Respiratory Viral Infection: An Underappreciated Cause of Acute Febrile Illness Admissions in Southern Sri Lanka

Patterns of Non-influenza Respiratory Viruses Among Severe Acute Respiratory Infection Cases in Burkina Faso: A Surveillance Study

BACKGROUND

Although influenza viruses cause only one-fifth of severe acute respiratory infections (SARI) in Burkina Faso, the other viral causes of SARI remain poorly investigated to inform clinical and preventive decision making.

METHODS

Between 2016 and 2019, we prospectively enrolled inpatients meeting the World Health Organization (WHO) case definition of SARI in Burkina Faso. Results of viral etiologies among inpatients tested negative for influenza using the Fast Track Diagnostics Respiratory Kits (FTD-33) were reported.

RESULTS

Of 1541 specimens tested, at least one respiratory virus was detected in 76.1% of the 1231 specimens negative for influenza virus. Human rhinoviruses (hRVs) were the most detected pathogens (476; 38.7%), followed by human adenoviruses (hAdV) (17.1%, 210/1231), human respiratory syncytial virus (hRSV) (15.4%, 189/1231), enterovirus (EnV) (11.2%, 138/1231), human bocavirus (hBoV) (7.9%, 97/1231), parainfluenza 3 (hPIV3) (6.1%, 75/1231), human metapneumovirus (hMPV) (6.0%,74/1321), parainfluenza 4 (hPIV4) (4.1%, 51/1231), human coronavirus OC43 (hCoV-OC43) (3.4%, 42/1231), human coronavirus HKU1(hCoV-HKU1) (2.7%, 33/1231), human coronavirus NL63 (hCoV-NL63) (2.5%, 31/1231), parainfluenza 1 (hPIV1) (2.0%, 25/1231), parainfluenza 2 (hPIV2) (1.8%, 22/1231), human parechovirus (PeV) (1.1%, 14/1231), and human coronavirus 229E (hCoV-229E) (0.9%, 11/1231). Among SARI cases, infants aged 1-4 years were mostly affected (50.7%; 622/1231), followed by those <1 year of age (35.7%; 438/1231). Most detected pathogens had year-long circulation patterns, with seasonal peaks mainly observed during the cold and dry seasons.

CONCLUSION

Several non-influenza viruses are cause of SARI in Burkina Faso. The integration of the most common pathogens into the routine influenza surveillance system might be beneficial.

Investigating the drivers for antibiotic use and misuse amongst medical undergraduates-perspectives from a Sri Lankan medical school

Medical undergraduates are a unique group who gain the theoretical knowledge on prescribing antibiotics but are not authorized to prescribe till full licensure. This unique situation may result in self-medication and unauthorized prescription of antibiotics. This cross-sectional study was conducted among medical students of the Faculty of Medicine, University of Peradeniya, Sri Lanka in 2021 to identify patterns and drivers for antibiotic use and misuse among medical undergraduates. A validated, self-administered Google forms-based online questionnaire was used to gather information on antibiotic use, misuse, and associated factors: demographics, knowledge and perceptions. Two scores; a practice score and a knowledge score were calculated to compare with the associated factors. The study population consisted of 347 medical students with a mean age of 24 (SD1.7) years and 142/347 (40.9%) were male participants. The patterns of misuses identified included; use of antibiotics without a prescription (161/347, 46.4%), keeping left-over antibiotics for future use (111/347, 32.0%), not completing the course of antibiotics (81/347, 23.3%), use of left-over antibiotics (74/347, 21.3%), prescribing to animals (61/347, 17.6%), prescribing antibiotics to family members or friends (51/347, 14.7%), antibiotic self-medication (25/347, 7.2%) and not following the dosage regime prescribed (24/347, 6.9%). The practice score ranged from 33% to 100% (median 87%, IQR 80.0-93.3) and did not differ significantly with either the gender or the year of study. The knowledge score ranged from 4% to 100% (median 87%, IQR: 71.5-95.4) differing significantly according to the year of study. Antibiotic prescription by medical undergraduates was perceived as unacceptable (329/347, 94.8%) by the majority. Individual misuse patterns were associated favourably or unfavourably with gender, year of study, having a health care worker at home and knowledge score. The knowledge score increased with the advancement in training at the medical school while the practice score remained indifferent, highlighting the need to identify the additional drivers of antibiotic misuse among medical undergraduates.

