Demographic variability, vaccination, and the spatiotemporal dynamics of rotavirus epidemics

Scenario design for infectious disease projections: Integrating concepts from decision analysis and experimental design

Across many fields, scenario modeling has become an important tool for exploring long-term projections and how they might depend on potential interventions and critical uncertainties, with relevance to both decision makers and scientists. In the past decade, and especially during the COVID-19 pandemic, the field of epidemiology has seen substantial growth in the use of scenario projections. Multiple scenarios are often projected at the same time, allowing important comparisons that can guide the choice of intervention, the prioritization of research topics, or public communication. The design of the scenarios is central to their ability to inform important questions. In this paper, we draw on the fields of decision analysis and statistical design of experiments to propose a framework for scenario design in epidemiology, with relevance also to other fields. We identify six different fundamental purposes for scenario designs (decision making, sensitivity analysis, situational awareness, horizon scanning, forecasting, and value of information) and discuss how those purposes guide the structure of scenarios. We discuss other aspects of the content and process of scenario design, broadly for all settings and specifically for multi-model ensemble projections. As an illustrative case study, we examine the first 17 rounds of scenarios from the U.S. COVID-19 Scenario Modeling Hub, then reflect on future advancements that could improve the design of scenarios in epidemiological settings.

Impact of rotavirus vaccination in Malawi from 2012 to 2022 compared to model predictions before, during, and after the COVID-19 pandemic

Background

Rotarix® rotavirus vaccine was introduced into the Malawi national immunization program in October 2012. We used a previously developed mathematical models to estimate overall vaccine effectiveness over a 10-year period following rotavirus vaccine introduction.

Methods

We analyzed data on children <5 years old hospitalized with acute gastroenteritis in Blantyre, Malawi from January 2012 to June 2022, compared to pre-vaccination data. We estimated vaccine coverage before, during, and after the COVID-19 pandemic using data from rotavirus-negative children. We compared model predictions for the weekly number of rotavirus-associated gastroenteritis (RVGE) cases to the observed number by age to validate model predictions and estimate overall vaccine effectiveness.

Results

The number of RVGE and rotavirus-negative acute gastroenteritis cases declined substantially following vaccine introduction. Vaccine coverage among rotavirus-negative controls was >90% with two doses by July 2014, and declined to a low of ~80% in October 2020, before returning to pre-pandemic levels by July 2021. Our models captured the post-vaccination trends in RVGE incidence, with 5.4% to 19.4% of observed weekly RVGE cases falling outside of the 95% prediction intervals. Comparing observed RVGE cases to the model-predicted incidence without vaccination, overall vaccine effectiveness was estimated to be 36.0% (95% prediction interval: 33.6%, 39.9%) peaking in 2014 and was highest in infants (52.5%; 95% prediction interval: 50.1%, 54.9%).

Conclusions

Overall effectiveness of rotavirus vaccination in Malawi is modest despite high vaccine coverage and has plateaued since 2016. Our mathematical models provide a validated platform for assessing strategies to improve rotavirus vaccine impact.

Prediction of effectiveness of universal rotavirus vaccination in Southwestern Vietnam based on a dynamic mathematical model

Vaccinating young children against rotavirus (RV) is a promising preventive strategy against rotavirus gastroenteritis (RVGE). We evaluated the relative risk reduction of RVGE induced by universal vaccination in Vietnam through dynamic model analysis. We developed an age-stratified dynamic Vaccinated-Susceptible-Infectious-Recovered-Susceptible model to analyze RV transmission and assess vaccine effectiveness (VE). We assumed 3 different vaccine efficacies: 55%, 70%, and 85%. For model calibration, we used a database of patients under 5 years of age admitted to Ho Chi Minh No.1 Hospital with RVGE between January 2013 and December 2018. Assuming a vaccination rate of 95%, the number of RVGE hospitalizations after 5 years from universal RV vaccination decreased from 92,502 cases to 45,626 with 85% efficacy, to 54,576 cases with 70% efficacy, and to 63,209 cases with 55% efficacy. Additionally, RVGE hospitalizations after 10 years decreased from 177,950 to 89,517 with 85% efficacy and to 121,832 cases with 55% efficacy. The relative risk reductions of RVGE after 10 years were 49.7% with 85% efficacy, 40.6% with 70% efficacy, and 31.5% with 55% efficacy. The VE was 1.10 times (95% CI, 1.01-1.22) higher in the 4-months to 1-year-old age group than in the other age groups (P = 0.038), when applying 85% efficacy with 95% coverage. In conclusion, despite its relatively lower efficacy compared to high-income countries, RV vaccination remains an effective intervention in Southwestern Vietnam. In particular, implementing universal RV vaccination with higher coverage would result in a decrease in RVGE hospitalizations among Vietnamese children under 5 years of age.

The success of publicly funded rotavirus vaccine programs for preventing community- and hospital-acquired rotavirus infections in Canadian pediatric hospitals: an observational study

BACKGROUND

Canadian immunization programs for rotavirus started in 2011. We sought to determine their effect on the burden of community-acquired admissions and hospital-acquired rotavirus at pediatric hospitals.

METHODS

The Canadian Immunization Monitoring Program Active (IMPACT) network conducted active surveillance for rotavirus-positive hospital admissions between 2005 and 2020 at 12 pediatric hospitals. We used yearly rates of community-acquired rotavirus per 10 000 admissions and hospital-acquired rotavirus infections per 1000 patient-days to determine changes in the pre- and post-vaccine program periods.

RESULTS

During the 15-year study period, 5691 rotavirus hospital admissions and hospital-acquired infections were detected, including 4323 (76%) community-acquired infections and 1368 (24%) hospital-acquired infections. The average community-acquired rate in the pre-vaccine period was 60.3 (95% confidence interval [CI] 53.7-68.3) per 10 000 admissions, with a decline to 11.0 (95% CI 7.5-15.1) per 10 000 admissions in the post-vaccine period, resulting in an average reduction of 81.7% (95% CI 74.4%-87.8%). The rate of hospital-acquired rotavirus declined from 0.35 (95% CI 0.29-0.41) per 1000 patient-days in the pre-vaccine period to 0.05 (95% CI 0.03-0.07) per 1000 patient-days in the post-vaccine period, resulting in an 85.3% (95% CI 77.7%-91.9%) average decline. Herd protection was present among children aged 2-16 years.

INTERPRETATION

Although start dates of rotavirus vaccine programs across provinces varied, there was around an 80% average decrease in both community-acquired and hospital-acquired rotavirus infections at pediatric hospitals in Canada in the 1- to 9-year interval after implementation of rotavirus vaccine programs. Herd protection is an important aspect of rotavirus vaccines for other children who are not vaccine eligible, and rotavirus vaccines continue to provide important benefits both for children and health care systems.

Scenario Design for Infectious Disease Projections: Integrating Concepts from Decision Analysis and Experimental Design

Across many fields, scenario modeling has become an important tool for exploring long-term projections and how they might depend on potential interventions and critical uncertainties, with relevance to both decision makers and scientists. In the past decade, and especially during the COVID-19 pandemic, the field of epidemiology has seen substantial growth in the use of scenario projections. Multiple scenarios are often projected at the same time, allowing important comparisons that can guide the choice of intervention, the prioritization of research topics, or public communication. The design of the scenarios is central to their ability to inform important questions. In this paper, we draw on the fields of decision analysis and statistical design of experiments to propose a framework for scenario design in epidemiology, with relevance also to other fields. We identify six different fundamental purposes for scenario designs (decision making, sensitivity analysis, value of information, situational awareness, horizon scanning, and forecasting) and discuss how those purposes guide the structure of scenarios. We discuss other aspects of the content and process of scenario design, broadly for all settings and specifically for multi-model ensemble projections. As an illustrative case study, we examine the first 17 rounds of scenarios from the U.S. COVID-19 Scenario Modeling Hub, then reflect on future advancements that could improve the design of scenarios in epidemiological settings.

Mumps epidemic dynamics in the United States before vaccination (1923-1932)

Mumps is a vaccine-preventable, reemerging, and highly transmissible infectious disease. Widespread vaccination dramatically reduced cases; however, case counts have been increasing over the past 20 years. To provide a quantitative overview of historical mumps dynamics that can act as baseline information to help identify causes of mumps reemergence, we analyzed timeseries of cases reported from 1923 to 1932 in the United States. During that time, 239,230 mumps cases were reported in 70 cities. Larger cities reported annual epidemics and smaller cities reported intermittent, sporadic outbreaks. The critical community size above which transmission continuously occurred was likely between 365,583 and 781,188 individuals but could range as high as 3,376,438 individuals. Mumps cases increased as city size increased, suggesting density-dependent transmission. Using a density-dependent SEIR model, we calculated a mean effective reproductive number (Re) of 1.2. Re varied by city and over time, with periodic high values that could characterize short periods of very high transmission known as superspreading events. Case counts most often peaked in March, with higher-than-average transmission from December through April and showed a correlation with weekly births. While certain city pairs in Midwestern states had synchronous outbreaks, most outbreaks were less synchronous and not driven by distance between cities. This work demonstrates the importance of long-term infectious disease surveillance data and will inform future studies on mumps reemergence and control.

