Mechanisms of replacement of circulating viruses by seasonal and pandemic influenza A viruses

Mathematical Modeling of Influenza Dynamics: Integrating Seasonality and Gradual Waning Immunity

The dynamics of influenza virus spread is one of the most complex to model due to two crucial factors involved: seasonality and immunity. These factors have been typically addressed separately in mathematical modeling in epidemiology. In this paper, we present a mathematical modeling approach to consider simultaneously both forced-seasonality and gradual waning immunity. A seasonal SIRn model that integrates seasonality and gradual waning immunity is constructed. Seasonality has been modeled classically, by defining the transmission rate as a periodic function, with higher values in winter seasons. The progressive decline of immunity after infection has been introduced into the model structure by considering multiple recovered subpopulations or recovery states with transmission rates attenuated by a susceptibility factor that varies with the age of infection. To show the applicability of the proposed mathematical modeling approach to a real-world scenario, we have carried out a calibration of the model with the data series of influenza infections reported in the 2010-2020 period at the General Hospital of Castellón de la Plana, Spain. The results of the case study show the feasibility of the mathematical approach. We provide a discussion of the main features and insights of the proposed mathematical modeling approach presented in this study.

The evolutionary cost of homophily: Social stratification facilitates stable variant coexistence and increased rates of evolution in host-associated pathogens

Coexistence of multiple strains of a pathogen in a host population can present significant challenges to vaccine development or treatment efficacy. Here we discuss a novel mechanism that can increase rates of long-lived strain polymorphism, rooted in the presence of social structure in a host population. We show that social preference of interaction, in conjunction with differences in immunity between host subgroups, can exert varying selection pressure on pathogen strains, creating a balancing mechanism that supports stable viral coexistence, independent of other known mechanisms. We use population genetic models to study rates of pathogen heterozygosity as a function of population size, host population composition, mutant strain fitness differences and host social preferences of interaction. We also show that even small periodic epochs of host population stratification can lead to elevated strain coexistence. These results are robust to varying social preferences of interaction, overall differences in strain fitnesses, and spatial heterogeneity in host population composition. Our results highlight the role of host population social stratification in increasing rates of pathogen strain diversity, with effects that should be considered when designing policies or treatments with a long-term view of curbing pathogen evolution.

The evolutionary cost of homophily: social stratification facilitates stable variant coexistence and increased rates of evolution in host-associated pathogens

Coexistence of multiple strains of a pathogen in a host population can present significant challenges to vaccine development or treatment efficacy. Here we discuss a novel mechanism that can increase rates of long-lived strain polymorphism, rooted in the presence of social structure in a host population. We show that social preference of interaction, in conjunction with differences in immunity between host subgroups, can exert varying selection pressure on pathogen strains, creating a balancing mechanism that supports stable viral coexistence, independent of other known mechanisms. We use population genetic models to study rates of pathogen heterozygosity as a function of population size, host population composition, mutant strain fitness differences and host social preferences of interaction. We also show that even small periodic epochs of host population stratification can lead to elevated strain coexistence. These results are robust to varying social preferences of interaction, overall differences in strain fitnesses, and spatial heterogeneity in host population composition. Our results highlight the role of host population social stratification in increasing rates of pathogen strain diversity, with effects that should be considered when designing policies or treatments with a long-term view of curbing pathogen evolution.

Competitive evolution of H1N1 and H3N2 influenza viruses in the United States: A mathematical modeling study

Seasonal influenza causes vast public health and economic impact globally. The prevention and control of the annual epidemics remain a challenge due to the antigenic evolution of the viruses. Here, we presented a novel modeling framework based on changes in amino acid sequences and relevant epidemiological data to retrospectively investigate the competitive evolution and transmission of H1N1 and H3N2 influenza viruses in the United States during October 2002 and April 2019. To do so, we estimated the time-varying disease transmission rate from the reported influenza cases and the time-varying antigenic change rate of the viruses from the changes in amino acid sequences. By incorporating the time-varying antigenic change rate into the transmission models, we found that the models could capture the evolutionary transmission dynamics of influenza viruses in the United States. Our modeling results also showed that the antigenic change of the virus plays an essential role in seasonal influenza dynamics.

[Comprehensive understanding of viral diseases by field, molecular, and theoretical studies]

Viral diseases are responsible for substantial morbidity and mortality and continue to be of great concern. To ensure better control of viral infections, I have been tackling the issue as a medical doctor, an academic researcher, and a public health officer. Especially, I have studied respiratory viruses, such as the influenza virus, from the perspectives of molecular virology, theoretical modeling, and field epidemiology. RNA biology and its involvement with viral life-cycle and pathogenicity are central topics of molecular study, while mathematical models of transmission dynamics and phylogenetics are major components of theoretical research. As a field epidemiologist, I work with public health authorities during viral disease outbreaks. I was deployed to West Africa for viral hemorrhagic fever outbreak responses as a WHO consultant, and I have served the Japanese Government as an advisor for COVID-19 countermeasures. I would like to integrate various approaches from clinical medicine to epidemiology, theoretical modeling, evolutionary biology, genetics, and molecular biology in my research. In that way, we could gain a more comprehensive understanding of viral diseases. I hope these findings will help ease the disease burden of viral infections around the world.

