Similar virus spectra and seasonality in paediatric patients with acute respiratory disease, Ghana and Germany

A combination of annual and nonannual forces drive respiratory disease in the tropics

INTRODUCTION

It is well known that influenza and other respiratory viruses are wintertime-seasonal in temperate regions. However, respiratory disease seasonality in the tropics is less well understood. In this study, we aimed to characterise the seasonality of influenza-like illness (ILI) and influenza virus in Ho Chi Minh City, Vietnam.

METHODS

We monitored the daily number of ILI patients in 89 outpatient clinics from January 2010 to December 2019. We collected nasal swabs and tested for influenza from a subset of clinics from May 2012 to December 2019. We used spectral analysis to describe the periodic signals in the system. We evaluated the contribution of these periodic signals to predicting ILI and influenza patterns through lognormal and gamma hurdle models.

RESULTS

During 10 years of community surveillance, 66 799 ILI reports were collected covering 2.9 million patient visits; 2604 nasal swabs were collected, 559 of which were PCR-positive for influenza virus. Both annual and nonannual cycles were detected in the ILI time series, with the annual cycle showing 8.9% lower ILI activity (95% CI 8.8% to 9.0%) from February 24 to May 15. Nonannual cycles had substantial explanatory power for ILI trends (ΔAIC=183) compared with all annual covariates (ΔAIC=263) in lognormal regression. Near-annual signals were observed for PCR-confirmed influenza but were not consistent over time or across influenza (sub)types. The explanatory power of climate factors for ILI and influenza virus trends was weak.

CONCLUSION

Our study reveals a unique pattern of respiratory disease dynamics in a tropical setting influenced by both annual and nonannual drivers, with influenza dynamics showing near-annual periodicities. Timing of vaccination campaigns and hospital capacity planning may require a complex forecasting approach.

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 respiratory infections in a rapidly changing climate: the need to prepare for the next pandemic

Viral respiratory infections (VRIs) cause seasonal epidemics and pandemics, with their transmission influenced by climate conditions. Despite the risks posed by novel VRIs, the relationships between climate change and VRIs remain poorly understood. In this review, we synthesized existing literature to explore the connections between changes in meteorological conditions, extreme weather events, long-term climate warming, and seasonal outbreaks, epidemics, and pandemics of VRIs from an interdisciplinary perspective. We proposed a comprehensive conceptual framework highlighting the potential biological, socioeconomic, and ecological mechanisms underlying the impact of climate change on VRIs. Our findings suggested that climate change increases the risk of VRI emergence and transmission by affecting the biology of viruses, host susceptibility, human behavior, and environmental conditions of both society and ecosystems. Further interdisciplinary research is needed to address the dual challenge of climate change and pandemics.

Solid waste motor tricycle operators in Kumasi, Ghana, harbour respiratory pathogens; a public health threat

BACKGROUND

The use of motor tricycles in transporting municipal solid waste (MSW) within urban and peri-urban towns in Ghana is on the increase. This activity often leads to the introduction of pathogen-containing bioaerosols into the environment, as well as to the tricycle operators. We sought to investigate the prevalence and associated risk factors of respiratory pathogens among solid waste tricycle operators.

METHODS

A cross-sectional study was conducted among 155 solid waste transporters who use motor tricycles using semi-structured interviews. Nasopharyngeal swabs were obtained from participants and screened for respiratory pathogens using Polymerase Chain Reaction (PCR).

RESULTS

Pathogens detected in participants were SARS-CoV-2 (n = 10, 6.5%) and Streptococcus pneumoniae (n = 10, 6.5%), constituting an overall prevalence of 12.9% and co-infection rate of 1.3%. The most common self-reported symptoms were cough (n = 67, 43.2%), sore throat (n = 44, 28.4%) and difficulty in breathing (n = 22, 14.2%). Adherence to the use of gloves (n = 117, 75.5%) and nose mask (n = 110, 71.0%) was high. There was a significant association between the detection of respiratory pathogens and the use of gloves, use of more than one PPE and exposure to other pollutants (p < 0.05). Individuals who were exposed to "other pollutants" significantly had lower odds of becoming infected with respiratory pathogens (Adj. OR (95% CI): 0.119(0.015,0.938).