Effectiveness of Pentavalent Rotavirus Vaccine in Shanghai, China: A Test-Negative Design Study

OBJECTIVE

To evaluate vaccine effectiveness (VE) of a live oral pentavalent rotavirus vaccine (RotaTeq, RV5) among young children in Shanghai, China, via a test-negative design study.

STUDY DESIGN

We consecutively recruited children visiting a tertiary children's hospital for acute diarrhea from November 2021 to February 2022. Information on clinical data and rotavirus vaccination was collected. Fresh fecal samples were obtained for rotavirus detection and genotyping. To evaluate VE of RV5 against rotavirus gastroenteritis among young children, unconditional logistic regression models were conducted to compare ORs for vaccination between rotavirus-positive cases and test-negative controls.

RESULTS

A total of 390 eligible children with acute diarrhea were enrolled, including 45 (11.54%) rotavirus-positive cases and 345 (88.46%) test-negative controls. After excluding 4 cases (8.89%) and 55 controls (15.94%) who had received the Lanzhou lamb rotavirus vaccine, 41 cases (12.39%) and 290 controls (87.61%) were included for the evaluation of RV5 VE. After adjustment for potential confounders, the 3-dose RV5 vaccination showed 85% (95% CI, 50%-95%) VE against mild to moderate rotavirus gastroenteritis among children aged 14 weeks to ≤4 years and 97% (95% CI, 83%-100%) VE among children aged 14 weeks to ≤2 years with genotypes G8P8, G9P8, and G2P4 represented 78.95%, 18.42%, and 2.63% of circulation strains, respectively.

CONCLUSIONS

A 3-dose vaccination of RV5 is highly protective against rotavirus gastroenteritis among young children in Shanghai. The G8P8 genotype prevailled in Shanghai after RV5 introduction.

Epidemiological impacts of post-infection mortality

Infectious diseases may cause some long-term damage to their host, leading to elevated mortality even after recovery. Mortality due to complications from so-called 'long COVID' is a stark illustration of this potential, but the impacts of such post-infection mortality (PIM) on epidemic dynamics are not known. Using an epidemiological model that incorporates PIM, we examine the importance of this effect. We find that in contrast to mortality during infection, PIM can induce epidemic cycling. The effect is due to interference between elevated mortality and reinfection through the previously infected susceptible pool. In particular, robust immunity (via decreased susceptibility to reinfection) reduces the likelihood of cycling; on the other hand, disease-induced mortality can interact with weak PIM to generate periodicity. In the absence of PIM, we prove that the unique endemic equilibrium is stable and therefore our key result is that PIM is an overlooked phenomenon that is likely to be destabilizing. Overall, given potentially widespread effects, our findings highlight the importance of characterizing heterogeneity in susceptibility (via both PIM and robustness of host immunity) for accurate epidemiological predictions. In particular, for diseases without robust immunity, such as SARS-CoV-2, PIM may underlie complex epidemiological dynamics especially in the context of seasonal forcing.

Charting the spatial dynamics of early SARS-CoV-2 transmission in Washington state

The spread of SARS-CoV-2 has been geographically uneven. To understand the drivers of this spatial variation in SARS-CoV-2 transmission, in particular the role of stochasticity, we used the early stages of the SARS-CoV-2 invasion in Washington state as a case study. We analysed spatially-resolved COVID-19 epidemiological data using two distinct statistical analyses. The first analysis involved using hierarchical clustering on the matrix of correlations between county-level case report time series to identify geographical patterns in the spread of SARS-CoV-2 across the state. In the second analysis, we used a stochastic transmission model to perform likelihood-based inference on hospitalised cases from five counties in the Puget Sound region. Our clustering analysis identifies five distinct clusters and clear spatial patterning. Four of the clusters correspond to different geographical regions, with the final cluster spanning the state. Our inferential analysis suggests that a high degree of connectivity across the region is necessary for the model to explain the rapid inter-county spread observed early in the pandemic. In addition, our approach allows us to quantify the impact of stochastic events in determining the subsequent epidemic. We find that atypically rapid transmission during January and February 2020 is necessary to explain the observed epidemic trajectories in King and Snohomish counties, demonstrating a persisting impact of stochastic events. Our results highlight the limited utility of epidemiological measures calculated over broad spatial scales. Furthermore, our results make clear the challenges with predicting epidemic spread within spatially extensive metropolitan areas, and indicate the need for high-resolution mobility and epidemiological data.

The Evolution of Post-Vaccine G8P[4] Group a Rotavirus Strains in Rwanda; Notable Variance at the Neutralization Epitope Sites

Africa has a high level of genetic diversity of rotavirus strains, which is suggested to be a possible reason contributing to the suboptimal effectiveness of rotavirus vaccines in this region. One strain that contributes to this rotavirus diversity in Africa is the G8P[4]. This study aimed to elucidate the entire genome and evolution of Rwandan G8P[4] strains. Illumina sequencing was performed for twenty-one Rwandan G8P[4] rotavirus strains. Twenty of the Rwandan G8P[4] strains had a pure DS-1-like genotype constellation, and one strain had a reassortant genotype constellation. Notable radical amino acid differences were observed at the neutralization sites when compared with cognate regions in vaccine strains potentially playing a role in neutralization escape. Phylogenetic analysis revealed that the closest relationship was with East African human group A rotavirus (RVA) strains for five of the genome segments. Two genome sequences of the NSP4 genome segment were closely related to bovine members of the DS-1-like family. Fourteen VP1 and eleven VP3 sequences had the closest relationships with the RotaTeq™ vaccine WC3 bovine genes. These findings suggest that the evolution of VP1 and VP3 might have resulted from reassortment events with RotaTeq™ vaccine WC3 bovine genes. The close phylogenetic relationship with East African G8P[4] strains from Kenya and Uganda suggests co-circulation in these countries. These findings highlight the need for continued whole-genomic surveillance to elucidate the evolution of G8P[4] strains, especially after the introduction of rotavirus vaccination.

Seasonal pattern in occurrence of rotavirus infection (RV) in diarrheic children, calves and piglets from Bareilly, India

Rapid and reliable diagnosis for diarrhoeal disease is critically important for the differentiation of etiological agents and subsequent suitable treatment modalities. The objective of the study is to reveal the seasonal pattern in the occurrence of rotavirus in diarrheic children, calves and piglets from Bareilly, Uttar Pradesh, India. A total of 115 diarrhoeal samples were collected, out of which 51 were collected during post-monsoon/autumn (September 2018-November 2018) and 64 during the winter season (December 2018-February 2019). The samples were collected from children <5 years (n = 50), piglets <3 months (n = 35) and calves <6 months of age (n = 30). These samples were screened by ribonucleic acid-polyacrylamide gel electrophoresis (RNA-PAGE) and reverse transcriptase-polymerase chain reaction (RT-PCR) by targeting the VP6 gene of rotavirus A (RVA) and the two were compared. In RNA-PAGE 29.4% (5/17), 6.3% (1/16) and 0% (0/18) samples collected from children, calves and piglets, respectively were rotavirus positive during the autumn season while 45.5% (15/33), 21.4% (3/14) and 17.7% (3/17) samples in the winter season. In RT-PCR, 41.2% (7/17), 12.5% (2/16) and 0% (0/18) samples were rotavirus positive in the autumn season while 51.5% (17/33), 28.6% (4/14) and 29.4% (5/17) samples in winter season collected from children, calves and piglets, respectively. On statistical analysis, no significant difference between the season and number of positives in children and calves (p > 0.05) was observed, however in piglets significantly higher number of RVA positives were detected in the winter season than autumn (p < 0.01). The diagnostic test comparison of RNA-PAGE and RT-PCR showed no statistically significant difference in detecting the RVA positives (p > 0.05). Overall the percent positivity showed a seasonal pattern with higher positivity in winter as compared to autumn season.

