Detection of influenza A virus in live bird markets in Kenya, 2009–2011

Please cite this paper as: Munyua et al. (2013) Detection of influenza A virus in live bird markets in Kenya, 2009–2011. Influenza and Other Respiratory Viruses 7(2), 113–119. Background Surveillance for influenza viruses within live bird markets (LBMs) has been recognized as an effective tool for detecting circulating avian influenza viruses (AIVs). In Sub‐Saharan Africa, limited data exist on AIVs in animal hosts, and in Kenya the presence of influenza virus in animal hosts has not been described. Objectives This surveillance project aimed to detect influenza A virus in poultry traded in five LBMs in Kenya. Methods We visited each market monthly and collected oropharyngeal and cloacal specimens from poultry and environmental specimens for virological testing for influenza A by real time RT‐PCR. On each visit, we collected information on the number and types of birds in each market, health status of the birds, and market practices. Results During March 24, 2009–February 28, 2011, we collected 5221 cloacal and oropharyngeal swabs. Of the 5199 (99·6%) specimens tested, influenza A virus was detected in 42 (0·8%), including 35/4166 (0·8%) specimens from chickens, 3/381 (0·8%) from turkeys, and 4/335 (1·2%) from geese. None of the 317 duck specimens were positive. Influenza was more commonly detected in oropharyngeal [33 (1·3%)] than in cloacal [9 (0·4%)] specimens. None of the 485 environmental specimens were positive. Virus was detected in all five markets during most (14/22) of the months. Ducks and geese were kept longer at the market (median 30 days) than chickens (median 2 days). Conclusions Influenza A was detected in a small percentage of poultry traded in LBMs in Kenya. Efforts should be made to promote practices that could limit the maintenance and transmission of AIVs in LBMs.     

Hospitalization following outpatient medical care for influenza: US influenza vaccine effectiveness network, 2011‐12—2015‐16

Over five seasons, we determined the proportion of outpatients with laboratory‐confirmed, influenza‐associated illness who were hospitalized within 30 days following the outpatient visit. Overall, 136 (1.7%) of 7813 influenza‐positive patients were hospitalized a median of 4 days after an outpatient visit. Patients aged ≥ 65 years and those with high‐risk conditions were at increased risk of hospitalization. After controlling for age and high‐risk conditions, vaccination status and infecting influenza virus type were not associated with hospitalization risk among adults.     

Risk factors for hospitalization and severe outcomes of 2009 pandemic H1N1 influenza in Quebec, Canada

BACKGROUND/ OBJECTIVE: This case-control study was carried out to estimate risk factors associated with hospitalizations and severe outcomes [intensive care unit (ICU) admission or death] among patients with illness because of laboratory-confirmed 2009 pandemic A/H1N1 virus (pH1N1) during the first wave of pH1N1 activity in the province of Quebec, Canada. PATIENTS/ METHODS: We collected epidemiologic information by phone using a standardized questionnaire from patients with laboratory-confirmed pH1N1 illness during the first spring/summer pandemic wave in Quebec, Canada. Risk factors associated with hospitalization were assessed by comparing hospitalized to community cases and for ICU admission or death through comparison with hospitalized cases. RESULTS: Cases (321 hospitalized patients including 47 ICU admissions and 15 deaths) were compared to controls (395 non-hospitalized patients) by using multivariable logistic regression adjusted for gender, age, education, being a health care worker, smoking, seasonal influenza vaccination, delay to consultation, antiviral use before admission, pregnancy, underlying medical conditions, and obesity. Age <5 years, underlying medical conditions (neuromuscular, cardiac, pulmonary, and renal conditions, diabetes, asthma, and other), and delayed consultation were associated with hospitalization. The strongest association with hospitalization was observed for neuromuscular disorders. Antiviral medication before hospital admission protected against severe disease. Association of obesity with hospitalization was not significant after adjustment in multivariable analysis. Among hospitalized patients, age ≥60 years and immune suppression were associated with death. CONCLUSIONS: Previously identified risk factors for seasonal influenza were also associated with increased risk of severe pH1N1 outcomes. The independent role of obesity needs to be further defined.     

Estimating influenza outpatients' and inpatients' incidences from 2009 to 2011 in a tropical urban setting in the Philippines

Objectives

Although the public health significance of influenza in regions with a temperate climate has been widely recognized, information on influenza burden in tropical countries, including the Philippines, remains limited. We aimed to estimate influenza incidence rates for both outpatients and inpatients then characterized their demographic features.

Design

An enhanced surveillance was performed from January 2009 to December 2011 in an urbanized highland city. The influenza-like illness (ILI) surveillance involved all city health centers and an outpatient department of a tertiary government hospital. The severe acute respiratory infection (sARI) surveillance was also conducted with one government and four private hospitals since April 2009. Nasal and/or oropharyngeal swabs were collected and tested for influenza A, influenza B, and respiratory syncytial virus.

