Respiratory viruses associated with patients older than 50 years presenting with ILI in Senegal, 2009 to 2011

Prevalence of Respiratory Pathogens in Nasopharyngeal Swabs of Febrile Patients with or without Respiratory Symptoms in the Niakhar Area of Rural Senegal

Acute respiratory tract infections are one of the leading causes of morbidity and mortality worldwide. More data are needed on circulating respiratory microorganisms in different geographical areas and ecosystems. We analyzed nasopharyngeal swabs from 500 febrile patients living in the Niakhar area (Senegal), using FTDTM multiplex qPCR and simplex qPCR to target a panel of 25 microorganisms. We detected at least one microorganism for 366/500 patients (73.2%), at least one virus for 193/500 (38.6%), and at least one bacterium for 324/500 (64.8%). The most frequently detected microorganisms were Streptococcus pneumoniae (36.8%), Haemophilus influenzae (35.8%), adenovirus (11.8%), influenza viruses (6.4%), rhinovirus (5.0%), SARS-CoV-2 (4.0%), and RSV (4.0%). The main microorganisms significantly associated with respiratory symptoms, with a p-value ≤ 0.05, were influenza virus (11.9% in patients with respiratory symptoms versus 2.9% in patients without), RSV (6.5% versus 2.6%), metapneumovirus (5.4% versus 1.3%), HPIVs (7.6% versus 1.0%), S. pneumoniae (51.9% versus 28.0%), and H. influenzae (54.6% versus 24.5%). Co-infections were significantly associated with respiratory symptoms (65.4% versus 32.9%). All the epidemiological data show a high level of circulation of respiratory pathogens among febrile patients, including those preventable by vaccination such as S. pneumoniae, raising the question of the serotypes currently circulating. Furthermore, the availability of affordable real-time etiological diagnostic tools would enable management to be adapted as effectively as possible.

Seasonal variation of asymptomatic viral and bacterial nasopharyngeal carriage in rural Senegal

BACKGROUND

The surveillance of respiratory pathogens in rural areas of West Africa has, to date, largely been focussed on symptoms. In this prospective study conducted prior to the COVID-19 pandemic, we aimed to assess the asymptomatic prevalence of respiratory pathogen carriage in a group of individuals living in a rural area of Senegalese.

METHODS

Longitudinal follow up was performed through monthly nasopharyngeal swabbing during the dry season and weekly swabbing during the rainy season. We enrolled 15 individuals from the village of Ndiop. A total of 368 nasopharyngeal swabs were collected over a one-year period. We investigated the prevalence of 18 respiratory viruses and eight respiratory bacteria in different age groups using singleplex and multiplex PCR.

RESULTS

In total, 19.56% of the samples (72/368) were positive for respiratory viruses and 13.60% of the samples (50/368) were positive for respiratory bacteria. Coronaviruses (19/72, 26.39%), adenoviruses (17/72, 23.61%), rhinoviruses (14/72, 19.44%), Streptococcus pneumoniae (17/50, 34%), and Moraxella catarrhalis (15/50, 30%) were the most frequently detected viruses. Interestingly, the carriage of respiratory pathogens was shown to be more frequent during the rainy season, as pluviometry was shown to be positively associated with the occurrence of respiratory viruses such as influenza (P = .0078, r2 =.523) and RSV (P = .0055, r2 =.554).

CONCLUSIONS

Our results show a non-negligible circulation of respiratory pathogens in a rural area in Senegal (West Africa) with an underestimated proportion of asymptomatic individuals. This study highlights the fact that the circulation of viruses and bacteria in the community has been overlooked.