Model-based estimation of the impact on rotavirus disease of RV3-BB vaccine administered in a neonatal or infant schedule

Rotavirus infection is a common cause of severe diarrheal disease and a major cause of deaths and hospitalizations among young children. Incidence of rotavirus has declined globally with increasing vaccine coverage. However, it remains a significant cause of morbidity and mortality in low-income countries where vaccine access is limited and efficacy is lower. The oral human neonatal vaccine RV3-BB can be safely administered earlier than other vaccines, and recent trials in Indonesia have demonstrated high efficacy. In this study, we use a stochastic individual-based model of rotavirus transmission and disease to estimate the anticipated population-level impact of RV3-BB following delivery according to either an infant (2, 4, 6 months) and neonatal (0, 2, 4 months) schedule. Using our model, which incorporated an age- and household-structured population and estimates of vaccine efficacy derived from trial data, we found both delivery schedules to be effective at reducing infection and disease. We estimated 95-96% reductions in infection and disease in children under 12 months of age when vaccine coverage is 85%. We also estimate high levels of indirect protection from vaccination, including 78% reductions in infection in adults over 17 years of age. Even for lower vaccine coverage of 55%, we estimate reductions of 84% in infection and disease in children under 12 months of age. While open questions remain about the drivers of observed lower efficacy in low-income settings, our model suggests RV3-BB could be effective at reducing infection and preventing disease in young infants at the population level.

Drivers of respiratory syncytial virus seasonal epidemics in children under 5 years in Kilifi, coastal Kenya

Respiratory syncytial virus (RSV) causes significant childhood morbidity and mortality in the developing world. The determinants of RSV seasonality are of importance in designing interventions. They are poorly understood in tropical and sub-tropical regions in low- and middle-income countries. Our study utilized long-term surveillance data on cases of RSV associated with severe or very severe pneumonia in children aged 1 day to 59 months admitted to the Kilifi County Hospital. A generalized additive model was used to investigate the association between RSV admissions and meteorological variables (maximum temperature, rainfall, absolute humidity); weekly number of births within the catchment population; and school term dates. Furthermore, a time-series-susceptible-infected-recovered (TSIR) model was used to reconstruct an empirical transmission rate which was used as a dependent variable in linear regression and generalized additive models with meteorological variables and school term dates. Maximum temperature, absolute humidity, and weekly number of births were significantly associated with RSV activity in the generalized additive model. Results from the TSIR model indicated that maximum temperature and absolute humidity were significant factors. Rainfall and school term did not yield significant relationships. Our study indicates that meteorological parameters and weekly number of births potentially play a role in the RSV seasonality in this region. More research is required to explore the underlying mechanisms underpinning the observed relationships.

Rotavirus epidemiology and genotype distribution in hospitalised children, Greece, 2008 to 2020: A prospective multicentre study

BackgroundTwo rotavirus (RV) vaccines were licensed in Greece in late 2006 and included in the national immunisation programme in 2012.AimTo study the epidemiology and genotype distribution of RV in children during the post-vaccination period and assess the impact of increased vaccination coverage.MethodsIn a prospective multicentre hospital-based study, hospitalised children (≤ 16 years) with an RV-positive faecal sample were recruited. Epidemiological and genotyping analyses were performed; periods of low (2008-12) and moderate (2012-20) RV vaccination coverage were compared. Statistical analysis was performed with a chi-squared or Mann-Whitney U test and logistic regression.ResultsA total of 3,874 children (55.6% male; n = 2,153) with median age of 1.4 years (IQR: 0.5-3.3) were studied during 2008-20. Most RV-infected children were aged ≤ 3 years (72.2%) and hospitalised during December-May (69.1%). Common RV genotypes (G1P[8], G2P[4], G3P[8], G4P[8], G9P[8], G12P[8]) were detected in 92.2% of samples; G-P combinations with prevalence above 1% were G4P[8] (44.1%), G1P[8] (25.4%), G2P[4] (14.9%), G9P[8] (3.5%), G12P[8] (2.2%), G3P[8] (2.1%), other (4.3%) and mixed (3.5%). Of all samples, 97.6% were homotypic or partially heterotypic to vaccines' genotypes. With moderate vaccination coverage, the seasonal peak was detected earlier, children were older and partially or fully heterotypic genotypes were increased (p < 0.001).ConclusionsIn the era of moderate RV vaccination coverage in Greece, epidemiology of RV in hospitalised children seemed to change. However, most circulating genotypes remain homotypic or partially heterotypic to RV vaccines. Continuous epidemiological surveillance and genotyping are important to monitor possible changes arising from RV vaccines' implementation.

Rotavirus epidemiology and genotype distribution in hospitalised children, Greece, 2008 to 2020: A prospective multicentre study

BackgroundTwo rotavirus (RV) vaccines were licensed in Greece in late 2006 and included in the national immunisation programme in 2012.AimTo study the epidemiology and genotype distribution of RV in children during the post-vaccination period and assess the impact of increased vaccination coverage.MethodsIn a prospective multicentre hospital-based study, hospitalised children (≤ 16 years) with an RV-positive faecal sample were recruited. Epidemiological and genotyping analyses were performed; periods of low (2008-12) and moderate (2012-20) RV vaccination coverage were compared. Statistical analysis was performed with a chi-squared or Mann-Whitney U test and logistic regression.ResultsA total of 3,874 children (55.6% male; n = 2,153) with median age of 1.4 years (IQR: 0.5-3.3) were studied during 2008-20. Most RV-infected children were aged ≤ 3 years (72.2%) and hospitalised during December-May (69.1%). Common RV genotypes (G1P[8], G2P[4], G3P[8], G4P[8], G9P[8], G12P[8]) were detected in 92.2% of samples; G-P combinations with prevalence above 1% were G4P[8] (44.1%), G1P[8] (25.4%), G2P[4] (14.9%), G9P[8] (3.5%), G12P[8] (2.2%), G3P[8] (2.1%), other (4.3%) and mixed (3.5%). Of all samples, 97.6% were homotypic or partially heterotypic to vaccines' genotypes. With moderate vaccination coverage, the seasonal peak was detected earlier, children were older and partially or fully heterotypic genotypes were increased (p < 0.001).ConclusionsIn the era of moderate RV vaccination coverage in Greece, epidemiology of RV in hospitalised children seemed to change. However, most circulating genotypes remain homotypic or partially heterotypic to RV vaccines. Continuous epidemiological surveillance and genotyping are important to monitor possible changes arising from RV vaccines' implementation.

Models with higher effective dimensions tend to produce more uncertain estimates

Mathematical models are getting increasingly detailed to better predict phenomena or gain more accurate insights into the dynamics of a system of interest, even when there are no validation or training data available. Here, we show through ANOVA and statistical theory that this practice promotes fuzzier estimates because it generally increases the model's effective dimensions, i.e., the number of influential parameters and the weight of high-order interactions. By tracking the evolution of the effective dimensions and the output uncertainty at each model upgrade stage, modelers can better ponder whether the addition of detail truly matches the model's purpose and the quality of the data fed into it.

Models with higher effective dimensions tend to produce more uncertain estimates

Mathematical models are getting increasingly detailed to better predict phenomena or gain more accurate insights into the dynamics of a system of interest, even when there are no validation or training data available. Here, we show through ANOVA and statistical theory that this practice promotes fuzzier estimates because it generally increases the model's effective dimensions, i.e., the number of influential parameters and the weight of high-order interactions. By tracking the evolution of the effective dimensions and the output uncertainty at each model upgrade stage, modelers can better ponder whether the addition of detail truly matches the model's purpose and the quality of the data fed into it.

Major Changes in Spatiotemporal Trends of US Rotavirus Laboratory Detections After Rotavirus Vaccine Introduction-2009-2021

For the 15 years before rotavirus vaccine introduction in 2006, annual rotavirus activity in the United States showed a distinct spatiotemporal pattern, peaking first in the Southwest and last in the Northeast. We modeled spatiotemporal trends in rotavirus laboratory detections from 2009 to 2021. Laboratories reporting to the National Respiratory and Enteric Virus Surveillance System were eligible for inclusion in a given surveillance year (July to June) if ≥1 polymerase chain reaction or enzyme immunoassay rotavirus test per week was reported during ≥26 weeks and totaling ≥100 annual tests. For each laboratory, the season peak was the week with the highest 7-week moving average of the number of rotavirus positive tests during the national season, defined as the period with a 3-week moving average of >10% rotavirus positivity lasting ≥2 consecutive weeks. We input peak week as a continuous variable and the geospatial coordinates of each laboratory into a spherical variogram model for Kriging spatial interpolation. We also created a state-level bivariate choropleth map using tertiles of the 2010-2019 average birth rates and rotavirus vaccine coverage. Following the established biennial trend, the 2010-2011, 2012-2013, 2014-2015, 2016-2017, and 2018-2019 surveillance years had >10% rotavirus positivity for ≥2 weeks and were included in the geospatial analysis. During all 5 seasons included in the geospatial analysis, the earliest peak week occurred in Oklahoma, Arkansas, and the western Gulf coast, a pattern markedly different from prevaccine seasons. These states also had the average lowest rotavirus vaccine coverage and highest birth rate, suggesting that more rapid accumulation of susceptible children drives annual rotavirus season activity. Increasing vaccine coverage remains a key tool in reducing rotavirus burden.