Results and Conclusions

We obtained 5915 specimens from 13 002 ILI cases and 2656 specimens from 10 726 sARI cases throughout the study period. We observed year-round influenza activity with two possible peaks each year. The overall influenza detection rate was 23% in the ILI surveillance and 9% in the sARI surveillance. The mean annual outpatient incidence rate of influenza was 5·4 per 1000 individuals [95% confidence interval (CI), 1·83–12·7], and the mean annual incidence of influenza-associated sARI was 1·0 per 1000 individuals (95% CI, 0·03–5·57). The highest incidence rates were observed among children aged <5 years, particularly those aged 6–23 months. Influenza posed a certain disease burden among inpatients and outpatients, particularly children aged <5 years, in an urbanized tropical city of the Philippines.     

Case fatality of SARS in mainland China and associated risk factors

Objective To analyse the case fatality ratio (CFR) and its risk factors for severe acute respiratory syndrome (SARS) in mainland China by using a comprehensive dataset of all probable cases.
Methods The data of all probable SARS cases were derived from the Infectious Disease Reporting System of the Center of Diseases Control and Hospital Information Systems, during the 2003 epidemic in mainland China. The definition of probable SARS case was consistent with the definition for clinically confirmed SARS issued by the Ministry of Health of the People's Republic of China. We performed univariate and multivariate logistic regression analysis to determine the association of CFR with age, sex, residence location, occupation, the period of the epidemic and the duration from symptom onset to admission into hospital.
Results The overall CFR was 6.4% among 5327 probable SARS cases in mainland China. Old age, being a patient during the early period of a local outbreak, and being from Tianjin led to a relatively higher CFR than young age, late stage of a local outbreak and cases from Beijing. Guangdong Province resulted in an even lower CFR compared with Beijing.
Conclusions Because of their deteriorated health status and apparent complications, SARS patients aged >60 years had a much higher risk of dying than younger patients. At the early stage of local outbreaks, lack of experience in patient care and perhaps treatment also led to a relatively higher CFR. The Tianjin SARS outbreak happened mainly within a hospital, leading to a high impact of co-morbidity. The relatively young age of the cases partly explains the low CFR in mainland China compared with other countries and areas affected by SARS.     

Influenza‐like illness sentinel surveillance in one hospital in Medellin,Colombia. 2007–2012

Background

The city of Medellin in Colombia has almost no documentation of the causes of acute respiratory infections (ARIs). As part of an ongoing collaboration, we conducted an epidemiologic surveillance for influenza and other respiratory viruses. It described the influenza strains that were circulating in the region along with their distribution over time, and performing molecular characterization to some of those strains. This will contribute to the knowledge of local and national epidemiology.

Objectives

To analyze viral etiologic agents associated with influenza like illness (ILI) in participants reporting to one General hospital in Medelllin, Colombia.

Results

From January 2007 to December 2012, a total of 2039 participants were enrolled. Among them, 1120 (54·9%) were male and 1364 (69%) were under the age of five. Only 124 (6%) were older than the age of 15. From all 2039 participants, 1040 samples were diagnosed by either isolation or RT-PCR. One or more respiratory viruses were found in 737 (36%) participants. Of those, 426 (57·8%) got influenza A or B. Adenoviral and parainfluenza infections represented 19·1% and 14·9% of viral infections, respectively. Influenza A was detected almost throughout the whole year except for the first quarter of 2010, right after the 2009 influenza A pandemic. Influenza B was detected in 2008, 2010, and 2012 with no pattern detected. During 2008 and 2010, both types circulated in about the same proportion. Unusually, in many months of 2012, the proportion of influenza B infections was higher than influenza A (ranging between 30% and 42%). The higher proportion of adenovirus was mainly detected in the last quarter of years 2007 and 2010. Adenoviral cases are more frequent in participants under the age of four.

Conclusions

The phylogenetic analysis of influenza viruses shows that only in the case of influenza A/H1N1, the circulating strains totally coincide with the vaccine strains each year.     

Timing of influenza epidemics and vaccines in the American tropics, 2002–2008, 2011–2014

Background

Influenza‐associated illness results in increased morbidity and mortality in the Americas. These effects can be mitigated with an appropriately chosen and timed influenza vaccination campaign. To provide guidance in choosing the most suitable vaccine formulation and timing of administration, it is necessary to understand the timing of influenza seasonal epidemics.

Objectives

Our main objective was to determine whether influenza occurs in seasonal patterns in the American tropics and when these patterns occurred.