CONCLUSION

Although prevalence of respiratory pathogens is generally low, strict adherence to PPE use could further reduce its rates to even lower levels. Governmental health institutions and informal solid waste transporters should address challenges related to exposure to pollutants, use of gloves, and multiple PPE.

Pathogens associated with hospitalization due to acute lower respiratory tract infections in children in rural Ghana: a case-control study

Respiratory infections are one of the most common causes of death among children under the age of five years. Data on prevalence and relevance of specific organisms in African children are still lacking. This case-control-study investigated prevalence and relevance of specific organisms in Ghanaian children admitted to hospital with symptoms of lower respiratory tract infection (LRTI). Pharyngeal swabs were taken and tested by PCR for 19 respiratory isolates. Adjusted odds ratios (aORs) were calculated to estimate associations between isolates and admission with LRTI. Population attributable fractions (PAFs) were calculated to assess the proportion of LRTI cases due to a particular pathogen. The study included 327 cases and 562 controls. We found associations between detection and admission for LRTI for influenza (aOR 98.6; 95% confidence interval (CI) 20.0-1789.6), respiratory syncytial virus (aOR 40.2; 95% CI 7.2-758.6), H. influenzae (aOR 4.1; 95% CI 2.2-7.9) and S. pneumoniae (aOR 2.4; 95% CI 1.7-3.4). PAFs ≥ 10% were observed for S. pneumoniae (30%; 95% CI 26-42), H. influenzae (10%; 95% CI 2-19) and influenza (10%; 95% CI 2-18). This study highlights the need for heightened surveillance and development of effective vaccines for respiratory pathogens other than SARS-CoV-2 in the future.

Molecular epidemiological surveillance of viral agents of acute lower respiratory tract infections in children in Accra, Ghana

BACKGROUND

Acute lower respiratory tract infection (ALRTI) in children under 5 years is known to be predominantly caused by respiratory syncytial virus (RSV). In recent times, however, human metapneumovirus (HMPV) has also been implicated. This study sought to investigate and genotype respiratory syncytial virus and human metapneumovirus in children presenting with ALRTIs infection at the Princess Marie Louis Children's Hospital in Accra, Ghana.

METHODS

Children below 5 years who were clinically diagnosed of ALRTI and on admission at the study site were recruited between September 2015 and November 2016 for this study. Demographic data information was obtained by means of a standardized questionnaire; and relevant clinical information was obtained from medical records. Nasopharyngeal swabs were collected from 176 children recruited for the study. Ribonucleic acid was extracted from swabs and cDNA syntheses were performed by RT-PCR. RSV-positive amplicons were sequenced and analyzed for genotype assignment.

RESULTS

RSV and HMPV prevalence among the sampled subjects were 11.4 and 1.7% respectively. Of the RSV positives, 8/20 (40%) were RSV-A and 12/20 (60%) were RSV-B. The highest prevalence was observed in children less than 12 months old. Phylogenetic analysis of the second hypervariable region of the RSV G-gene revealed that all RSV group A viruses belonged to the "novel" ON1 genotype containing the 72-nucleotide duplication; and RSV group B viruses belong to the BA IX genotype.

CONCLUSION

RSV is frequently detected in children aged under 5 years admitted with ALRTI in Ghana. Continued surveillance of viral aetiological agents is warranted to elucidate the prevalence and transmission patterns of viral pathogens that cause respiratory tract infections among children. This will help inform appropriate intervention approaches.

Nonurgent Visits to the Pediatric Emergency Department before and during the First Peak of the COVID-19 Pandemic

Background

Nonurgent visits in pediatric Emergency Departments are a growing burden. In order to find predictors for those nonurgent visits, we performed a retrospective analysis of unscheduled visits at the Pediatric Emergency Department of the University Hospital of Bonn, Germany, in the year 2017. Additionally, we compared these findings to unscheduled visits during the first peak of the worldwide pandemic of the Coronavirus disease 2019, to see if there would be an effect on nonurgent pediatric Emergency Department attendances.