Rotavirus Strain Trends in United States, 2009–2016: Results from the National Rotavirus Strain Surveillance System (NRSSS)

Before the introduction of vaccines, group A rotaviruses (RVA) were the leading cause of acute gastroenteritis in children worldwide. The National Rotavirus Strain Surveillance System (NRSSS) was established in 1996 by the Centers for Disease Control and Prevention (CDC) to perform passive RVA surveillance in the USA. We report the distribution of RVA genotypes collected through NRSSS during the 2009–2016 RVA seasons and retrospectively examine the genotypes detected through the NRSSS since 1996. During the 2009–2016 RVA seasons, 2134 RVA-positive fecal specimens were sent to the CDC for analysis of the VP7 and VP4 genes by RT-PCR genotyping assays and sequencing. During 2009–2011, RVA genotype G3P[8] dominated, while G12P[8] was the dominant genotype during 2012–2016. Vaccine strains were detected in 1.7% of specimens and uncommon/unusual strains, including equine-like G3P[8] strains, were found in 1.9%. Phylogenetic analyses showed limited VP7 and VP4 sequence variation within the common genotypes with 1–3 alleles/lineages identified per genotype. A review of 20 years of NRSSS surveillance showed two changes in genotype dominance, from G1P[8] to G3P[8] and then G3P[8] to G12P[8]. A better understanding of the long-term effects of vaccine use on epidemiological and evolutionary dynamics of circulating RVA strains requires continued surveillance.

The influence of demographic and meteorological factors on temporal patterns of rotavirus infection in Dhaka, Bangladesh

To quantify the potential impact of rotavirus vaccines and identify strategies to improve vaccine performance in Bangladesh, a better understanding of the drivers of pre-vaccination rotavirus patterns is required. We developed and fitted mathematical models to 23 years (1990-2012) of weekly rotavirus surveillance data from Dhaka with and without incorporating long-term and seasonal variation in the birth rate and meteorological factors. We performed external model validation using data between 2013 and 2019 from the regions of Dhaka and Matlab. The models showed good agreement with the observed age distribution of rotavirus cases and captured the observed shift in seasonal patterns of rotavirus hospitalizations from biannual to annual peaks. The declining long-term trend in the birth rate in Bangladesh was the key driver of the observed shift from biannual to annual winter rotavirus patterns. Meteorological indices were also important: a 1°C, 1% and 1 mm increase in diurnal temperature range, surface water presence and degree of wetness were associated with a 19%, 3.9% and 0.6% increase in the transmission rate, respectively. The model demonstrated reasonable predictions for both Dhaka and Matlab, and can be used to evaluate the impact of rotavirus vaccination in Bangladesh against changing patterns of disease incidence.

Projecting the SARS-CoV-2 transition from pandemicity to endemicity: Epidemiological and immunological considerations

In this review, we discuss the epidemiological dynamics of different viral infections to project how the transition from a pandemic to endemic Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) might take shape. Drawing from theories of disease invasion and transmission dynamics, waning immunity in the face of viral evolution and antigenic drift, and empirical data from influenza, dengue, and seasonal coronaviruses, we discuss the putative periodicity, severity, and age dynamics of SARS-CoV-2 as it becomes endemic. We review recent studies on SARS-CoV-2 epidemiology, immunology, and evolution that are particularly useful in projecting the transition to endemicity and highlight gaps that warrant further research.

Rotaviruses: From Pathogenesis to Disease Control—A Critical Review

Since their first recognition in human cases about four decades ago, rotaviruses have remained the leading cause of acute severe dehydrating diarrhea among infants and young children worldwide. The WHO prequalification of oral rotavirus vaccines (ORV) a decade ago and its introduction in many countries have yielded a significant decline in the global burden of the disease, although not without challenges to achieving global effectiveness. Poised by the unending malady of rotavirus diarrhea and the attributable death cases in developing countries, we provide detailed insights into rotavirus biology, exposure pathways, cellular receptors and pathogenesis, host immune response, epidemiology, and vaccination. Additionally, recent developments on the various host, viral and environmental associated factors impacting ORV performance in low-and middle-income countries (LMIC) are reviewed and their significance assessed. In addition, we review the advances in nonvaccine strategies (probiotics, candidate anti-rotaviral drugs, breastfeeding) to disease prevention and management.

Dissecting recurrent waves of pertussis across the boroughs of London

Pertussis has resurfaced in the UK, with incidence levels not seen since the 1980s. While the fundamental causes of this resurgence remain the subject of much conjecture, the study of historical patterns of pathogen diffusion can be illuminating. Here, we examined time series of pertussis incidence in the boroughs of Greater London from 1982 to 2013 to document the spatial epidemiology of this bacterial infection and to identify the potential drivers of its percolation. The incidence of pertussis over this period is characterized by 3 distinct stages: a period exhibiting declining trends with 4-year inter-epidemic cycles from 1982 to 1994, followed by a deep trough until 2006 and the subsequent resurgence. We observed systematic temporal trends in the age distribution of cases and the fade-out profile of pertussis coincident with increasing national vaccine coverage from 1982 to 1990. To quantify the hierarchy of epidemic phases across the boroughs of London, we used the Hilbert transform. We report a consistent pattern of spatial organization from 1982 to the early 1990s, with some boroughs consistently leading epidemic waves and others routinely lagging. To determine the potential drivers of these geographic patterns, a comprehensive parallel database of borough-specific features was compiled, comprising of demographic, movement and socio-economic factors that were used in statistical analyses to predict epidemic phase relationships among boroughs. Specifically, we used a combination of a feed-forward neural network (FFNN), and SHapley Additive exPlanations (SHAP) values to quantify the contribution of each covariate to model predictions. Our analyses identified a number of predictors of a borough's historical epidemic phase, specifically the age composition of households, the number of agricultural and skilled manual workers, latitude, the population of public transport commuters and high-occupancy households. Univariate regression analysis of the 2012 epidemic identified the ratio of cumulative unvaccinated children to the total population and population of Pakistan-born population to have moderate positive and negative association, respectively, with the timing of epidemic. In addition to providing a comprehensive overview of contemporary pertussis transmission in a large metropolitan population, this study has identified the characteristics that determine the spatial spread of this bacterium across the boroughs of London.

Infectious disease in an era of global change

The twenty-first century has witnessed a wave of severe infectious disease outbreaks, not least the COVID-19 pandemic, which has had a devastating impact on lives and livelihoods around the globe. The 2003 severe acute respiratory syndrome coronavirus outbreak, the 2009 swine flu pandemic, the 2012 Middle East respiratory syndrome coronavirus outbreak, the 2013-2016 Ebola virus disease epidemic in West Africa and the 2015 Zika virus disease epidemic all resulted in substantial morbidity and mortality while spreading across borders to infect people in multiple countries. At the same time, the past few decades have ushered in an unprecedented era of technological, demographic and climatic change: airline flights have doubled since 2000, since 2007 more people live in urban areas than rural areas, population numbers continue to climb and climate change presents an escalating threat to society. In this Review, we consider the extent to which these recent global changes have increased the risk of infectious disease outbreaks, even as improved sanitation and access to health care have resulted in considerable progress worldwide.

Impact of rotavirus vaccination on rotavirus hospitalizations in Taiwanese children

In 2006, two rotavirus vaccines were licensed in Taiwan but were not added to the national immunization schedule. National Health Insurance data from 2003 through 2017 were used to compare rotavirus-associated pediatric hospitalizations before and after vaccine introduction. Rotavirus hospitalization rates among children < 5 years of age significantly declined by 24% (95% confidence interval [CI] 23 - 25%) in post-vaccine compared to pre-vaccine rotavirus seasons. Rotavirus hospitalization rates declined by 42% (95% CI 39 - 44%) among infants < 12 months of age, and by 38% (95% CI 36 - 40%) among children 12 - 23 months of age. These findings suggest that, despite not being included in the national immunization schedule, rotavirus vaccines had a measurable impact on reducing rotavirus hospitalization burden among Taiwanese children.

Analysis of spatiotemporal mobility of shared-bike usage during COVID-19 pandemic in Beijing

The entire world is experiencing a crisis in public health and the economy owing to the coronavirus disease 2019 (COVID-19) pandemic. Understanding human mobility during the pandemic helps to formulate interventional strategies and resilient measures. The widely used bike-sharing system (BSS) could illustrate the activities of urban dwellers over time and space in big cities; however, it is rarely reported in epidemiological research. In this article, we analyze the BSS data to examine the human mobility of shared-bike users, detecting the key time nodes of different pandemic stages and demonstrating the evolution of human mobility owing to the onset of the COVID-19 threat and administrative restrictions. We assessed the net impact of the pandemic using the results of co-location analysis between shared-bike usage and points of interest. Our results demonstrate that the pandemic has reduced overall bike usage by 64.8%; however, a subsequent average increase (15.9%) in shared-bike usage has been observed, suggesting partial recovery of productive and residential activities, although far from normal times. These findings could be a reference for epidemiological research, and thereby aid policymaking in the context of the current COVID-19 outbreak and other epidemic events at the city scale.