Methods

Publicly available, monthly seasonal influenza data from the Pan American Health Organization and WHO, from countries in the American tropics, were obtained during 2002–2008 and 2011–2014 (excluding unseasonal pandemic activity during 2009–2010). For each country, we calculated the monthly proportion of samples that tested positive for influenza. We applied the monthly proportion data to a logistic regression model for each country.

Results

We analyzed 2002–2008 and 2011–2014 influenza surveillance data from the American tropics and identified 13 (81%) of 16 countries with influenza epidemics that, on average, started during May and lasted 4 months.

Conclusions

The majority of countries in the American tropics have seasonal epidemics that start in May. Officials in these countries should consider the impact of vaccinating persons during April with the Southern Hemisphere formulation.     

Decline of influenza and respiratory syncytial virus detection in facility-based surveillance during the COVID-19 pandemic,South Africa,January to October 2020

BackgroundIn South Africa, COVID-19 control measures to prevent SARS-CoV-2 spread were initiated on 16 March 2020. Such measures may also impact the spread of other pathogens, including influenza virus and respiratory syncytial virus (RSV) with implications for future annual epidemics and expectations for the subsequent northern hemisphere winter.MethodsWe assessed the detection of influenza and RSV through facility-based syndromic surveillance of adults and children with mild or severe respiratory illness in South Africa from January to October 2020, and compared this with surveillance data from 2013 to 2019.ResultsFacility-based surveillance revealed a decline in influenza virus detection during the regular season compared with previous years. This was observed throughout the implementation of COVID-19 control measures. RSV detection decreased soon after the most stringent COVID-19 control measures commenced; however, an increase in RSV detection was observed after the typical season, following the re-opening of schools and the easing of measures.ConclusionCOVID-19 non-pharmaceutical interventions led to reduced circulation of influenza and RSV in South Africa. This has limited the country’s ability to provide influenza virus strains for the selection of the annual influenza vaccine. Delayed increases in RSV case numbers may reflect the easing of COVID-19 control measures. An increase in influenza virus detection was not observed, suggesting that the measures may have impacted the two pathogens differently. The impact that lowered and/or delayed influenza and RSV circulation in 2020 will have on the intensity and severity of subsequent annual epidemics is unknown and warrants close monitoring.     

Influenza‐associated mortality in Thailand, 2006–2011

Background

Influenza-associated mortality in subtropical or tropical regions, particularly in developing countries, remains poorly quantified and often underestimated. We analyzed data in Thailand, a middle-income tropical country with good vital statistics and influenza surveillance data.

Methods

We obtained weekly mortality data for all-cause and three underlying causes of death (circulatory and respiratory diseases, and pneumonia and influenza), and weekly influenza virus data, from 2006 to 2011. A negative binomial regression model was used to estimate deaths attributable to influenza in two age groups (<65 and ≥65 years) by incorporating influenza viral data as covariates in the model.

Results

From 2006 to 2011, the average annual influenza-associated mortality per 100 000 persons was 4·0 (95% CI: −18 to 26). Eighty-three percent of influenza-associated deaths occurred among persons aged > 65 years. The average annual rate of influenza-associated deaths was 0·7 (95% CI: −8·2 to 10) per 100 000 population for person aged <65 years and 42 (95% CI: −137 to 216) for person aged ≥ 65 years.

Discussion

In Thailand, estimated excess mortality associated with influenza was considerable even during non-pandemic years. These data provide support for Thailand''s seasonal influenza vaccination campaign. Continued monitoring of mortality data is important to assess impact.     

Hospital‐based influenza morbidity and mortality surveillance system for influenza‐like illnesses: a comparison with national influenza surveillance systems

The Hospital‐based Influenza Morbidity and Mortality (HIMM) surveillance system is an emergency room (ER)‐based influenza surveillance system in Korea that was established in 2011. The system was established under the assumption that integrated clinical and virologic surveillance could be performed rapidly and easily at seven tertiary hospitals' ER. Here, we assessed the correlation between data generated from the HIMM surveillance system and the Korean national influenza surveillance systems during the 2011–2012 influenza season using cross‐correlation analysis and found strong correlations. Rapid antigen‐test‐based HIMM surveillance would predict the start of influenza epidemic earlier than pre‐existing influenza‐like‐illness‐based surveillance.     