Influence of Microbiota on Clinical Expressions of Respiratory Viral Infections

Respiratory infections, mainly due to viruses, are among the leading causes of worldwide morbidity and mortality. We investigated the prevalence of viruses and bacteria in a cross-sectional survey conducted in Dielmo, a village in rural Senegal with a population of 481 inhabitants. Nasopharyngeal sampling was performed in 50 symptomatic subjects and 101 asymptomatic subjects. Symptomatic subjects were defined as individuals presenting with clinical signs of respiratory infection, whereas asymptomatic subjects were recruited in the same households. The identification of pathogens was performed by polymerase chain reaction for 18 respiratory viruses and eight respiratory bacteria. The prevalence results for respiratory viruses detected in each study group demonstrated that 83.6% of symptomatic samples were positive for at least one respiratory virus, and 21.8% were detected in asymptomatic samples. Influenza A (P = 0.0001), metapneumovirus (P = 0.04), and enterovirus (P = 0.001) were significantly more prevalent in symptomatic patients. Overall, 82.0% of symptomatic subjects and 26.9% of asymptomatic subjects were positive for at least one respiratory bacterium. The most frequent pathogenic bacteria detected were Moraxella catarrhalis (56%) and Streptococcus pneumoniae (48.0%) among symptomatic individuals, whereas in asymptomatic subjects Corynebacterium propinquum was more prevalent (18%). A principal component analysis showed that parainfluenzas 2 and 4 were associated with asymptomatic subjects, whereas influenza A was associated with the presence of symptoms. Considering these results, a large epidemiological surveillance of the circulation of these respiratory pathogens in the general population should be conducted to provide a better understanding of their carriage and to potentially prevent epidemics.

Prevalence and Molecular Epidemiology of Human Coronaviruses in Africa Prior to the SARS-CoV-2 Outbreak: A Systematic Review

Coronaviruses, re-emerging in human populations, cause mild or severe acute respiratory diseases, and occasionally epidemics. This study systematically reviewed human coronavirus (HCoVs) infections in Africa prior to the SARS-CoV-2 outbreak. Forty studies on the prevalence or molecular epidemiology of HCoVs were available from 13/54 African countries (24%). The first published data on HCoV was from South Africa in 2008. Eight studies (20%) reported on HCoV molecular epidemiology. Endemic HCoV prevalence ranged from 0.0% to 18.2%. The prevalence of zoonotic MERS-CoV ranged from 0.0% to 83.5%. Two studies investigated SARS-CoV infection, for which a prevalence of 0.0% was reported. There was heterogeneity in the type of tests used in determining HCoV prevalence. Two studies reported that risk factors for HCoV include exposure to infected animals or humans. The quantity of virologic investigations on HCoV on the African continent was scant, and Africa was not prepared for SARS-CoV-2.

Viral etiology of lower respiratory tract infections in adults in the pre-COVID-19 pandemic era: A cross-sectional study in a single center experience from Cameroon

Background and Aims

Respiratory viruses are responsible for the majority of lower respiratory tract infections (LRTIs) worldwide. However, there is a gap on the epidemiology of viral LRTIs in adults in sub-Saharan African countries. In Cameroon, like in other countries, the role of viral respiratory pathogens in the etiology of LRTIs in adults is helpful for clinical management. This study aimed to determine the viral aetiologies of LRTIs among hospitalized adults in a reference center for respiratory diseases in the town of Yaounde in Cameroon and its surroundings.

Methods

A cross-sectional study was conducted from January 2017 to January 2018 at Jamot Hospital in Yaounde (Cameroon). Clinical and demographic information; BAL and sputa were collected from hospitalized patients meeting LRTI case definitions. The clinical samples were investigated for respiratory pathogens with a commercial Reverse Transcriptase Real-Time Polymerase Chain Reaction (RT-PCR) targeting 21 viruses, cultures for bacterial and fungal infections.

Results

The 77 included adult patients with LRTIs had an appropriate clinical sample for microbial investigations. A viral agent was detected in 22.1% (17/77) samples. The main viruses detected included rhinovirus (10/77), coronavirus (hCoV-OC43 and hCoV-229E), and influenza A virus (3/77 each). A concomitant viral and bacterial co-infection occurred in 7.8% of patients (6/77) while viral co-infection occurred in one patient (1.3%). No Severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) was detected in clinical samples. Most patients were under antimicrobials before getting diagnosed.