The impact of infection-derived immunity on disease dynamics

When modeling infectious diseases, it is common to assume that infection-derived immunity is either (1) non-existent or (2) perfect and lifelong. However there are many diseases in which infection-derived immunity is known to be present but imperfect. There are various ways in which infection-derived immunity can fail, which can ultimately impact the probability that an individual be reinfected by the same pathogen, as well as the long-run population-level prevalence of the pathogen. Here we discuss seven different models of imperfect infection-derived immunity, including waning, leaky and all-or-nothing immunity. For each model we derive the probability that an infected individual becomes reinfected during their lifetime, given that the system is at endemic equilibrium. This can be thought of as the impact that each of these infection-derived immunity failures have on reinfection. This measure is useful because it provides us with a way to compare different modes of failure of infection-derived immunity.

Impact analysis of rotavirus vaccination in various geographic regions in Western Europe

BACKGROUND

Universal mass vaccination (UMV) against rotavirus has been implemented in many but not all European countries. This study investigated the impact of UMV on rotavirus incidence trends by comparing European countries with UMV: Belgium, England/Wales and Germany versus countries without UMV: Denmark and the Netherlands.

METHODS

For this observational retrospective cohort study, time series data (2001-2016) on rotavirus detections, meteorological factors and population demographics were collected. For each country, several meteorological and population factors were investigated as possible predictors of rotavirus incidence. The final set of predictors were incorporated in negative binomial models accounting for seasonality and serial autocorrelation, and time-varying incidence rate ratios (IRR) were calculated for each age group and country separately. The overall vaccination impact two years after vaccine implementation was estimated by pooling the results using a random effects meta-analyses. Independent t-tests were used to compare annual epidemics in the pre-vaccination and post-vaccination era to explore any changes in the timing of rotavirus epidemics.

RESULTS

The population size and several meteorological factors were predictors for the rotavirus epidemiology. Overall, we estimated a 42% (95%-CI 23;56%) reduction in rotavirus incidence attributable to UMV. Strongest reductions were observed for age-groups 0-, 1- and 2-years (IRR 0.47, 0.48 and 0.63, respectively). No herd effect induced by UMV in neighbouring countries was observed. In all UMV countries, the start and/or stop and corresponding peak of the rotavirus season was delayed by 4-7 weeks.

CONCLUSIONS

The introduction of rotavirus UMV resulted in an overall reduction of 42% in rotavirus incidence in Western European countries two years after vaccine introduction and caused a change in seasonal pattern. No herd effect induced by UMV neighbouring countries was observed for Denmark and the Netherlands.

All-cause gastroenteritis hospitalisations of children decreased after the introduction of rotavirus vaccine in Stockholm

BACKGROUND

In Stockholm, Sweden, rotavirus vaccination was offered to children born after 1 March 2014. Our aim was to describe rates of hospitalisation due to community-acquired gastroenteritis before and after the introduction of the vaccine, and aetiology, underlying medical conditions and complications in admitted children.

METHODS

We retrospectively included patients from our catchment area hospitalised with a diagnosis of gastroenteritis during ten infection seasons 2008/2009-2017/2018, whereof six seasons prevaccination and four seasons postvaccination. We studied virus detection data and the patients' medical records.

RESULTS

We included 3718 episodes in 3513 children. In 2967 (80%), stools were tested with virus isolation, ELISA, PCR, or bacterial culture; 479 (16%) tested negative. The incidence rates, with 95% confidence intervals, for children <5 years hospitalised for rotavirus gastroenteritis were 2.9 (2.8-3.1) per 1000 person-years prevaccination and 0.65 (0.56-0.74) postvaccination, for a rate ratio (RR) of 0.22 (0.19-0.26, p < .001). The rates for all-cause gastroenteritis were 5.6 (5.4-5.9) prevaccination and 2.5 (2.3-2.7) postvaccination, RR 0.45 (0.42-0.50, p < .001). In 5-17-year-old children norovirus dominated with little change over time. Of patients <5 years, those with underlying conditions constituted a larger proportion postvaccination than prevaccination (30.7% vs. 24.2%, p < .001). A complication other than dehydration, most commonly seizures, arose in 8.8% of the patients <5 years prevaccination and 11.4% postvaccination (p < .05).

CONCLUSIONS

Rotavirus vaccination reduced the number of children <5 years requiring hospital care for gastroenteritis. We saw no replacement of rotavirus by other viruses.

The Statewide Economic Impact of Child Care-Associated Viral Acute Gastroenteritis Infections

INTRODUCTION

More than 65% of children aged ≤5 years in the United States require out-of-home child care. Child care attendance has been associated with an elevated risk of respiratory illness and acute gastroenteritis (AGE). While child care-associated respiratory disease cases are more numerous, AGE is associated with more severe symptoms and more than double the number of absences from child care. In addition, viral pathogens such as norovirus, rotavirus, and adenovirus are highly infectious and may be spread to parents and other household members. As a result, child care-associated viral AGE may incur substantial economic costs due to healthcare service usage and lost productivity.

METHODS

We used surveillance data from a network of child care centers in Washtenaw County, Michigan, as well as a household transmission model to estimate the annual cost of child care-associated viral AGE in the state of Michigan.

RESULTS

We estimated that child care-associated viral AGE in Michigan costs between $15 million and $31 million annually, primarily due to lost productivity.

CONCLUSIONS

The economic burden of child care-associated infections is considerable. Effective targeted interventions are needed to mitigate this impact.

RSV genomic diversity and the development of a globally effective RSV intervention

Respiratory syncytial virus (RSV) is the most common cause of serious lower respiratory tract illness in infants and children and causes significant disease in the elderly and immunocompromised. Recently there has been an acceleration in the development of candidate RSV vaccines, monoclonal antibodies and therapeutics. However, the effects of RSV genomic variability on the implementation of vaccines and therapeutics remain poorly understood. To address this knowledge gap, the National Institute of Allergy and Infectious Diseases and the Fogarty International Center held a workshop to summarize what is known about the global burden and transmission of RSV disease, the phylogeographic dynamics and genomics of the virus, and the networks that exist to improve the understanding of RSV disease. Discussion at the workshop focused on the implications of viral evolution and genomic variability for vaccine and therapeutics development in the context of various immunization strategies. This paper summarizes the meeting, highlights research gaps and future priorities, and outlines what has been achieved since the meeting took place. It concludes with an examination of what the RSV community can learn from our understanding of SARS-CoV-2 genomics and what insights over sixty years of RSV research can offer the rapidly evolving field of COVID-19 vaccines.

A Multivariate Spatiotemporal Model of COVID-19 Epidemic Using Ensemble of ConvLSTM Networks

The high R-naught factor of SARS-CoV-2 has created a race against time for mankind, and it necessitates rapid containment actions to control the spread. In such scenario short-term accurate spatiotemporal predictions can help understanding the dynamics of the spread in a geographic region and identify hotspots. However, due to the novelty of the disease there is very little disease-specific data generated yet. This poses a difficult problem for machine learning methods to learn a model of the epidemic spread from data. A proposed ensemble of convolutional LSTM-based spatiotemporal model can forecast the spread of the epidemic with high resolution and accuracy in a large geographic region. The feature construction method creates geospatial frames of features with or without temporal component based on latitudes and longitudes thus avoiding the need of location specific adjacency matrix. The model has been trained with available data for USA and Italy. It achieved 5.57% and 0.3% mean absolute percent error for total number of predicted infection cases in a 5-day prediction period for USA and Italy, respectively.

Continued Evidence of the Impact of Rotavirus Vaccine in Children Less Than 3 Years of Age From the United States New Vaccine Surveillance Network: A Multisite Active Surveillance Program, 2006-2016

BACKGROUND

Since 2006, the New Vaccine Surveillance Network has conducted active, population-based surveillance for acute gastroenteritis (AGE) hospitalizations and emergency department (ED) visits in 3 United States counties. Trends in the epidemiology and disease burden of rotavirus hospitalizations and ED visits were examined from 2006 to 2016.

METHODS

Children < 3 years of age hospitalized or visiting the ED with AGE were enrolled from January 2006 through June 2016. Bulk stool specimens were collected and tested for rotavirus. Rotavirus-associated hospitalization and ED visit rates were calculated annually with 2006-2007 defined as the prevaccine period and 2008-2016 as the postvaccine period. Rotavirus genotype trends were compared over time.

