Repeatability and timing of tropical influenza epidemics

Servadio, Joseph L.; Thái, Phạm Quang; Choisy, Marc; Boni, Maciej F.

doi:10.1101/2022.11.04.22281944

Cited by 5 publications

(13 citation statements)

References 76 publications

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“…4D). A single influenza peak per year does not guarantee that peak timing is repeatable or consistent 14 . In addition, the peak timings and the periodic signals are not consistent across subtypes (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…The percentage of ILI patients among total outpatient visits per day (%ILI) in each clinic from January 1, 2010 to December 31, 2019 is used as the primary data type in the analysis. The %ILI time series for each clinic was detrended to an ILI ζ -score (“zeta” score) to remove long-term decreasing trends seen in seven clinics 13,14 (see S1 Text). Daily data were detrended using the ζ -score for each clinic, and then the arithmetic mean among all clinics reporting that day was calculated to get an aggregated ILI time series.…”

Section: Methodsmentioning

confidence: 99%

“…To validate the molecular surveillance trends in our community-based study, we compared our ILI+ data to the ILI+ time series seen in hospital-based surveillance via the Vietnam's National Influenza Sentinel Surveillance System 14,20,21 in HCMC. The 186 weeks that overlapped during 2012 and 2015 between two time series showed similar circulation pattern of influenza and its subtypes, confirming the reporting consistency between our system and sentinel surveillance (Pearson's correlation ρ = 0.568 (95% CI: 0.456-0.662) for overall influenza, ρ = 0.784 (95% CI: 0.719-0.836) for subtype A/H1N1, ρ = 0.706 (95% CI: 0.621-0.774) for subtype A/H3N2, and ρ = 0.523 (95% CI: 0.404-0.624) for influenza B; all p < 10 -4 , Fig.…”

Section: Periodic Signals In Influenza Datamentioning

confidence: 99%

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A combination of annual and nonannual forces drive respiratory disease in the tropics

Yang

Servadio

Thanh

et al. 2023

Preprint

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Background: It is well known that influenza and other respiratory viruses are wintertime-seasonal in temperate regions. However, respiratory disease seasonality in the tropics remains elusive. In this study, we aimed to characterize the seasonality of influenza-like illness (ILI) and influenza virus in Ho Chi Minh City (HCMC), Vietnam. Methods: We monitored the daily number of ILI patients in 89 outpatient clinics from January 2010 to December 2019. We collected nasal swabs and tested for influenza from a subset of clinics from May 2012 to December 2019. We used spectral analysis to describe the periodicities in the system. We evaluated the contribution of these periodicities to predicting ILI and influenza patterns through lognormal and gamma hurdle models. Findings: During ten years of community surveillance, 66,799 ILI reports were collected covering 2.9 million patient visits; 2604 nasal swabs were collected 559 of which were PCR-positive for influenza virus. Both annual and nonannual cycles were detected in the ILI time series, with the annual cycle showing 8.9% lower ILI activity (95% CI: 8.8%-9.0%) from February 24 to May 15. Nonannual cycles had substantial explanatory power for ILI trends (ΔAIC = 183) compared to all annual covariates (ΔAIC = 263). Near-annual signals were observed for PCR-confirmed influenza but were not consistent along in time or across influenza (sub)types. Interpretation: Our study reveals a unique pattern of respiratory disease dynamics in a tropical setting influenced by both annual and nonannual drivers. Timing of vaccination campaigns and hospital capacity planning may require a complex forecasting approach. Funding: National Institutes of Health, Wellcome Trust.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Periodic Signals In Influenza Datamentioning

confidence: 99%

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A combination of annual and nonannual forces drive respiratory disease in the tropics

Yang

Servadio

Thanh

et al. 2023

Preprint

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“…We adjusted the transmission levels in the model for future projections based on influenza dynamics in the US. Seasonal wintertime forcing in transmissibility was introduced starting in season 2023-2024, where transmission increases by up to 20 percent in a sinusoidal curve between October and February, estimated from influenza transmission during winter in the northeastern US (46). The baseline transmission rate after March 1, 2023 was assumed to be the mean of the transmission parameter throughout the entire third year.…”

Section: Projecting Future Disease Burdenmentioning

confidence: 99%

Benefits of near-universal vaccination and treatment access to manage COVID-19 burden in the United States