Methods

For our retrospective cohort study, we analyzed more than 5.000 visits at the pediatric Emergency Department of the University Hospital of Bonn, Germany, before and during the first peak of the ongoing worldwide pandemic of the Coronavirus disease 2019, particularly with regard to their urgency. Data included gender, age, zip code, urgency, and preexisting conditions.

Results

Our study shows that more than half of unscheduled pediatric Emergency Department visits (69%) at the University Hospital in Bonn are for nonurgent reasons, with short living distance being a factor to present children to a pediatric Emergency Department, even with minor complaints. During the first peak of the pandemic of the Coronavirus disease 2019, nonurgent visits decreased significantly, potentially due to hesitation to attend a pediatric Emergency Department with minor issues, fearing an infection with SARS-CoV-2 at the hospital.

Conclusion

Many people use pediatric Emergency Departments for nonemergency complaints. In order to address the reasons for nonurgent visits to pediatric Emergency Departments and to prevent parents from doing so, further studies and targeted education concepts for parents are needed.

Two novel human coronavirus OC43 genotypes circulating in hospitalized children with pneumonia in China

HCoV-OC43 is one of the mildly pathogenic coronaviruses with high infection rates in common population. Here, 43 HCoV-OC43 related cases with pneumonia were reported, corresponding genomes of HCoV-OC43 were obtained. Phylogenetic analyses based on complete genome, orf1ab and spike genes revealed that two novel genotypes of HCoV-OC43 have emerged in China. Obvious recombinant events also can be detected in the analysis of the evolutionary dynamics of novel HCoV-OC43 genotypes. Estimated divergence time analysis indicated that the two novel genotypes had apparently independent evolutionary routes. Efforts should be conducted for further investigation of genomic diversity and evolution analysis of mildly pathogenic coronaviruses.

Crystal structures of human coronavirus NL63 main protease at different pH values

Human coronavirus NL63 (HCoV-NL63), which belongs to the genus Alphacoronavirus, mainly infects children and the immunocompromized and is responsible for a series of clinical manifestations, including cough, fever, rhinorrhoea, bronchiolitis and croup. HCoV-NL63, which was first isolated from a seven-month-old child in 2004, has led to infections worldwide and accounts for 10% of all respiratory illnesses caused by etiological agents. However, effective antivirals against HCoV-NL63 infection are currently unavailable. The HCoV-NL63 main protease (Mpro), also called 3C-like protease (3CLpro), plays a vital role in mediating viral replication and transcription by catalyzing the cleavage of replicase polyproteins (pp1a and pp1ab) into functional subunits. Moreover, Mpro is highly conserved among all coronaviruses, thus making it a prominent drug target for antiviral therapy. Here, four crystal structures of HCoV-NL63 Mpro in the apo form at different pH values are reported at resolutions of up to 1.78 Å. Comparison with Mpro from other human betacoronaviruses such as SARS-CoV-2 and SARS-CoV reveals common and distinct structural features in different genera and extends knowledge of the diversity, function and evolution of coronaviruses.

Evolutionary Dynamics and Epidemiology of Endemic and Emerging Coronaviruses in Humans, Domestic Animals, and Wildlife