RESULTS

Over 11 seasons, 6954 children with AGE were enrolled and submitted a stool specimen (2187 hospitalized and 4767 in the ED). Comparing pre- and postvaccine periods, the proportion of children with rotavirus dramatically declined for hospitalization (49% vs 10%) and ED visits (49% vs 8%). In the postvaccine era, a biennial pattern of rotavirus rates was observed, with a trend toward an older median age. G1P[8] (63%) was the predominant genotype in the prevaccine period with a significantly lower proportion (7%) in the postvaccine period (P < .001). G2P[4] remained stable (8% to 14%) in both periods, whereas G3P[8] and G12P[8] increased in proportion from pre- to postvaccine periods (1% to 25% and 17% to 40%), respectively.

CONCLUSIONS

The epidemiology and disease burden of rotavirus has been altered by rotavirus vaccination with a biennial disease pattern, sustained low rates of rotavirus in children < 3 years of age, and a shift in the residual genotypes from G1P[8] to other genotypes.

The impact of COVID-19 nonpharmaceutical interventions on the future dynamics of endemic infections

Nonpharmaceutical interventions (NPIs) have been employed to reduce the transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), yet these measures are already having similar effects on other directly transmitted, endemic diseases. Disruptions to the seasonal transmission patterns of these diseases may have consequences for the timing and severity of future outbreaks. Here we consider the implications of SARS-CoV-2 NPIs for two endemic infections circulating in the United States of America: respiratory syncytial virus (RSV) and seasonal influenza. Using laboratory surveillance data from 2020, we estimate that RSV transmission declined by at least 20% in the United States at the start of the NPI period. We simulate future trajectories of both RSV and influenza, using an epidemic model. As susceptibility increases over the NPI period, we find that substantial outbreaks of RSV may occur in future years, with peak outbreaks likely occurring in the winter of 2021-2022. Longer NPIs, in general, lead to larger future outbreaks although they may display complex interactions with baseline seasonality. Results for influenza broadly echo this picture, but are more uncertain; future outbreaks are likely dependent on the transmissibility and evolutionary dynamics of circulating strains.

Immune life history, vaccination, and the dynamics of SARS-CoV-2 over the next 5 years

The future trajectory of the coronavirus disease 2019 (COVID-19) pandemic hinges on the dynamics of adaptive immunity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); however, salient features of the immune response elicited by natural infection or vaccination are still uncertain. We use simple epidemiological models to explore estimates for the magnitude and timing of future COVID-19 cases, given different assumptions regarding the protective efficacy and duration of the adaptive immune response to SARS-CoV-2, as well as its interaction with vaccines and nonpharmaceutical interventions. We find that variations in the immune response to primary SARS-CoV-2 infections and a potential vaccine can lead to markedly different immune landscapes and burdens of critically severe cases, ranging from sustained epidemics to near elimination. Our findings illustrate likely complexities in future COVID-19 dynamics and highlight the importance of immunological characterization beyond the measurement of active infections for adequately projecting the immune landscape generated by SARS-CoV-2 infections.

Spatio-temporal impact of self-financed rotavirus vaccination on rotavirus and acute gastroenteritis hospitalisations in the Valencia region, Spain

BACKGROUND

Several studies have shown a substantial impact of Rotavirus (RV) vaccination on the burden of RV and all-cause acute gastroenteritis (AGE). However, the results of most impact studies could be confused by a dynamic and complex space-time process. Therefore, there is a need to analyse the impact of RV vaccination on RV and AGE hospitalisations in a space-time framework to detect geographical-time patterns while avoiding the potential confusion caused by population inequalities in the impact estimations.

METHODS

A retrospective population-based study using real-world data from the Valencia Region was performed among children aged less than 3 years old in the period 2005-2016. A Bayesian spatio-temporal model was constructed to analyse RV and AGE hospitalisations and to estimate the vaccination impact measured in averted hospitalisations.

RESULTS

We found important spatio-temporal patterns in RV and AGE hospitalisations, RV vaccination coverage and in their associated adverted hospitalisations. Overall, ~ 1866 hospital admissions for RV were averted by RV vaccination during 2007-2016. Despite the low-medium vaccine coverage (~ 50%) in 2015-2016, relevant 36 and 20% reductions were estimated in RV and AGE hospitalisations respectively.

CONCLUSIONS

The introduction of the RV vaccines has substantially reduced the number of RV hospitalisations, averting ~ 1866 admissions during 2007-2016 which were space and time dependent. This study improves the methodologies commonly used to estimate the RV vaccine impact and their interpretation.

Evaluating strategies to improve rotavirus vaccine impact during the second year of life in Malawi

Rotavirus vaccination has substantially reduced the incidence of rotavirus-associated gastroenteritis (RVGE) in high-income countries, but vaccine impact and estimated effectiveness are lower in low-income countries for reasons that are poorly understood. We used mathematical modeling to quantify rotavirus vaccine impact and investigate reduced vaccine effectiveness, particularly during the second year of life, in Malawi, where vaccination was introduced in October 2012 with doses at 6 and 10 weeks. We fitted models to 12 years of prevaccination data and validated the models against postvaccination data to evaluate the magnitude and duration of vaccine protection. The observed rollout of vaccination in Malawi was predicted to lead to a 26 to 77% decrease in the overall incidence of moderate-to-severe RVGE in 2016, depending on assumptions about waning of vaccine-induced immunity and heterogeneity in vaccine response. Vaccine effectiveness estimates were predicted to be higher among 4- to 11-month-olds than 12- to 23-month-olds, even when vaccine-induced immunity did not wane, due to differences in the rate at which vaccinated and unvaccinated individuals acquire immunity from natural infection. We found that vaccine effectiveness during the first and second years of life could potentially be improved by increasing the proportion of infants who respond to vaccination or by lowering the rotavirus transmission rate. An additional dose of rotavirus vaccine at 9 months of age was predicted to lead to higher estimated vaccine effectiveness but to only modest (5 to 16%) reductions in RVGE incidence over the first 3 years after introduction, regardless of assumptions about waning of vaccine-induced immunity.

Investigation of two suspected diarrhoeal-illness outbreaks in Northern Cape and KwaZulu-Natal provinces, South Africa, April-July 2013: The role of rotavirus

BACKGROUND

Suspected diarrhoeal-illness outbreaks affecting mostly children < 5 years were investigated between May and July 2013 in Northern Cape province (NCP) and KwaZulu-Natal (KZN) province. This study describes the epidemiological, environmental and clinical characteristics and diarrhoeal-illnesses causative agent(s).

METHODS

A descriptive cross-sectional study was conducted. Cases were patients presenting at healthcare facilities with diarrhoeal-illness between 09 April and 09 July 2013 in NCP and 01 May and 31 July 2013 in KZN. Laboratory investigations were performed on stools and water samples using microscopy, culture and sensitivity screening and molecular assays.

RESULTS

A total of 953 cases including six deaths (case fatality rate [CFR]: 0.6%) were recorded in the Northern Cape province outbreak. Children < 5 years accounted for 58% of cases. Enteric viruses were detected in 51% of stools, with rotavirus detected in 43%. The predominant rotavirus strains were G3P[8] (45%) and G9P[8] (42%). Other enteric viruses were detected, with rotavirus co-infections (63%). No enteric pathogens detected in water specimens. KwaZulu-Natal outbreak: A total of 1749 cases including 26 deaths (CFR: 1.5%) were recorded. Children < 5 years accounted for 95% of cases. Rotavirus was detected in 55% of stools; other enteric viruses were detected, mostly as rotavirus co-infections. The predominant rotavirus strains were G2P[4] (54%) and G9P[8] (38%).

CONCLUSION

Although source(s) of the outbreaks were not identified, the diarrhoeal-illnesses were community-acquired. It is difficult to attribute the outbreaks to one causative agent(s) because of rotavirus co-infections with other enteric pathogens. While rotavirus was predominant, the outbreaks coincided with the annual rotavirus season.

Modeling of rotavirus transmission dynamics and impact of vaccination in Ghana

Background:

Rotavirus incidence remains relatively high in low-income countries (LICs) compared to high-income countries (HICs) after vaccine introduction. Ghana introduced monovalent rotavirus vaccine in April 2012 and despite the high coverage, vaccine performance has been modest compared to developed countries. The predictors of low vaccine effectiveness in LICs are poorly understood, and the drivers of subnational heterogeneity in rotavirus vaccine impact are unknown.

Methods:

We used mathematical models to investigate variations in rotavirus incidence in children <5 years old in Ghana. We fit models to surveillance and case-control data from three different hospitals: Korle-Bu Teaching Hospital in Accra, Komfo Anokye Teaching Hospital in Kumasi, and War Memorial Hospital in Navrongo. The models were fitted to both pre- and post-vaccine data to estimate parameters describing the transmission rate, waning of maternal immunity, and vaccine response rate.

