Viral etiology, seasonality and severity of hospitalized patients with severe acute respiratory infections in the Eastern Mediterranean Region, 2007-2014.

INTRODUCTION: Little is known about the role of viral respiratory pathogens in the etiology, seasonality or severity of severe acute respiratory infections (SARI) in the Eastern Mediterranean Region. METHODS: Sentinel surveillance for SARI was conducted from December 2007 through February 2014 at 20 hospitals in Egypt, Jordan, Oman, Qatar and Yemen. Nasopharyngeal and oropharyngeal swabs were collected from hospitalized patients meeting SARI case definitions and were analyzed for infection with influenza, respiratory syncytial virus (RSV), adenovirus (AdV), human metapneumovirus (hMPV) and human parainfluenza virus types 1-3 (hPIV1-3). We analyzed surveillance data to calculate positivity rates for viral respiratory pathogens, describe the seasonality of those pathogens and determine which pathogens were responsible for more severe outcomes requiring ventilation and/or intensive care and/or resulting in death. RESULTS: At least one viral respiratory pathogen was detected in 8,753/28,508 (30.7%) samples tested for at least one pathogen and 3,497/9,315 (37.5%) of samples tested for all pathogens-influenza in 3,345/28,438 (11.8%), RSV in 3,942/24,503 (16.1%), AdV in 923/9,402 (9.8%), hMPV in 617/9,384 (6.6%), hPIV1 in 159/9,402 (1.7%), hPIV2 in 85/9,402 (0.9%) and hPIV3 in 365/9,402 (3.9%). Multiple pathogens were identified in 501/9,316 (5.4%) participants tested for all pathogens. Monthly variation, indicating seasonal differences in levels of infection, was observed for all pathogens. Participants with hMPV infections and participants less than five years of age were significantly less likely than participants not infected with hMPV and those older than five years of age, respectively, to experience a severe outcome, while participants with a pre-existing chronic disease were at increased risk of a severe outcome, compared to those with no reported pre-existing chronic disease. CONCLUSIONS: Viral respiratory pathogens are common among SARI patients in the Eastern Mediterranean Region. Ongoing surveillance is important to monitor changes in the etiology, seasonality and severity of pathogens of interest

S1 Dataset for "Viral etiology, seasonality and severity of hospitalized patients with severe acute respiratory infections in the Eastern Mediterranean Region, 2007–2014"

Little is known about the role of viral respiratory pathogens in the etiology, seasonality or severity of severe acute respiratory infections (SARI) in the Eastern Mediterranean Region. Sentinel surveillance for SARI was conducted from December 2007 through February 2014 at 20 hospitals in Egypt, Jordan, Oman, Qatar and Yemen. Nasopharyngeal and oropharyngeal swabs were collected from hospitalized patients meeting SARI case definitions and were analyzed for infection with influenza, respiratory syncytial virus (RSV), adenovirus (AdV), human metapneumovirus (hMPV) and human parainfluenza virus types 1-3 (hPIV1-3). We analyzed surveillance data to calculate positivity rates for viral respiratory pathogens, describe the seasonality of those pathogens and determine which pathogens were responsible for more severe outcomes requiring ventilation and/or intensive care and/or resulting in death. At least one viral respiratory pathogen was detected in 8,753/28,508 (30.7%) samples tested for at least one pathogen and 3,497/9,315 (37.5%) of samples tested for all pathogens-influenza in 3,345/28,438 (11.8%), RSV in 3,942/24,503 (16.1%), AdV in 923/9,402 (9.8%), hMPV in 617/9,384 (6.6%), hPIV1 in 159/9,402 (1.7%), hPIV2 in 85/9,402 (0.9%) and hPIV3 in 365/9,402 (3.9%). Multiple pathogens were identified in 501/9,316 (5.4%) participants tested for all pathogens. Monthly variation, indicating seasonal differences in levels of infection, was observed for all pathogens. Participants with hMPV infections and participants less than five years of age were significantly less likely than participants not infected with hMPV and those older than five years of age, respectively, to experience a severe outcome, while participants with a pre-existing chronic disease were at increased risk of a severe outcome, compared to those with no reported pre-existing chronic disease. Viral respiratory pathogens are common among SARI patients in the Eastern Mediterranean Region. Ongoing surveillance is important to monitor changes in the etiology, seasonality and severity of pathogens of interest

Indicators of severity of disease by pathogen (influenza, RSV, AdV, hMPV, PIV1, PIV2, PIV3 and any coinfection).

<p>Severe outcome is defined as illness requiring ventilation or intensive care or resulting in death. For each pathogen of interest, tested SARI patients with a positive result for that pathogen were compared to a reference group of tested SARI patients with a negative result for that pathogen. For “any coinfection”, tested SARI patients with any coinfection were compared to a reference group of tested SARI patients with test results for all pathogens of interest and no identified coinfection.</p

Proportion of positive samples for each viral respiratory pathogen by month.

<p>Proportion of positive samples out of total samples tested for each pathogen are shown.</p

Coinfections by viral respiratory pathogen (n = 501).

<p>Includes 5 patients with influenza, RSV and AdV; 3 with influenza, RSV and hMPV; 3 with RSV, AdV and hMPV; 3 with RSV, AdV and hPIV1; 2 with RSV, AdV and hPIV3; 2 with AdV, hMPV and hPIV3; 1 with influenza, AdV and hMPV; 1 with RSV, AdV and hPIV2; 1 with RSV, hPIV1 and hPIV2; 1 with influenza, RSV, AdV and hMPV; 1 with RSV, AdV, hMPV and hPIV3; 1 with RSV, AdV, hPIV1 and hPIV3.</p

Proportion of tested SARI cases positive for viral respiratory pathogens (influenza, RSV, AdV, hMPV, hPIV1, hPIV2, hPIV3) by country, year, age and sex.

<p>Proportion of tested SARI cases positive for viral respiratory pathogens (influenza, RSV, AdV, hMPV, hPIV1, hPIV2, hPIV3) by country, year, age and sex.</p

Univariate and multivariate logistic regression examining predictors of severe outcomes.

<p>Includes only individuals for whom testing for the full panel of viral respiratory viruses was performed and for whom data on demographics and clinical risk factors are complete. Severe outcome is defined as illness requiring ventilation or intensive care or resulting in death.</p