Diverse coronavirus (CoV) strains can infect both humans and animals and produce various diseases. CoVs have caused three epidemics and pandemics in the last two decades, and caused a severe impact on public health and the global economy. Therefore, it is of utmost importance to understand the emergence and evolution of endemic and emerging CoV diversity in humans and animals. For diverse bird species, the Infectious Bronchitis Virus is a significant one, whereas feline enteric and canine coronavirus, recombined to produce feline infectious peritonitis virus, infects wild cats. Bovine and canine CoVs have ancestral relationships, while porcine CoVs, especially SADS-CoV, can cross species barriers. Bats are considered as the natural host of diverse strains of alpha and beta coronaviruses. Though MERS-CoV is significant for both camels and humans, humans are nonetheless affected more severely. MERS-CoV cases have been reported mainly in the Arabic peninsula since 2012. To date, seven CoV strains have infected humans, all descended from animals. The severe acute respiratory syndrome coronaviruses (SARS-CoV and SARS-CoV-2) are presumed to be originated in Rhinolopoid bats that severely infect humans with spillover to multiple domestic and wild animals. Emerging alpha and delta variants of SARS-CoV-2 were detected in pets and wild animals. Still, the intermediate hosts and all susceptible animal species remain unknown. SARS-CoV-2 might not be the last CoV to cross the species barrier. Hence, we recommend developing a universal CoV vaccine for humans so that any future outbreak can be prevented effectively. Furthermore, a One Health approach coronavirus surveillance should be implemented at human-animal interfaces to detect novel coronaviruses before emerging to humans and to prevent future epidemics and pandemics.

An overview on the seven pathogenic human coronaviruses

To date, seven human coronaviruses (HCoVs) have been detected: HCoV-NL63, HCoV-229E, HCoV-HKU1, HCoV-OC43, severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV) and SARS-CoV-2. Four of these viruses, including HCoV-NL63, -229E, -HKU1 and -OC43, usually cause mild-to-moderate respiratory diseases with a seasonal pattern. Since 2000, three new HCoVs have emerged with a significant mortality rate. Although SARS-CoV and MERS-CoV caused an epidemic in some countries, SARS-CoV-2 escalated into a pandemic. All HCoVs can cause severe complications in the elderly and immunocompromised individuals. The bat origin of HCoVs, the presence of intermediate hosts and the nature of their viral replication suggest that other new coronaviruses may emerge in the future. Despite the fact that all HCoVs share similarities in viral replication, they differ in their accessory proteins, incubation period and pathogenicity. This study aims to review these differences between the seven HCoVs.

Impaired performance of SARS-CoV-2 antigen-detecting rapid diagnostic tests at elevated and low temperatures

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Analytical sensitivity of SARS-CoV-2 Ag-RDTs ranges from 1.0 × 10⁶-5.5 × 10⁷ copies/mL.

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Even short-term exposure to 37 °C reduces sensitivity of SARS-CoV-2 Ag-RDTs.

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Elevated temperatures impair sensitivity at clinically relevant virus concentrations.

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Low temperatures limit SARS-CoV-2 Ag-RDT specificity.

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Storage and operation of SARS-CoV-2 Ag-RDTs at recommended conditions is essential.

Antigen-detecting rapid diagnostic tests (Ag-RDTs) can complement molecular diagnostics for COVID-19. The recommended temperature for storage of SARS-CoV-2 Ag-RDTs ranges between 2−30 °C. In the global South, mean temperatures can exceed 30 °C. In the global North, Ag-RDTs are often used in external testing facilities at low ambient temperatures.

We assessed analytical sensitivity and specificity of eleven commercially-available SARS-CoV-2 Ag-RDTs using different storage and operational temperatures, including short- or long-term storage and operation at recommended temperatures or at either 2−4 °C or at 37 °C. The limits of detection of SARS-CoV-2 Ag-RDTs under recommended conditions ranged from 1.0×10⁶- 5.5×10⁷ genome copies/mL of infectious SARS-CoV-2 cell culture supernatant. Despite long-term storage at recommended conditions, 10 min pre-incubation of Ag-RDTs and testing at 37 °C resulted in about ten-fold reduced sensitivity for five out of 11 SARS-CoV-2 Ag-RDTs, including both Ag-RDTs currently listed for emergency use by the World Health Organization. After 3 weeks of storage at 37 °C, eight of the 11 SARS-CoV-2 Ag-RDTs exhibited about ten-fold reduced sensitivity. Specificity of SARS-CoV-2 Ag-RDTs using cell culture supernatant from common respiratory viruses was not affected by storage and testing at 37 °C, whereas false-positive results occurred at outside temperatures of 2−4 °C for two out of six tested Ag-RDTs, again including an Ag-RDT recommended by the WHO.

