| Literature DB >> 32415751 |
Marta Galanti1, Devon Comito1,2, Chanel Ligon1, Benjamin Lane1, Nelsa Matienzo1, Sadiat Ibrahim1, Atinuke Shittu1, Eudosie Tagne1, Ruthie Birger1,3,4, Minhaz Ud-Dean1, Ioan Filip5, Haruka Morita1, Raul Rabadan5, Simon Anthony6, Greg A Freyer1, Peter Dayan7, Bo Shopsin8, Jeffrey Shaman1.
Abstract
BACKGROUND: Respiratory viral infections are a leading cause of disease worldwide. However, the overall community prevalence of infections has not been properly assessed, as standard surveillance is typically acquired passively among individuals seeking clinical care.Entities:
Keywords: ILI; medically attended respiratory infections; population-based estimate of respiratory infections; respiratory illness surveillance
Year: 2020 PMID: 32415751 PMCID: PMC7276732 DOI: 10.1111/irv.12753
Source DB: PubMed Journal: Influenza Other Respir Viruses ISSN: 1750-2640 Impact factor: 4.380
Outcomes associated with respiratory infections: MA stands for medical attention, HOME for sick days, and MEDS indicates medicine intake for a respiratory illness. P(−|vi) indicates the probability of a specific outcome given infection with a particular virus. Estimates are obtained from cohort diaries and samples from October 2016 through April 2018. Viral co‐infections are excluded from the table, and analysis including co‐infections is reported in Table S3
| Virus | Episodes | MA | P(MA|vi) | 95% CI | HOME | P(HOME|vi) | 95% CI | MEDS | P(MEDS|vi) | 95% CI |
|---|---|---|---|---|---|---|---|---|---|---|
| Influenza | 27 | 5 | 0.19 | 0.04‐0.33 | 12 | 0.44 | 0.26‐0.63 | 16 | 0.59 | 0.40‐0.78 |
| RSV | 27 | 1 | 0.04 | 0‐0.1 | 4 | 0.15 | 0.04‐0.34 | 9 | 0.33 | 0.17‐0.54 |
| PIV | 26 | 2 | 0.07 | 0‐0.18 | 4 | 0.15 | 0.02‐0.29 | 8 | 0.31 | 0.13‐0.49 |
| HMPV | 20 | 4 | 0.20 | 0.03‐0.38 | 7 | 0.35 | 0.14‐0.56 | 10 | 0.50 | 0.28‐0.72 |
| HRV | 243 | 18 | 0.07 | 0.04‐ 0.11 | 27 | 0.11 | 0.07‐0.15 | 69 | 0.28 | 0.23‐0.34 |
| Adenovirus | 37 | 5 | 0.13 | 0.04‐0.29 | 5 | 0.13 | 0.04‐0.29 | 9 | 0.24 | 0.11‐0.38 |
| Coronavirus | 123 | 5 | 0.04 | 0.01‐0.09 | 9 | 0.07 | 0.03‐0.12 | 32 | 0.26 | 0.18‐0.34 |
FIGURE 1Differences in viral distribution among EDs and the general population. Comparison of the distribution of viruses within patients at pediatric hospitals and among a cohort of children and teenagers tested regularly irrespective of symptoms. The median age associated with specimens was the same for the hospital and cohort (4 y). We restricted the analysis to samples testing positive for a single respiratory virus at PedsED (258) and to samples taken from the children/teenagers cohort (257) within the same time period: October 2016 to April 2018. The pie chart on the right represents data from the pediatric hospitals rescaled by the likelihood of seeking care for a specific virus (Table 1), following the Bayes mapping reported in Methods. We did not consider RSV positivity in either dataset because children in the cohort did not include young infants, who are most subject to severe RSV infections. To estimate the relative proportion of viruses, we can disregard the numerator of the scaling factor and use from Table 1
Evaluation of MA‐ILI (medically attended ILI) as a measure of respiratory infection, ILI, viral infection, and influenza infection. Estimates are obtained from cohort diaries and samples from October 2016 through April 2018. Symbol ~ denotes negation. A subanalysis is reported in Table S4, where we evaluate the same probabilities using a stricter definition of ILI (typically used by the WHO) requiring specifically fever and cough
| Description | Formula | Estimate | 95% CI |
|---|---|---|---|
| ILI missed by surveillance | P (~MA|ILI) | 0.71 | 0.64‐0.78 |
| MA‐respiratory disease not recognized by the ILI classification | P (~ILI|MA) | 0.54 | 0.44‐0.64 |
| MA‐ILI without an identified viral infection | P (~infected|MA ∩ ILI) | 0.32 | 0.19‐0.45 |
| MA‐ILI not attributable to influenza | P (~influenza|MA ∩ ILI) | 0.82 | 0.66‐0.92 |
|
False negative: viral infection that is not MA‐ILI *if MA‐ILI is a proxy for viral infections | P (~(MA ∩ ILI)|infected) | 0.95 | 0.93‐0.97 |
|
False negative: viral infection that is not MA‐ILI *if MA‐ILI is a proxy for influenza | P (~(MA ∩ ILI)|influenza) | 0.79 | 0.62‐0.91 |
|
False negative: viral infection accompanied by ILI that is not MA‐ILI *if MA‐ILI is a proxy for viral infections associated with ILI symptoms | P (~(MA ∩ ILI)|i ∩ ILI) | 0.64 | 0.53‐0.75 |
Average number of infections by respiratory virus per person per cold/flu season. Summer months are not included due to decreased participation in the cohort during summer
| HRV | coronavirus | influenza | PIV | adenovirus | HMPV | RSV | All | |
|---|---|---|---|---|---|---|---|---|
| 2016/2017 | 1.60 | 1.18 | 0.21 | 0.17 | 0.36 | 0.08 | 0.28 | 3.9 |
| 2017/2018 | 1.76 | 0.73 | 0.22 | 0.09 | 0.31 | 0.16 | 0.14 | 3.4 |