Clinical and epidemiological characteristics of influenza virus infection in hospitalized children with acute respiratory infections in Sri Lanka

Influenza viruses (Inf-V) are an important cause of acute respiratory infection (ARI) in children. This study was undertaken to describe the clinical and epidemiological characteristics of Inf-V infections in a sample of hospitalized children with ARI. Nasopharyngeal aspirates (NPA) from 500 children between 1 month to 5 years old with symptoms of ARI were collected at the Teaching Hospital Kegalle Sri Lanka From May 2016 to June 2018, NPAs were tested for influenza A (Inf-A) and B (Inf-B) viruses, human respiratory syncytial virus (hRSV), human parainfluenza virus (hPIV) 1–3 using an immunofluorescence assay. The Inf-V were then subtyped using a multiplex RT-PCR. Inf-V were detected in 10.75% (54/502) of the hospitalized children with ARI and in that 5.57% (28/502) were positive for Inf-A and 5.17% (26/502) were positive for Inf-B. Of the 54 Inf-V positive children, 33 were aged between 6 and 20 months. Of the 28 children infected with Inf-A, 15 had uncharacterized lower respiratory infection, 7 had bronchopneumonia and 6 had bronchiolitis. Of the 26 children infected with Inf-B, 11 had uncharacterized lower respiratory infection, 10 had bronchiolitis, and 4 had bronchopneumonia. Inf-B circulated throughout the year with a few peaks, one in June and then in August followed by November to December in 2016 and one in April 2017 and January 2018. Inf-A circulated throughout the year with a major peak in March to April 2017 and July 2018. ARI was more common in boys compared to girls. Majority of the children infected with Inf-V were diagnosed with uncharacterized lower respiratory infection and mild to moderate bronchiolitis. Inf-V infections were prevalent throughout the year in the study area of Sri Lanka with variations in the type of the circulating virus.

Viral burden and diversity in acute respiratory tract infections in hospitalized children in wet and dry zones of Sri Lanka

The present study was done to identify the viral diversity, seasonality and burden associated with childhood acute respiratory tract infection (ARTI) in Sri Lanka. Nasopharyngeal aspirates (NPA) of hospitalized children (1 month-5 years) with ARTI were collected in 2 centers (wet and dry zones) from March 2013 to August 2014. Respiratory viral antigen detection by immunofluorescence assay (IFA) was used to identify the infecting viruses. IFA negative 100 NPA samples were tested for human metapeumovirus (hMPV), human bocavirus and corona viruses by polymerase chain reaction. Of the 443 and 418 NPAs, 37.2% and 39.4% were positive for any of the 8 different respiratory viruses tested from two centers studied. Viral co-infection was detected with respiratory syncytial virus (RSV) in both centers. Peak viral detection was noted in the wet zone from May-July 2013 and 2014 and in the dry zone from December-January 2014 suggesting a local seasonality for viral ARTI. RSV showed a clear seasonality with a direct correlation of monthly RSV infections with rainy days in the wet zone and an inverse correlation with temperature in both centers. The case fatality rate was 2.7% for RSV associated ARTI. The overall disability adjusted life years was 335.9 and for RSV associated ARTI it was 241.8. RSV was the commonly detected respiratory virus with an annual seasonality and distribution in rainy seasons in the dry and wet zones of Sri Lanka. Identifying the virus and seasonality will contribute to employ preventive measures and reduce the empirical use of antibiotics in resource limited settings.

Viral etiology and seasonal trends of pediatric acute febrile illness in southern Puerto Rico; a seven-year review

BACKGROUND

Acute febrile illness (AFI) is an important cause for seeking health care among children. Knowledge of the most common etiologic agents of AFI and its seasonality is limited in most tropical regions.