In summary, elevated temperatures impair sensitivity, whereas low temperatures impair specificity of SARS-CoV-2 Ag-RDTs. Consequences may include false-negative test results at clinically relevant virus concentrations compatible with transmission and false-positive results entailing unwarranted quarantine assignments. Storage and operation of SARS-CoV-2 Ag-RDTs at recommended conditions is essential for successful usage during the pandemic.

Factors associated with diarrhoea and acute respiratory infection in children under-5 years old in Ghana: an analysis of a national cross-sectional survey

BACKGROUND

Diarrhoea and acute respiratory infection (ARI) are major causes of morbidity and mortality in children under-5 years old in Ghana. The aim of the study was to assess factors associated with diarrhoea and ARI in children under-5 years old.

METHODS

We analysed nationally representative data from the 2017-2018 Ghana Multiple Indicator Cluster Survey (MICS) on 8879 children under-5 years old. Multivariable logistic regression was used to assess the factors associated with diarrhoea and ARI. We applied sample weights, stratification and clustering to account for the sampling design of the MICS.

RESULTS

The prevalence of diarrhoea was 17.0% (95% CI: 15.70, 18.24%). Children aged 6-11 months [Adjusted prevalence odds ratio (aPOR): 2.06, 95% CI: 1.45, 2.92], and 12-23 months (aPOR: 2.37, 95% CI: 1.67, 3.35), had higher prevalence of diarrhoea compared to children aged 0-5 months. Children whose mothers had a college or higher education (aPOR: 0.41, 95% CI: 0.22, 0.78), and a secondary education (aPOR: 0.66, 95% CI: 0.51, 0.86), had 59% and 34% lower odds of diarrhoea respectively, compared to children whose mothers had no formal education. Children from the richest households (aPOR: 0.58, 95% CI: 0.39, 0.86), had 42% lower odds of diarrhoea compared to children from the poorest households. Children resident in rural areas had 22% lower odds of diarrhoea compared to their peers in urban areas (aPOR: 0.78, 95% CI: 0.63, 0.98). The prevalence of ARI was 33.3% (95% CI: 31.72, 34.82%). Children aged 6-11 months (aPOR: 1.43, 95% CI: 1.06, 1.93), and 12-23 months (aPOR: 1.41, 95% CI: 1.10, 1.82), had higher prevalence of ARI compared to children aged 0-5 months.

CONCLUSIONS

This study suggests that the prevalence of diarrhoea and ARI among children aged 6-11 and 12-23 months was higher compared to children aged 0-5 months. Children under-5 years old whose mothers had a secondary or higher education had a lower prevalence of diarrhoea compared to children whose mothers had no formal education.

COVID-19 in Colombia endpoints. Are we different, like Europe?

The infection by the new coronavirus (SARS-CoV-2) has taken the dimension of a pandemic, affecting more than 160 countries in a few weeks. In Colombia, despite the implementation of the rules established by the national government, exists an elevate concern both for mortality and for the limited capacity of the health system to respond effectively to the needs of patients infected. For Colombia, assuming a case fatality rate among people infected with SARS-CoV-2 of 0.6% (average data from the information reported for Latin American countries for March 18) (Table 1), the number of deaths, in one or two weeks, could be 16 and 243, respectively. These estimates differ markedly from those documented in countries such as Spain and Italy, in which COVID-19 case fatality rates exceed 8% (case of Italy) and from the percentage of patients who have required intensive care, which has ranged from 9% to 11% of patients in Mediterranean European countries. These differences could be explained due to: a) the percentage of the population at risk (individuals older than 60 years); b) a higher epidemiological exposure to viral respiratory infections associated with more frequent exposure to them, due to geographic and climatic conditions; c) less spread of the virus by location in the tropical zone; and d) earlier preventive measures to contain the spread of SARS-CoV-2 infection. Therefore, it is possible to establish that the situation in this country will be different from in European Mediterranean and that Colombia could have different endpoints from Spain and Italy.

Coronavirus Detection in the Clinical Microbiology Laboratory: Are We Ready for Identifying and Diagnosing a Novel Virus?