Spotlight influenza: Extending influenza surveillance to detect non-influenza respiratory viruses of public health relevance: analysis of surveillance data,Belgium, 2015 to 2019

BackgroundSeasonal influenza-like illness (ILI) affects millions of people yearly. Severe acute respiratory infections (SARI), mainly influenza, are a leading cause of hospitalisation and mortality. Increasing evidence indicates that non-influenza respiratory viruses (NIRV) also contribute to the burden of SARI. In Belgium, SARI surveillance by a network of sentinel hospitals has been ongoing since 2011.AimWe report the results of using in-house multiplex qPCR for the detection of a flexible panel of viruses in respiratory ILI and SARI samples and the estimated incidence rates of SARI associated with each virus.MethodsWe defined ILI as an illness with onset of fever and cough or dyspnoea. SARI was defined as an illness requiring hospitalisation with onset of fever and cough or dyspnoea within the previous 10 days. Samples were collected in four winter seasons and tested by multiplex qPCR for influenza virus and NIRV. Using catchment population estimates, we calculated incidence rates of SARI associated with each virus.ResultsOne third of the SARI cases were positive for NIRV, reaching 49.4% among children younger than 15 years. In children younger than 5 years, incidence rates of NIRV-associated SARI were twice that of influenza (103.5 vs 57.6/100,000 person-months); co-infections with several NIRV, respiratory syncytial viruses, human metapneumoviruses and picornaviruses contributed most (33.1, 13.6, 15.8 and 18.2/100,000 person-months, respectively).ConclusionEarly testing for NIRV could be beneficial to clinical management of SARI patients, especially in children younger than 5 years, for whom the burden of NIRV-associated disease exceeds that of influenza.     

Estimating the hospitalization burden associated with influenza and respiratory syncytial virus in New York City, 2003–2011

Background

Hospitalization burden associated with influenza and respiratory syncytial virus (RSV) is uncertain due to ambiguity in the inference methodologies employed for its estimation.

Objectives

Utilization of a new method to quantitate the above burden.

Methods

Weekly hospitalization rates for several principal diagnoses from 2003 to 2011 in New York City by age group were regressed linearly against incidence proxies for the major influenza subtypes and RSV adjusting for temporal trends and seasonal baselines.

Results

Average annual rates of influenza-associated respiratory hospitalizations per 100 000 were estimated to be 129 [95% CI (79, 179)] for age <1, 36·3 (21·6, 51·4) for ages 1–4, 10·6 (7·5, 13·7) for ages 5–17, 25·6 (21·3, 29·8) for ages 18–49, 65·5 (54·0, 76·9) for ages 50–64, 125 (105, 147) for ages 65–74, and 288 (244, 331) for ages ≥75. Additionally, influenza had a significant contribution to hospitalization rates with a principal diagnosis of septicemia for ages 5–17 [0·76 (0·1, 1·4)], 18–49 [1·02 (0·3, 1·7)], 50–64 [4·0 (1·7, 6·3)], 65–74 [8·8 (2·2, 15·6)], and ≥75 [38·7 (25·7, 52·9)]. RSV had a significant contribution to the rates of respiratory hospitalizations for age <1 [1900 (1740, 2060)], ages 1–4 [117 (70, 167)], and ≥75 [175 (44, 312)] [including chronic lower respiratory disease, 90 (43, 140)] as well as pneumonia & influenza hospitalizations for ages 18–49 [6·2 (1·1, 11·3)] and circulatory hospitalizations for ages ≥75 [199 (13, 375)].

Conclusions

The high burden of RSV hospitalizations among young children and seniors age ≥75 suggests the need for additional control measures such as vaccination to mitigate the impact of annual RSV epidemics. Our estimates for influenza-associated hospitalizations provide further evidence of the burden of morbidity associated with influenza, supporting current guidelines regarding influenza vaccination and antiviral treatment.     

Effectiveness and knowledge,attitudes and practices of seasonal influenza vaccine in primary healthcare settings in South Africa, 2010–2013

Objectives

Influenza vaccine effectiveness (VE) and coverage data for sub-Saharan Africa are scarce. Using a test-negative case–control design, we estimated influenza VE annually among individuals with influenza-like illness presenting to an outpatient sentinel surveillance programme in South Africa from 2010 to 2013. A knowledge, attitudes and practices (KAP) influenza vaccine survey of programme clinicians was conducted in 2013.

Sample

In total, 9420 patients were enrolled in surveillance of whom 5344 (56.7%) were included in the VE analysis: 2678 (50.1%) were classified as controls (influenza test-negative) and 2666 (49.9%) as cases (influenza test-positive).

Results

Mean annual influenza vaccine coverage among controls was 4.5% for the four years. Annual VE estimates adjusted for age, underlying medical conditions and seasonality for 2010-2013 were 54.2% (95% confidence interval (CI): 2.4–78.6%), 57.1% (95% CI: 15.5–78.2%), 38.4% (95% CI: −71.7–78.1%) and 87.2% (95% CI: 67.2–95.0%), respectively. The KAP survey showed that >90% of clinicians were familiar with the indications for and the benefits of influenza vaccination.

Conclusions

Our study showed that the vaccine was significantly protective in 2010, 2011 and 2013, but not in 2012 when the circulating A(H3N2) strain showed genetic drift. Vaccine coverage was low despite good clinician knowledge of vaccination indications. Further studies are needed to investigate the reason for the low uptake of influenza vaccine.