Yang

Tran

Howerton

et al. 2023

Preprint

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Background: As we enter the fourth year of the COVID-19 pandemic, SARS-CoV-2 infections still cause high morbidity and mortality in the United States. During 2020-2022, COVID-19 was one of the leading causes of death in the United States and by far the leading cause among infectious diseases. Vaccination uptake remains low despite this being an effective burden reducing intervention. The development of COVID-19 therapeutics provides hope for mitigating severe clinical outcomes. This modeling study examines combined strategies of vaccination and treatment to reduce the burden of COVID-19 epidemics over the next decade. Methods: We use a validated mathematical model to evaluate the reduction of incident cases, hospitalized cases, and deaths in the United States through 2033 under various levels of vaccination and treatment coverage. We assume that future seasonal transmission patterns for COVID-19 will be similar to those of influenza virus. We account for the waning of infection-induced immunity and vaccine-induced immunity in a future with stable COVID-19 dynamics. Due to uncertainty in the duration of immunity following vaccination or infection, we consider two exponentially-distributed waning rates, with means of 365 days (one year) and 548 days (1.5 years). We also consider treatment failure, including rebound frequency, as a possible treatment outcome. Results: As expected, universal vaccination is projected to eliminate transmission and mortality. Under current treatment coverage (13.7%) and vaccination coverage (49%), averages of 89,000 annual deaths (548-day waning) and 120,000 annual deaths (365-day waning) are expected by the end of this decade. Annual mortality in the United States can be reduced below 50,000 per year with >81% annual vaccination coverage, and below 10,000 annual deaths with >84% annual vaccination coverage. Universal treatment reduces hospitalizations by 88% and deaths by 93% under current vaccination coverage. A reduction in vaccination coverage requires a comparatively larger increase in treatment coverage in order for hospitalization and mortality levels to remain unchanged. Conclusions: Adopting universal vaccination and universal treatment goals in the United States will likely lead to a COVID-19 mortality burden below 50,000 deaths per year, a burden comparable to that of influenza virus.

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“…The absence of winter in tropical regions makes the yearly patterns of influenza and influenza-like illness (ILI) less seasonal and less predictable 9. Thus far, it has been found that influenza in tropical regions shows lower variation in incidence,10 11 higher variation in epidemic timing10 12 and different periodicities geographically,10 13–18 making it difficult to forecast periods of high incidence. Although some studies in tropical areas have shown associations between climate or environmental factors and influenza transmission,11 19–23 this relationship remains elusive16 24 25 and caution is needed in interpreting these results and drawing inferences on a ‘typical’ tropical influenza season.…”

Section: Introductionmentioning

confidence: 99%

A combination of annual and nonannual forces drive respiratory disease in the tropics

Yang,

Servadio,

Thanh

et al. 2023

BMJ Glob Health

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IntroductionIt is well known that influenza and other respiratory viruses are wintertime-seasonal in temperate regions. However, respiratory disease seasonality in the tropics is less well understood. In this study, we aimed to characterise the seasonality of influenza-like illness (ILI) and influenza virus in Ho Chi Minh City, Vietnam.MethodsWe monitored the daily number of ILI patients in 89 outpatient clinics from January 2010 to December 2019. We collected nasal swabs and tested for influenza from a subset of clinics from May 2012 to December 2019. We used spectral analysis to describe the periodic signals in the system. We evaluated the contribution of these periodic signals to predicting ILI and influenza patterns through lognormal and gamma hurdle models.ResultsDuring 10 years of community surveillance, 66 799 ILI reports were collected covering 2.9 million patient visits; 2604 nasal swabs were collected, 559 of which were PCR-positive for influenza virus. Both annual and nonannual cycles were detected in the ILI time series, with the annual cycle showing 8.9% lower ILI activity (95% CI 8.8% to 9.0%) from February 24 to May 15. Nonannual cycles had substantial explanatory power for ILI trends (ΔAIC=183) compared with all annual covariates (ΔAIC=263) in lognormal regression. Near-annual signals were observed for PCR-confirmed influenza but were not consistent over time or across influenza (sub)types. The explanatory power of climate factors for ILI and influenza virus trends was weak.ConclusionOur study reveals a unique pattern of respiratory disease dynamics in a tropical setting influenced by both annual and nonannual drivers, with influenza dynamics showing near-annual periodicities. Timing of vaccination campaigns and hospital capacity planning may require a complex forecasting approach.

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Repeatability and timing of tropical influenza epidemics

Cited by 5 publications

References 76 publications

A combination of annual and nonannual forces drive respiratory disease in the tropics

A combination of annual and nonannual forces drive respiratory disease in the tropics

Benefits of near-universal vaccination and treatment access to manage COVID-19 burden in the United States

A combination of annual and nonannual forces drive respiratory disease in the tropics

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