Endemic species of coronavirus (HCoV-OC43, HCoV-229E, HCoV-NL63, and HCoV-HKU1) are frequent causes of upper respiratory tract infections. Three highly pathogenic coronaviruses have been associated with outbreaks and epidemics and have challenged clinical microbiology laboratories to quickly develop assays for diagnosis. Their initial characterization was achieved by molecular methods. With the great advance in metagenomic whole-genome sequencing directly from clinical specimens, diagnosis of novel coronaviruses could be quickly implemented into the workflow of managing cases of pneumonia of unknown cause, which will markedly affect the time of the initial characterization and accelerate the initiation of outbreak control measures.

Bibliometric and Visualization Analysis of Human Coronaviruses: Prospects and Implications for COVID-19 Research

Human coronaviruses, which can cause a range of infectious diseases, have been studied for nearly 60 years. The field has gained renewed interest from researchers around the world due to the COVID-19 outbreak in late 2019. Despite a large amount of research, little is known about the knowledge structure and developing trends of this topic. Here, we apply bibliometric analysis along with visualization tools to analyze 15,207 publications related to human coronavirus from the Scopus database, using indicators on publication and citation, journal, country or territory, affiliation and international cooperation, author, and keyword co-occurrence cluster. The results show that research on human coronavirus is dominated by SARS-CoV. Although there have been many publications, only 626 publications (4.1% of total) have more than 100 citations. The top 20 journals with most publications account for 20.6% of total publications and 41% of total citations. In addition to the United States and some European countries, many Asian and African countries are involved in this research, with China holding an important position in this area. Leading researchers from various fields of human coronavirus research are listed to facilitate collaboration and promote effective disease prevention and control. The keywords co-occurrence analysis reveals that the research focus on virology, public health, drugs and other hotspot fields, and uncovers changes in the direction of coronavirus research. The research map on human coronavirus obtained by our analysis are expected to help researchers to efficiently and effectively explore COVID-19.

COVID-19: Immunology and treatment options

The novel coronavirus SARS-CoV2 causes COVID-19, a pandemic threatening millions. As protective immunity does not exist in humans and the virus is capable of escaping innate immune responses, it can proliferate, unhindered, in primarily infected tissues. Subsequent cell death results in the release of virus particles and intracellular components to the extracellular space, which result in immune cell recruitment, the generation of immune complexes and associated damage. Infection of monocytes/macrophages and/or recruitment of uninfected immune cells can result in massive inflammatory responses later in the disease. Uncontrolled production of pro-inflammatory mediators contributes to ARDS and cytokine storm syndrome. Antiviral agents and immune modulating treatments are currently being trialled. Understanding immune evasion strategies of SARS-CoV2 and the resulting delayed massive immune response will result in the identification of biomarkers that predict outcomes as well as phenotype and disease stage specific treatments that will likely include both antiviral and immune modulating agents.

Typical epidemiology of respiratory virus infections in a Brazilian slum

Host population size, density, immune status, age structure, and contact rates are critical elements of virus epidemiology. Slum populations stand out from other settings and may present differences in the epidemiology of acute viral infections. We collected nasopharyngeal specimens from 282 children aged ≤5 years with acute respiratory tract infection (ARI) during 2005 to 2006 in one of the largest Brazilian slums. We conducted real‐time reverse transcription‐polymerase chain reaction (RT‐PCR) for 16 respiratory viruses, nested RT‐PCR‐based typing of rhinoviruses (HRVs), and collected clinical symptoms. Viruses were common causes of respiratory disease; with ≥1 virus being detected in 65.2% of patients. We detected 15 different viruses during 1 year with a predominance of HRV (33.0%) and human respiratory syncytial virus (hRSV, 12.1%) infections, and a high rate of viral coinfections (28.3%). We observed seasonality of hRSV, HRV and human coronavirus infections, more severe symptoms in hRSV and influenza virus (FLU) infections and prolonged circulation of seven HRV clusters likely representing distinct serotypes according to genomic sequence distances. Potentially unusual findings included the absence of human metapneumovirus detections and lack of typical FLU seasonal patterns, which may be linked to the population size and density of the slum. Nonetheless, most epidemiological patterns were similar to other studies globally, suggesting surprising similarities of virus‐associated ARI across highly diverse settings and a complex impact of population characteristics on respiratory virus epidemiology.