Conclusions

Respiratory viruses account for 22.1% of LRTIs in hospitalized patients in this study. Despite prior antimicrobial therapy and delay, rhinovirus, coronavirus and influenza A virus were the most detected in patients in the pre-COVID-19 pandemic era in a single center experience from Cameroon.

PCR investigation of infections in patients consulting at a healthcare centre over a four-year period during the Grand Magal of Touba

BACKGROUND

Respiratory and gastrointestinal symptoms and febrile illness are the most common complaints among ill pilgrims attending the Grand Magal of Touba (GMT) in Senegal.

METHODS

Patients presenting with respiratory or gastrointestinal symptoms or febrile systemic illnesses were recruited between 2018 and 2021 at a healthcare centre close to Touba. Respiratory, gastrointestinal and blood samples were tested for potential pathogens using qPCR.

RESULTS

538 patients were included. 45.5% of these were female, with a median age of 17 years. Of the 326 samples collected from patients with a cough, 62.8% tested positive for at least one virus, including influenza viruses (33.1%). A high positivity rate of bacterial carriage was observed for Haemophilus influenzae (72.7%), Streptococcus pneumoniae (51.2%) and Moraxella catarrhalis (46.0%). Of the 95 samples collected from patients with diarrhoea, 71.3% were positive, with high rates of bacterial carriage, ranging from 4.2% for Tropheryma whipplei to 45.3% for Entero-pathogenic Escherichia coli. Of the 141 blood samples collected from patients with fever, 31.9% were positive including Plasmodium falciparum (21.3%), Borrelia sp. (5.7%) and dengue virus (5.0%).

CONCLUSION

This study provides insight into the aetiology of most common infections at the GMT on which to base therapeutic options.

The epidemiology of seasonal influenza after the 2009 influenza pandemic in Africa: a systematic review

Background

Influenza infection is a serious public health problem that causes an estimated 3 to 5 million cases and 250,000 deaths worldwide every year. The epidemiology of influenza is well-documented in high- and middle-income countries, however minimal effort had been made to understand the epidemiology, burden and seasonality of influenza in Africa. This study aims to assess the state of knowledge of seasonal influenza epidemiology in Africa and identify potential data gaps for policy formulation following the 2009 pandemic.

Method

We reviewed articles from Africa published into four databases namely: MEDLINE (PubMed), Google Scholar, Cochrane Library and Scientific Research Publishing from 2010 to 2019.

Results

We screened titles and abstracts of 2070 studies of which 311 were selected for full content evaluation and 199 studies were considered. Selected articles varied substantially on the basis of the topics they addressed covering the field of influenza surveillance (n=80); influenza risk factors and co-morbidities (n=15); influenza burden (n=37); influenza vaccination (n=40); influenza and other respiratory pathogens (n=22) and influenza diagnosis (n=5).

Conclusion

Significant progress has been made since the last pandemic in understanding the influenza epidemiology in Africa. However, efforts still remain for most countries to have sufficient data to allow countries to prioritize strategies for influenza prevention and control.

The burden of respiratory syncytial virus in adults: a systematic review and meta-analysis

Respiratory syncytial virus (RSV) is the most common pathogen associated with acute lower respiratory tract infections in young children. RSV is also a major viral pathogen causing severe lung disease in the adult population, particularly among the elderly. We conducted a review of adult RSV studies published from January 1970 to February 2017 to determine the burden of disease among adults worldwide. There were no restrictions on health care setting or definition of RSV infection. A total of 1530 published studies were identified, 95 of which were included in this review. The incidence rates of hospitalised RSV acute respiratory tract infection (ARI) in adults >65 years old ranged from 7.3 to 13.0/10⁵ population in Africa and Asia and from 190 to 254/10⁵ population in the USA. Higher incidence rates (195–1790/10⁵ population) were observed in adults ≥50 years old for outpatient or emergency visits in the USA. Of all ARI patients, RSV accounted for 1–10% in adults and 2–14% in patients with chronic diseases or transplantation. Given the limitations in the existing data, significant efforts should be made to generate evidence on the burden of RSV infections in adults and to estimate the potential impact of future preventive interventions.