METHODOLOGY/PRINCIPAL FINDINGS

To describe the viral etiology of AFI in pediatric patients (≤18 years) recruited through a sentinel enhanced dengue surveillance system (SEDSS) in Southern Puerto Rico, we analyzed data for patients enrolled from 2012 to May 2018. To identify seasonal patterns, we applied time-series analyses to monthly arboviral and respiratory infection case data. We calculated coherence and phase differences for paired time-series to quantify the association between each time series. A viral pathogen was found in 47% of the 14,738 patients. Influenza A virus was the most common pathogen detected (26%). The incidence of Zika and dengue virus etiologies increased with age. Arboviral infections peaked between June and September throughout the times-series. Respiratory infections have seasonal peaks occurring in the fall and winter months of each year, though patterns vary by individual respiratory pathogen.

CONCLUSIONS/SIGNIFICANCE

Distinct seasonal patterns and differences in relative frequency by age groups seen in this study can guide clinical and laboratory assessment in pediatric patients with AFI in Puerto Rico.

Outbreak of severe acute respiratory infection in Southern Province, Sri Lanka in 2018: a cross-sectional study

OBJECTIVES

To determine aetiology of illness among children and adults presenting during outbreak of severe respiratory illness in Southern Province, Sri Lanka, in 2018.

DESIGN

Prospective, cross-sectional study.

SETTING

1600-bed, public, tertiary care hospital in Southern Province, Sri Lanka.

PARTICIPANTS

410 consecutive patients, including 371 children and 39 adults, who were admitted with suspected viral pneumonia (passive surveillance) or who met case definition for acute respiratory illness (active surveillance) in May to June 2018.

RESULTS

We found that cocirculation of influenza A (22.6% of cases), respiratory syncytial virus (27.8%) and adenovirus (AdV) (30.7%; type B3) was responsible for the outbreak. Mortality was noted in 4.5% of paediatric cases identified during active surveillance. Virus type and viral coinfection were not significantly associated with mortality.

CONCLUSIONS

This is the first report of intense cocirculation of multiple respiratory viruses as a cause of an outbreak of severe acute respiratory illness in Sri Lanka, and the first time that AdV has been documented as a cause of a respiratory outbreak in the country. Our results emphasise the need for continued vigilance in surveying for known and emerging respiratory viruses in the tropics.

Previously Derived Host Gene Expression Classifiers Identify Bacterial and Viral Etiologies of Acute Febrile Respiratory Illness in a South Asian Population

Background

Pathogen-based diagnostics for acute respiratory infection (ARI) have limited ability to detect etiology of illness. We previously showed that peripheral blood-based host gene expression classifiers accurately identify bacterial and viral ARI in cohorts of European and African descent. We determined classifier performance in a South Asian cohort.

Methods

Patients ≥15 years with fever and respiratory symptoms were enrolled in Sri Lanka. Comprehensive pathogen-based testing was performed. Peripheral blood ribonucleic acid was sequenced and previously developed signatures were applied: a pan-viral classifier (viral vs nonviral) and an ARI classifier (bacterial vs viral vs noninfectious).

Results

Ribonucleic acid sequencing was performed in 79 subjects: 58 viral infections (36 influenza, 22 dengue) and 21 bacterial infections (10 leptospirosis, 11 scrub typhus). The pan-viral classifier had an overall classification accuracy of 95%. The ARI classifier had an overall classification accuracy of 94%, with sensitivity and specificity of 91% and 95%, respectively, for bacterial infection. The sensitivity and specificity of C-reactive protein (>10 mg/L) and procalcitonin (>0.25 ng/mL) for bacterial infection were 100% and 34%, and 100% and 41%, respectively.

Conclusions

Previously derived gene expression classifiers had high predictive accuracy at distinguishing viral and bacterial infection in South Asian patients with ARI caused by typical and atypical pathogens.