Large epidemiological study of respiratory viruses in children from one of the biggest Brazilian slums using sensitive molecular PCR assays

Viruses are common causes of respiratory disease in pediatric patients from a Brazilian slum

15 distinct viruses circulate in the Brazilian slum, with highest prevalence of rhinoviruses and human respiratory syncytial virus

The epidemiology of virus‐associated respiratory infections presents surprising similarities worldwide despite drastic differences in socioeconomic status and population characteristics

Epidemiology of human respiratory viruses in children with acute respiratory tract infection in a 3-year hospital-based survey in Northern Italy

Acute respiratory tract infections (ARTIs) are among the leading causes of morbidity and mortality in children. The viral etiology of ARTIs was investigated over 3 years (October 2012–September 2015) in 2575 children in Parma, Italy, using indirect immunofluorescent staining of respiratory samples for viral antigens, cell culture, and molecular assays. Respiratory viruses were detected in 1299 cases (50.44%); 1037 (79.83%) were single infections and 262 (20.17%) mixed infections. The highest infection incidence was in children aged >6 months to ≤3 years (57.36%). Human respiratory syncytial virus (27.12%) and human adenovirus (23.58%) were the most common viruses identified. The virus detection rate decreased significantly between the first and third epidemic season (53.9% vs. 43.05%, P < 0.0001). The simultaneous use of different diagnostic tools allowed us to identify a putative viral etiology in half the children examined and to provide an estimate of the epidemiology and seasonality of respiratory viruses associated with ARTIs.

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Respiratory viruses were assessed in children from October 2012 to September 2015.

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Viruses were detected using antigen and molecular assays, and cell culture.

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Respiratory syncytial virus and adenovirus were the most common viruses detected.

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Influenza virus and respiratory syncytial virus detection showed seasonal variation.

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Respiratory virus detection was highest in children aged >6 months to ≤3 years.

Hosts and Sources of Endemic Human Coronaviruses

The four endemic human coronaviruses HCoV-229E, -NL63, -OC43, and -HKU1 contribute a considerable share of upper and lower respiratory tract infections in adults and children. While their clinical representation resembles that of many other agents of the common cold, their evolutionary histories, and host associations could provide important insights into the natural history of past human pandemics. For two of these viruses, we have strong evidence suggesting an origin in major livestock species while primordial associations for all four viruses may have existed with bats and rodents. HCoV-NL63 and -229E may originate from bat reservoirs as assumed for many other coronaviruses, but HCoV-OC43 and -HKU1 seem more likely to have speciated from rodent-associated viruses. HCoV-OC43 is thought to have emerged from ancestors in domestic animals such as cattle or swine. The bovine coronavirus has been suggested to be a possible ancestor, from which HCoV-OC43 may have emerged in the context of a pandemic recorded historically at the end of the 19th century. New data suggest that HCoV-229E may actually be transferred from dromedary camels similar to Middle East respiratory syndrome (MERS) coronavirus. This scenario provides important ecological parallels to the present prepandemic pattern of host associations of the MERS coronavirus.

Mixed viral infections of the respiratory tract; an epidemiological study during consecutive winter seasons