Results:

The seasonal pattern and age distribution of rotavirus cases varied among the three study sites in Ghana. Our model was able to capture the spatio-temporal variations in rotavirus incidence across the three sites and showed good agreement with the age distribution of observed cases. The rotavirus transmission rate was highest in Accra and lowest in Navrongo, while the estimated duration of maternal immunity was longer (∼5 months) in Accra and Kumasi and shorter (∼3 months) in Navrongo. The proportion of infants who responded to the vaccine was estimated to be high in Accra and Kumasi and low in Navrongo.

Conclusions:

Rotavirus vaccine impact varies within Ghana. A low vaccine response rate was estimated for Navrongo, where rotavirus is highly seasonal and incidence limited to a few months of the year. Our findings highlight the need to further explore the relationship between rotavirus seasonality, maternal immunity, and vaccine response rate to determine how they influence vaccine effectiveness and to develop strategies to improve vaccine impact.

Longer-term Direct and Indirect Effects of Infant Rotavirus Vaccination Across All Ages in the United States in 2000-2013: Analysis of a Large Hospital Discharge Data Set

BACKGROUND

Rotavirus disease rates dramatically declined among children <5 years of age since the rotavirus vaccine was introduced in 2006; population-level impacts remain to be fully elucidated.

METHODS

Data from the Healthcare Cost and Utilization Project State Inpatient Databases were used to conduct a time-series analysis of monthly hospital discharges across age groups for acute gastroenteritis and rotavirus from 2000 to 2013. Rate ratios were calculated comparing prevaccine and postvaccine eras.

RESULTS

Following vaccine introduction, a decrease in rotavirus hospitalizations occurred with a shift toward biennial patterns across all ages. The 0-4-year age group experienced the largest decrease in rotavirus hospitalizations (rate ratio, 0.14; 95% confidence interval, .09-.23). The 5-19-year and 20-59-year age groups experienced significant declines in rotavirus hospitalization rates overall; the even postvaccine calendar years were characterized by progressively lower rates, and the odd postvaccine years were associated with reductions in rates that diminished over time. Those aged ≥60 years experienced the smallest change in rotavirus hospitalization rates overall, with significant reductions in even postvaccine years compared with prevaccine years (rate ratio, 0.51; 95% confidence interval, .39-.66).

CONCLUSIONS

Indirect impacts of infant rotavirus vaccination are apparent in the emergence of biennial patterns in rotavirus hospitalizations that extend to all age groups ineligible for vaccination. These observations are consistent with the notion that young children are of primary importance in disease transmission and that the initial postvaccine period of dramatic population-wide impacts will be followed by more complex incidence patterns across the age range in the long term.

Ensemble forecast and parameter inference of childhood diarrhea in Chobe District, Botswana

Diarrheal disease is the second largest cause of mortality in children younger than 5, yet our ability to anticipate and prepare for outbreaks remains limited. Here, we develop and test an epidemiological forecast model for childhood diarrheal disease in Chobe District, Botswana. Our prediction system uses a compartmental susceptible-infected-recovered-susceptible (SIRS) model coupled with Bayesian data assimilation to infer relevant epidemiological parameter values and generate retrospective forecasts. Our model inferred two system parameters and accurately simulated weekly observed diarrhea cases from 2007-2017. Accurate retrospective forecasts for diarrhea outbreaks were generated up to six weeks before the predicted peak of the outbreak, and accuracy increased over the progression of the outbreak. Many forecasts generated by our model system were more accurate than predictions made using only historical data trends. Accurate real-time forecasts have the potential to increase local preparedness for coming outbreaks through improved resource allocation and healthcare worker distribution.

Disease burden and seasonal impact of improving rotavirus vaccine coverage in the United States: A modeling study

Background

Prior to vaccine introduction in 2006, rotavirus was the leading cause of severe diarrhea in children under five years of age in the U.S. Vaccination of infants has led to major reductions in disease burden, a shift in the seasonal peak and the emergence of a biennial pattern of disease. However, rotavirus vaccine coverage has remained relatively low (70–75%) compared to other infant immunizations in the U.S. Part of the reason for this lower coverage is that children whose care is provided by family practitioners (FP) have considerably lower probability of being vaccinated compared to those seen be pediatricians (PE). We used a dynamic transmission model to assess the impact of improving rotavirus vaccine coverage by FP and/or PE on rotavirus gastroenteritis (RVGE) incidence and seasonal patterns.

Methods

A deterministic age-structured dynamic model with susceptible, infectious, and recovered compartments (SIRS model) was used to simulate rotavirus transmission and vaccination. We estimated the reduction of RVGE cases by 2 doses of rotavirus vaccine with three vaccination scenarios: (Status Quo: 85% coverage by pediatricians and 45% coverage by family practitioners; Improved FP: 85% coverage by pediatricians and family practitioners; Improved FP+PE: 95% coverage by pediatricians and family practitioners). In addition, we tested the sensitivity of the model to the assumption of random mixing patterns between children visiting pediatricians and children visiting family practitioners.

Results

In this model, higher vaccine coverage provided by family practitioners and pediatricians leads to lower incidence of severe RVGE cases (23% averted in Improved FP and 57% averted in Improved FP+PE compared to Status Quo) including indirect effects. One critical impact of higher total vaccine coverage is the effect on rotavirus epidemic patterns in the U.S.; the biennial rotavirus epidemic patterns shifted to reduced annual epidemic patterns. Additionally, assortative mixing patterns in children visiting pediatricians and family practitioners amplify the impact of increasing vaccine coverage.

Conclusion

Other high-income countries that introduced vaccine have not experienced biennial patterns, like the U.S. Our results suggest that increasing overall vaccine coverage to 85% among infants would lead to an overall reduction in incidence with annual epidemic patterns.

Surveillance data confirm multiyear predictions of rotavirus dynamics in New York City

Prediction skill is a key test of models for epidemic dynamics. However, future validation of models against out-of-sample data is rare, partly because of a lack of timely surveillance data. We address this gap by analyzing the response of rotavirus dynamics to infant vaccination. Syndromic surveillance of emergency department visits for diarrhea in New York City reveals a marked decline in diarrheal incidence among infants and young children, in line with data on rotavirus-coded hospitalizations and laboratory-confirmed cases, and a shift from annual to biennial epidemics increasingly affecting older children and adults. A published mechanistic model qualitatively predicted these patterns more than 2 years in advance. Future efforts to increase vaccination coverage may disrupt these patterns and lead to further declines in the incidence of rotavirus-attributable gastroenteritis.

Identifying signatures of the impact of rotavirus vaccines on hospitalizations using sentinel surveillance data from Latin American countries

BACKGROUND

Passive surveillance data are often the only available source of data that can be used to evaluate the population-level impact of vaccination, but such data often suffer from important limitations such as changes in surveillance efforts. This study provides an example of how to identify important signatures of rotavirus vaccine impact, including evaluating the overall effectiveness and changes in rotavirus seasonal dynamics.

METHODS

We used data from a standardized sentinel rotavirus surveillance network in six Latin American countries (Bolivia, El Salvador, Guatemala, Honduras, Paraguay, and Venezuela) from 2004 to 2017. A random-effects model was used to evaluate changes in the proportion of rotavirus-associated hospitalizations following vaccine introduction. Harmonic regression models were used to estimate vaccine impact on the number of rotavirus hospitalizations, controlling for trends in rotavirus-negative cases. Changes to rotavirus seasonality were evaluated using center of gravity analysis, wavelet analysis, and harmonic regression.

RESULTS

All countries observed declines in the proportion of rotavirus-positive acute diarrhea samples with a mean reduction of 16% (95% confidence interval: 10-22%). We estimate that each 10% increase in vaccine coverage was associated with declines in the number of rotavirus-positive cases, ranging from 4.3% (1.3-7.2%) in Honduras to 21.4% (16.8-25.9%) in Venezuela. The strength of the seasonal peak in rotavirus incidence became smaller after vaccine introduction in Guatemala, Honduras, and Venezuela. Seasonal peaks also shifted later in the surveillance year, especially in higher-mortality countries.

CONCLUSIONS

The combination of methods we applied have different strengths that allow us to identify common signatures of rotavirus vaccine impact.