Estimation of the burden of flu-association influenza-like illness visits on total clinic visits through the sentinel influenza monitoring system in Senegal during the 2013-2015 influenza seasons

Knowing the burden of influenza is helpful for policy decisions. Here we estimated the contribution of influenza-like illness (ILI) visits associated with laboratory-confirmed influenza among all clinic visits in a Senegal sentinel network. ILI data from ten sentinel sites were collected from January 2013 to December 2015. ILI was defined as an axillary measured fever of more than 37.5 °C with a cough or a sore throat. Collected nasopharyngeal swabs were tested for influenza viruses by rRT-PCR. Influenza-associated ILI was defined as ILI with laboratory-confirmed influenza. For the influenza disease burden estimation, we used all-case outpatient visits during the study period who sought care at selected sites. Of 4030 ILI outpatients tested, 1022 were influenza positive. The estimated proportional contribution of influenza-associated ILI was, per 100 outpatients, 1.2 (95% CI 1.1-1.3), 0.32 (95% CI 0.28-0.35), 1.11 (95% CI 1.05-1.16) during 2013, 2014, 2015, respectively. The age-specific outpatient visits proportions of influenza-associated ILI were higher among children under 5 years (0.68%, 95% CI: 0.62-0.70). The predominant virus during years 2013 and 2015 was influenza B while A/H3N2 subtype was predominant during 2014. Influenza viruses cause a substantial burden of outpatient visits particularly among children under 5 of age in Senegal and highlight the need of vaccination in risk groups.

Clinical Features, Severity, and Incidence of RSV Illness During 12 Consecutive Seasons in a Community Cohort of Adults ≥60 Years Old

Background

The epidemiology and burden of respiratory syncytial virus (RSV) illness are not well defined in older adults.

Methods

Adults ≥60 years old seeking outpatient care for acute respiratory illness were recruited from 2004–2005 through 2015–2016 during the winter seasons. RSV was identified from respiratory swabs by multiplex polymerase chain reaction. Clinical characteristics and outcomes were ascertained by interview and medical record abstraction. The incidence of medically attended RSV was estimated for each seasonal cohort.

Results

RSV was identified in 243 (11%) of 2257 enrollments (241 of 1832 individuals), including 121 RSV type A and 122 RSV type B. The RSV clinical outcome was serious in 47 (19%), moderate in 155 (64%), and mild in 41 (17%). Serious outcomes included hospital admission (n = 29), emergency department visit (n = 13), and pneumonia (n = 23) and were associated with lower respiratory tract symptoms during the enrollment visit. Moderate outcomes included receipt of a new antibiotic prescription (n = 144; 59%), bronchodilator/nebulizer (n = 45; 19%), or systemic corticosteroids (n = 28; 12%). The relative risk of a serious outcome was significantly increased in persons aged ≥75 years (vs 60–64 years) and in those with chronic obstructive pulmonary disease or congestive heart failure. The average seasonal incidence was 139 cases/10 000, and it was significantly higher in persons with cardiopulmonary disease compared with others (rate ratio, 1.89; 95% confidence interval, 1.44–2.48).

Conclusions

RSV causes substantial outpatient illness with lower respiratory tract involvement. Serious outcomes are common in older patients and those with cardiopulmonary disease.

Prevalence of human respiratory syncytial virus infection in people with acute respiratory tract infections in Africa: A systematic review and meta-analysis

AIM

The epidemiology of human respiratory syncytial virus (HRSV) infection has not yet been systematically investigated in Africa. This systematic review and meta-analysis are to estimate the prevalence of HRSV infections in people with acute respiratory tract infections (ARTI) in Africa.