The current study aimed to describe the molecular epidemiology of mixed respiratory viral infections during consecutive winter seasons in a tertiary care hospital. Patients with symptoms of respiratory tract infection were evaluated during the 2009‐2011 and 2013‐15 winter seasons. A clinical microarray technique was used for viral detection. Clinical and epidemiological data were correlated with mixed viral detection and the need for hospitalization. In 332 out of 604 (54.4%) evaluated patients (17.6% children) a respiratory virus was identified. Mixed viral infections were diagnosed in 68/332 (20.5%) patients with virus detection (66.2% mixed Influenza‐RSV infections). Mixed viral infections were more commonly detected in children (OR 3.7; 95%CI 1.9‐5.6, P < 0.01) and patients with comorbidities. In logistic regression analyses, mixed viral infections were associated with younger age (mean age 30.4 years vs. 41.8 years, P ≤ 0.001) and increased rates of fever (OR: 2.7; 95%CI 1.04‐7.2, P < 0.05) but no adverse outcomes or increased rates of hospitalization. High rates of mixed viral infections were noted during all winter seasons (especially Influenza and RSV) and were more common in younger patients. The clinical significance of mixed respiratory viral infection needs further elucidation.

Burden of influenza among hospitalized febrile children in Ghana

BACKGROUND

Influenza surveillance data from Africa indicate a substantial disease burden with high mortality. However, local influenza data from district hospitals with limited laboratory facilities are still scarce.

OBJECTIVES

To identify the frequency and seasonal distribution of influenza among hospitalized febrile children in a rural hospital in Ghana and to describe differential diagnoses to other severe febrile infections.

METHODS

Between January 2014 and April 2015, all children with a temperature of ≥38°C admitted to a district hospital in Ghana were screened for influenza A and B by RT-PCR and differentiated to subtypes A(H1N1)pdm09 and A(H3N2). Malaria microscopy and blood cultures were performed for each patient.

RESULTS

A total of 1063 children with a median age of 2 years (IQR: 1-4 years) were recruited. Of those, 271 (21%) were classified as severe acute respiratory infection (SARI) and 47 (4%) were positive for influenza, namely 26 (55%) influenza B, 15 (32%) A(H1N1)pdm09, and 6 (13%) A(H3N2) cases. Influenza predominantly occurred in children aged 3-5 years and was more frequently detected in the major rainy season (OR = 2.9; 95% CI: 1.47-6.19) during the first half of the year. Two (4%) and seven (15%) influenza-positive children were co-diagnosed with an invasive bloodstream infection or malaria, respectively.

CONCLUSION

Influenza contributes substantially to the burden of hospitalized febrile children in Ghana being strongly dependent on age and corresponds with the major rainy season during the first half-year.

Nasal Carriage of Staphylococcus aureus among Children in the Ashanti Region of Ghana

Background

Nasal carriage with Staphylococcus aureus is a common risk factor for invasive infections, indicating the necessity to monitor prevalent strains, particularly in the vulnerable paediatric population. This surveillance study aims to identify carriage rates, subtypes, antimicrobial susceptibilities and virulence markers of nasal S. aureus isolates collected from children living in the Ashanti region of Ghana.

Methods

Nasal swabs were obtained from children < 15 years of age on admission to the Agogo Presbyterian Hospital between April 2014 and January 2015. S. aureus isolates were characterized by their antimicrobial susceptibility, the presence of genes encoding for Panton-Valentine leukocidin (PVL) and toxic shock syndrome toxin-1 (TSST-1) and further differentiated by spa-typing and multi-locus-sequence-typing.

Results

Out of 544 children 120 (22.1%) were colonized with S. aureus, with highest carriage rates during the rainy seasons (27.2%; p = 0.007), in females aged 6–8 years (43.7%) and males aged 8–10 years (35.2%). The 123 isolates belonged to 35 different spa-types and 19 sequence types (ST) with the three most prevalent spa-types being t355 (n = 25), t84 (n = 18), t939 (n = 13), corresponding to ST152, ST15 and ST45. Two (2%) isolates were methicillin-resistant S. aureus (MRSA), classified as t1096 (ST152) and t4454 (ST45), and 16 (13%) were resistant to three or more different antimicrobial classes. PVL and TSST-1 were detected in 71 (58%) and 17 (14%) isolates respectively.

Conclusion

S. aureus carriage among Ghanaian children seems to depend on age, sex and seasonality. While MRSA rates are low, the high prevalence of PVL is of serious concern as these strains might serve not only as a source for severe invasive infections but may also transfer genes, leading to highly virulent MRSA clones.