Evaluation of changes in pediatric emergency department utilization during COVID-19 pandemic: Changes during COVID-19 pandemic

Background

During the coronavirus disease 2019 (COVID-19) pandemic period, the use of emergency services with pediatric non-COVID patients has decreased considerably. We aimed to examine whether there was a change in the demographic data, triage profile, causes, management, and cost of pediatric emergency department (PED) visits of non-COVID patients during the pandemic period.

Methods

This study was a retrospective, single-center, observational comparative study that was conducted at the PED. Patient records were examined during “the pandemic spring” and the same period of the previous year. Patient demographics, waiting time, and outcome of the PED visit were analyzed in the entire population of children admitted to the PED during the study period, whereas more precise data such as the reason for PED use, duration of symptoms, urgency levels according to the Emergency Severity Index (ESI), final diagnosis, management, and cost of patient care were analyzed in a sample of admitted patients. We used the chi-square test, Fisher's exact test, and Mann–Whitney U test for statistical analyses.

Results

A total of 62,593 PED visits occurred. During the pandemic period, PED visits showed a decrease of 55.8% compared to the previous year. Patients included in the sampling study group were selected using a systematic random sampling method. The median waiting time during the pandemic period was significantly shorter than the previous year (median 14 min [IQR: 5–32] vs. median 5 min [IQR: 2–16]; p<0.001). The median duration of symptoms was 1 day (1–2) in both groups. Emergency Severity Index (ESI) levels I, II, and III showed a significant increase (27.7% vs. 37.3%) in triage scoring compared to levels IV and V (72.3% vs. 62.7%) during the pandemic period (p<0.001). The median cost per patient during the pandemic period was statistically higher compared to the previous year ($19.57 [19.57–40.50] vs. $25.34 [31.50–52.01]; p<0.001). Overall costs during the pandemic period had a 1.6-fold decline.

Conclusion

We highlighted the changes in an ordinary PED profile during an extraordinary period. A shift in ESI levels in a more emergent direction was observed. While the number of nonurgent patients, especially those with infections, decreased, the rates of surgical cases, acute neurological and heart diseases, home accidents, and poisoning increased relative to the pre-pandemic period.

Viruses That Can and Cannot Coexist With Humans and the Future of SARS-CoV-2

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a worldwide pandemic. Many projections concerning the outbreak, such as the estimated number of cases and deaths in upcoming months, have been made available. However, what happens to the virus after the pandemic subsides has not been fully explored. In this article, we discuss the ways that past and present human viruses have emerged via zoonotic transmission, the mechanisms that they have acquired the ability for effective transmission among humans, the process to sustain a chain of transmission to coexist with humans, and the factors important for complete containment leading to eradication of viruses. These aspects of viral disease may provide clues for the future path that SARS-CoV-2 might take in relation to human infection.

Genotypic diversity, circulation patterns and co-detections among rhinoviruses in Queensland, 2001

Purpose

Rhinoviruses (RVs) occur more frequently than other viruses and more often in people displaying symptoms than in those without. We sought to estimate the spectrum of RV diversity, RV species seasonality and to analyse RV involvement in respiratory virus co-detections.

Methodology

A convenience collection of 1179 airway sample extracts from patients with suspected respiratory infections, collected during 2001, was subjected to comprehensive molecular testing.

Results

RVs were the most common virus detected. We were able to genotype ~90 % of RV detections, identifying 70 distinct RVs, spanning all three species. RV-Bs were under-represented. We found RV species co-circulated at times, although one species usually dominated. Each species displayed a bimodal distribution.

Conclusion

Notably, RVs and influenza A viruses (IFAV) seldom co-occurred, supporting their roles as primary pathogens of the airway among acutely ill infants. Whether RV circulation has a moderating or controlling effect on the IFAV season or is controlled by it cannot be determined from these data. Despite the frequent perception that RVs commonly co-occur with another virus, our findings indicated this was not always the case. Nearly 80 % of RV detections occurred alone. Understanding more about population-level interference between viruses may allow us to harness aspects of it to generate a non-specific antiviral intervention that mimics a putative protective effect. For routine respiratory virus screening to best serve the patient, RV testing should be a principal component of any acute respiratory illness testing algorithm throughout the year.