METHOD

We searched PubMed, EMBASE, Africa Journal Online, and Global Index Medicus to identify observational studies published from January 1, 2000, to August 1, 2017. We used a random-effects model to estimate the prevalence across studies. Heterogeneity (I2 ) was assessed via the chi-square test on Cochran's Q statistic. Review registration: PROSPERO CRD42017076352.

RESULTS

A total of 67 studies (154 000 participants) were included. Sixty (90%), seven (10%), and no studies had low, moderate, and high risk of bias, respectively. The prevalence of HRSV infection varied widely (range 0.4%-60.4%). The pooled prevalence was 14.6% (95% CI 13.0-16.4, I2  = 98.8%). The prevalence was higher in children (18.5%; 95% CI 15.8-21.5) compared to adults (4.0%; 95% CI 2.2-6.1) and in people with severe respiratory tract infections (17.9%; 95% CI 15.8-20.1) compared to those with benign forms (9.4%; 95% CI 7.4-11.5); P-values <0.0001. The HRSV prevalence was not associated with sex, subregion in Africa, setting, altitude, latitude, longitude, and seasonality.

CONCLUSION

This study suggests a high prevalence of HRSV in people with ARTI in Africa, particularly among children and people with severe clinical form. All innovative strategies to curb the burden should first focus on children which present the highest HRSV-related burden.

Contemporaneous data on the prevalence of Human Respiratory Syncytial Virus infection in people with acute respiratory tract infections in Africa (2000-2017)

Availability of accurate data on the burden of the Human Respiratory Syncytial Virus (HRSV) can help to implement better strategies to curb this burden in Africa continent among people with acute respiratory tract infections (ARTI). We summarize here available contemporaneous data published from January 1, 2000 to August 31, 2017 on the prevalence of HSRV infection among people with ARTI in the continent.

Prevalence of Human Bocavirus in Africa and Other Developing Countries between 2005 and 2016: A Potential Emerging Viral Pathogen for Diarrhea

BACKGROUND

Human Bocavirus (HBoV) is an emerging virus discovered in 2005 from individuals suffering gastroenteritis and respiratory tract infections. Numerous studies related to the epidemiology and pathogenesis of HBoV have been conducted worldwide. This review reports on HBoV studies in individuals with acute gastroenteritis, with and without respiratory tract infections in Africa between 2005 and 2016.

MATERIAL AND METHOD

The search engines of PubMed, Google Scholar, and Embase database for published articles of HBoV were used to obtain data between 2005 and 2016. The search words included were as follows: studies performed in Africa or/other developing countries or/worldwide; studies for the detection of HBoV in patients with/without diarrhea and respiratory tract infection; studies using standardized laboratory techniques for detection.

RESULTS

The search yielded a total of 756 publications with 70 studies meeting the inclusion criteria. Studies included children and individuals of all age groups. HBoV prevalence in Africa was 13% in individuals suffering gastroenteritis with/without respiratory tract infection.

CONCLUSION

Reports suggest that HBoV infections are increasingly being recognized worldwide. Therefore, surveillance of individuals suffering from infections in Africa is required to monitor the prevalence of HBoV and help understand the role of HBoV in individuals suffering from gastroenteritis with/without respiratory tract infection.

Update on Human Rhinovirus and Coronavirus Infections

Human rhinovirus (HRV) and coronavirus (HCoV) infections are associated with both upper respiratory tract illness (“the common cold”) and lower respiratory tract illness (pneumonia). New species of HRVs and HCoVs have been diagnosed in the past decade. More sensitive diagnostic tests such as reverse transcription-polymerase chain reaction have expanded our understanding of the role these viruses play in both immunocompetent and immunosuppressed hosts. Recent identification of severe acute respiratory syndrome and Middle East respiratory syndrome viruses causing serious respiratory illnesses has led to renewed efforts for vaccine development. The role these viruses play in patients with chronic lung disease such as asthma makes the search for antiviral agents of increased importance.