary patterns.

Language: Английский

Citations

17
The airborne transmission of viruses causes tight transmission bottlenecks DOI Creative Commons

Patrick Sinclair,

Lei Zhao, Clive Beggs

et al.

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: April 26, 2024

The transmission bottleneck describes the number of viral particles that initiate an infection in a new host. Previous studies have used genome sequence data to suggest bottlenecks for influenza and SARS-CoV-2 involve few particles, but general principles virus are not fully understood. Here we show that, across broad range circumstances, tight simple consequence physical process airborne transmission. We use mathematical modelling describe emission inhalation infectious deriving result great majority particles. While exceptions this rule exist, circumstances needed create these likely very rare. thus provide explanation previous inferences size, while predicting prevail more generally respiratory

Language: Английский

Citations

6
The effects of amino acid substitution of spike protein and genomic recombination on the evolution of SARS-CoV-2 DOI Creative Commons

Letian Fang,

Jie Xu,

Yue Zhao

et al.

Frontiers in Microbiology, Journal Year: 2023, Volume and Issue: 14

Published: July 25, 2023

Over three years’ pandemic of 2019 novel coronavirus disease (COVID-19), multiple variants and subvariants have emerged successively, outcompeted earlier become predominant. The sequential emergence reflects the evolutionary process mutation-selection-adaption severe acute respiratory syndrome 2 (SARS-CoV-2). Amino acid substitution/insertion/deletion in spike protein causes altered viral antigenicity, transmissibility, pathogenicity SARS-CoV-2. Early pandemic, D614G mutation conferred virus with advantages over previous increased it also laid a conservative background for subsequent substantial mutations. role genomic recombination evolution SARS-CoV-2 raised increasing concern occurrence recombinants such as Deltacron, XBB.1.5, XBB.1.9.1, XBB.1.16 late phase pandemic. Co-circulation different co-infection immunocompromised patients accelerate recombinants. Surveillance variations, particularly recombination, is essential to identify ongoing changes genome antigenic epitopes thus leads development new vaccine strategies interventions.

Language: Английский

Citations

15
Innate immune responses yield tissue-specific bottlenecks that scale with pathogen dose DOI Creative Commons
Karthik Hullahalli, Katherine G. Dailey, Matthew K. Waldor

et al.

Proceedings of the National Academy of Sciences, Journal Year: 2023, Volume and Issue: 120(37)

Published: Sept. 5, 2023

To cause infection, pathogens must overcome bottlenecks imposed by the host immune system. These restrict inoculum and largely determine whether pathogen exposure results in disease. Infection therefore quantify effectiveness of barriers. Here, using a model

Language: Английский

Citations

11
Genetic consequences of effective and suboptimal dosing with mutagenic drugs in a hamster model of SARS-CoV-2 infection DOI Creative Commons
Christopher J. R. Illingworth, José Afonso Guerra‐Assunção, Samuel Gregg

et al.

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

Published: Jan. 1, 2024

Abstract Mutagenic antiviral drugs have shown promise against multiple viruses, but concerns been raised about whether their use might promote the emergence of new and harmful viral variants. Recently, genetic signatures associated with molnupiravir identified in global SARS-COV-2 population. Here, we examine consequences using favipiravir to treat SARS-CoV-2 infection a hamster model, comparing genome sequence data collected from (1) untreated hamsters, (2) hamsters receiving effective suboptimal doses treatment. We identify broadly linear relationship between drug dose extent variation treated populations, high proportion this being composed variants at frequencies less than 1 per cent, below typical thresholds for variant calling. Treatment an was gain 7 10 relative drug-free controls: even after short period treatment population founded by transmitted virus could contain differences that original host. showed intermediate gains No dose-dependent signal numbers single-nucleotide reaching excess 5 cent. did not find evidence support resistance or novel immune phenotypes. Our study suggests where onward transmission occurs, mutagenic may be sufficient generate significant increase number transmitted.

Language: Английский

Citations

4
The Asymptomatic Proportion of SARS‐CoV‐2 Omicron Variant Infections in Households: A Systematic Review DOI Creative Commons
Nancy D. J. Shi, Adrian J. Marcato, Violeta Spirkoska

et al.

Influenza and Other Respiratory Viruses, Journal Year: 2024, Volume and Issue: 18(7)

Published: July 1, 2024

ABSTRACT Understanding the clinical spectrum of SARS‐CoV‐2 infection, including asymptomatic fraction, is important as individuals are still able to infect other and contribute ongoing transmission. The WHO Unity Household transmission investigation (HHTI) protocol provides a platform for prospective systematic collection high‐quality clinical, epidemiological, serological virological data from confirmed cases their household contacts. These can be used understand key severity transmissibility parameters—including proportion—in relation local epidemic context help inform public health response. We aimed estimate proportion Omicron variant infections in Unity‐aligned HHTIs. conducted review meta‐analysis alignment with PRISMA 2020 guidelines registered our on PROSPERO (CRD42022378648). searched EMBASE, Web Science, MEDLINE bioRxiv medRxiv 1 November 2021 22 August 2023. identified 8368 records, which 98 underwent full text review. only three studies extraction, substantial variation study design corresponding estimates proportion. As result, we did not generate pooled or I 2 metric. limited number quality that highlights need improved preparedness response capabilities facilitate robust HHTI implementation, analysis reporting, better national, regional global risk assessments policymaking.

Language: Английский

Citations

4
What have we learnt from the COVID-19 pandemic? DOI
Shampa Chatterjee, Amaro Nunes Duarte‐Neto, Marco Cascella

et al.

Elsevier eBooks, Journal Year: 2025, Volume and Issue: unknown, P. 867 - 892

Published: Jan. 1, 2025

Language: Английский

Citations

0
Barcoded SARS-CoV-2 viruses define the impact of duration and route of exposure on the transmission bottleneck in a hamster model DOI Creative Commons
Reed Trende, Tamarand L. Darling, Tianyu Gan

et al.

Science Advances, Journal Year: 2025, Volume and Issue: 11(3)

Published: Jan. 15, 2025

The transmission bottleneck, defined as the number of viruses shed from one host to infect another, is an important determinant rate virus evolution and level immunity required protect against transmission. Despite its importance, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) bottleneck remains poorly characterized. We adapted a SARS-CoV-2 reverse genetics system generate pool >200 isogenic harboring specific 6-nucleotide barcodes, infected donor hamsters with this pool, exposed contact paired donors, varying duration route exposure. Following exposure, nasal turbinates, trachea, lungs were collected barcodes in each tissue was enumerated. found that longer more direct exposures increased upper airway primary source transmitted model. Together, these findings highlight utility barcoded tools rigorously study

Language: Английский

Citations

0