Heterogeneous susceptibility to rotavirus infection and gastroenteritis in two birth cohort studies: Parameter estimation and epidemiological implications

Cohort studies, randomized trials, and post-licensure studies have reported reduced natural and vaccine-derived protection against rotavirus gastroenteritis (RVGE) in low- and middle-income countries. While susceptibility of children to rotavirus is known to vary within and between settings, implications for estimation of immune protection are not well understood. We sought to re-estimate naturally-acquired protection against rotavirus infection and RVGE, and to understand how differences in susceptibility among children impacted estimates. We re-analyzed data from studies conducted in Mexico City, Mexico and Vellore, India. Cumulatively, 573 rotavirus-unvaccinated children experienced 1418 rotavirus infections and 371 episodes of RVGE over 17,636 child-months. We developed a model that characterized susceptibility to rotavirus infection and RVGE among children, accounting for aspects of the natural history of rotavirus and differences in transmission rates between settings. We tested whether model-generated susceptibility measurements were associated with demographic and anthropometric factors, and with the severity of RVGE symptoms. We identified greater variation in susceptibility to rotavirus infection and RVGE in Vellore than in Mexico City. In both cohorts, susceptibility to rotavirus infection and RVGE were associated with male sex, lower birth weight, lower maternal education, and having fewer siblings; within Vellore, susceptibility was also associated with lower socioeconomic status. Children who were more susceptible to rotavirus also experienced higher rates of rotavirus-negative diarrhea, and higher risk of moderate-to-severe symptoms when experiencing RVGE. Simulations suggested that discrepant estimates of naturally-acquired immunity against RVGE can be attributed, in part, to between-setting differences in susceptibility of children, but result primarily from the interaction of transmission rates with age-dependent risk for infections to cause RVGE. We found that more children in Vellore than in Mexico City belong to a high-risk group for rotavirus infection and RVGE, and demonstrate that unmeasured individual- and age-dependent susceptibility may influence estimates of naturally-acquired immune protection against RVGE.

Differences in susceptibility can help explain why some individuals, and not others, acquire infection and exhibit symptoms when exposed to infectious disease agents. However, it is difficult to distinguish between differences in susceptibility versus exposure in epidemiological studies. We developed a modeling approach to distinguish transmission intensity and susceptibility in data from cohort studies of rotavirus infection among children in Mexico City, Mexico, and Vellore, India, and evaluated how these factors may have contributed to differences in estimates of naturally-acquired immune protection between the studies. Given the same exposure, more children were at high risk of acquiring rotavirus infection, and of experiencing gastroenteritis when infected, in Vellore than in Mexico City. The probability of belonging to this high-risk stratum was associated with well-known individual factors such as lower socioeconomic status, lower birth weight, and incidence of diarrhea due to other causes. We also found the risk for rotavirus infections to cause symptoms declined with age, independent of acquired immunity. These findings can, in part, account for estimates of lower protective efficacy of acquired immunity against rotavirus gastroenteritis in high-incidence settings, mirroring estimates of reduced effectiveness of live oral rotavirus vaccines in low- and middle-income countries.

Prevalence and molecular typing of rotavirus in children with acute diarrhoea in Northeastern Colombia

After the introduction of the rotavirus vaccine, the number of rotavirus-associated deaths and the predicted annual rotavirus detection rate had slightly declined worldwide. Taking in account that in Colombia, Rotarix vaccine was introduced in 2009, the purpose of this study was to evaluate the presence of rotavirus A in children under five years who were treated for acute diarrhoea in Bucaramanga, Colombia and, moreover, to determine the genotypes of rotavirus present in those children. We performed an analytical cross-sectional study of rotavirus A in faecal samples from children up to five years of age. Stool samples were screened for rotavirus A using a lateral-flow immunochromatographic assay and confirmed using a VP6 sandwich ELISA. Genotyping of rotavirus A-positive samples was performed by PCR and sequencing of VP7 and VP4 genes. The overall prevalence of rotavirus was 30.53% (95% confidence interval [CI] 21.2 - 39.7). Most of the children with rotavirus (86.2%) had received two doses of the rotavirus vaccine. G3 strains accounted for the vast majority of cases (82.8%), followed by G12 strains (13.8%) and G3/G9 coinfections (3.4%). Among the P genotypes, P[8] was the most prevalent (69%), followed by P[9] (31%). The most common G[P] genotype combination was G3P[8], followed by G3P[9]. The main finding in this study was that rotavirus, in a Colombian region, is still an important pathogen in children under five years old, previously vaccinated. The results showed that different factors, such as kindergarten attendance, could explain the epidemiology and transmission of rotavirus in Bucaramanga.

First detection of a reassortant G3P[8] rotavirus A strain in Italy: a case report in an 8-year-old child

Background

Acute gastroenteritis (AGE) due to group A rotavirus (RVA) agent is one of the major causes of hospitalization in paediatric age. The G3P[8] RVA genotype has been usually considered as one of the major human genotypes, largely circulating in Asia, but showing low detection rates in the European countries. In recent years, the G3P[8] RVAs emerged also in Europe as a predominant genotype and the viral strains detected revealed high similarities with equine-like G3P[8] RVA strains, resulting in a new variant circulating in humans and able to cause AGE in the paediatric population.

Case presentation

An 8-year-old boy was admitted to the Emergency Room because he had suffered from severe diarrhoea, vomiting, and high fever over the previous two days. Severe dehydration was evident based on low serum concentrations of potassium and sodium, low glycaemia, and pre-renal failure (creatinine 2.48 mg/dL, urea 133 mg/dL). Immunological tests were within normal range. Enzyme immunoassay for the detection of RV was positive, and a sample of faeces was collected in order to perform the molecular characterization of the viral strain. The phylogenetic trees revealed relatedness between the VP7 and VP4 genes of the G3P[8] RVA Italian strain (namely PG2) and those belonging to recent G3P[8] RVAs detected worldwide. The G3 VP7 belonged to the G3-I lineage and shared the highest nucleotide sequence identity (99.8%) with the equine-like G3 previously identified in other countries. The P [8] VP4 revealed a similar clustering pattern to that observed for the VP7. In addition, the molecular characterization of the 11 gene segments of strain PG2 revealed a G3-P[8]-I2-R2-C2-M2-A2-N2-T2-E2-H2 genomic constellation.

Conclusions

This case shows the first detection in Italy of a reassortant G3P[8] RVA associated with a severe AGE, which is unusual in a school-age child without any known severe underlying problems. The findings reported in this paper highlight the importance of continuously monitoring the RVA strains circulating in paediatric age in order to detect novel viral variants able to spread in the general population.

Effects of the rotavirus vaccine program across age groups in the United States: analysis of national claims data, 2001-2016

BACKGROUND

The direct effectiveness of infant rotavirus vaccination implemented in 2006 in the United States has been evaluated extensively, however, understanding of population-level vaccine effectiveness (VE) is still incomplete.

METHODS

We analyzed time series data on rotavirus gastroenteritis (RVGE) and all-cause acute gastroenteritis (AGE) hospitalization rates in the United States from the MarketScan® Research Databases for July 2001-June 2016. Individuals were grouped into ages 0-4, 5-9, 10-14, 15-24, 25-44, and 45-64 years. Negative binomial regression models were fitted to monthly RVGE and AGE data to estimate the direct, indirect, overall, and total VE.

RESULTS

A total of 9211 RVGE and 726,528 AGE hospitalizations were analyzed. Children 0-4 years of age had the largest declines in RVGE hospitalizations with direct VE of 87% (95% CI: 83, 90%). Substantial indirect effects were observed across age groups and generally declined in each older group. Overall VE against RVGE hospitalizations for all ages combined was 69% (95% CI: 62, 76%). Total VE was highest among young children; a vaccinated child in the post-vaccine era has a 95% reduced risk of RVGE hospitalization compared to a child in the pre-vaccine era. We observed higher direct VE in odd post-vaccine years and an opposite pattern for indirect VE.

CONCLUSIONS

Vaccine benefits extended to unvaccinated individuals in all age groups, suggesting infants are important drivers of disease transmission across the population. Imperfect disease classification and changing disease incidence may lead to bias in observed direct VE.

TRIAL REGISTRATION

Not applicable.

Timing of Birth as an Emergent Risk Factor for Rotavirus Hospitalization and Vaccine Performance in the Postvaccination Era in the United States

Rotavirus vaccines were introduced in the United States in 2006, and in the years since they have fundamentally altered the seasonality of rotavirus infection and have shifted disease outbreaks from annual epidemics to biennial epidemics. We investigated whether season and year of birth have emerged as risk factors for rotavirus or have affected vaccine performance. We constructed a retrospective birth cohort of US children under age 5 years using the 2001-2014 MarketScan database (Truven Health Analytics, Chicago, Illinois). We evaluated the associations of season of birth, even/odd year of birth, and interactions with vaccination. We fitted Cox proportional hazards models to estimate the hazard of rotavirus hospitalization according to calendar year of birth and season of birth assessed for interaction with vaccination. After the introduction of rotavirus vaccine, we observed monotonically decreasing rates of rotavirus hospitalization for each subsequent birth cohort but a biennial incidence pattern by calendar year. In the postvaccine period, children born in odd calendar years had a higher hazard of rotavirus hospitalization than those born in even years. Children born in winter had the highest hazard of hospitalization but also had greater vaccine effectiveness than children born in spring, summer, or fall. With the emergence of a strong biennial pattern of disease following vaccine introduction, the timing of a child's birth has become a risk factor for rotavirus infection.