Epidemiology and molecular characterization of influenza viruses in Burkina Faso, sub-Saharan Africa

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.

Etiologies of influenza-like illness and severe acute respiratory infections in Tanzania, 2017-2019

In 2016, Tanzania expanded sentinel surveillance for influenza-like illness (ILI) and severe acute respiratory infection (SARI) to include testing for non-influenza respiratory viruses (NIRVs) and additional respiratory pathogens at 9 sentinel sites. During 2017-2019, respiratory specimens from 2730 cases underwent expanded testing: 2475 specimens (90.7%) were tested using a U.S. Centers for Disease Control and Prevention (CDC)-developed assay covering 7 NIRVs (respiratory syncytial virus [RSV], rhinovirus, adenovirus, human metapneumovirus, parainfluenza virus 1, 2, and 3) and influenza A and B viruses. Additionally, 255 specimens (9.3%) were tested using the Fast-Track Diagnostics Respiratory Pathogens 33 (FTD-33) kit which covered the mentioned viruses and additional viral, bacterial, and fungal pathogens. Influenza viruses were identified in 7.5% of all specimens; however, use of the CDC assay and FTD-33 kit increased the number of specimens with a pathogen identified to 61.8% and 91.5%, respectively. Among the 9 common viruses between the CDC assay and FTD-33 kit, the most identified pathogens were RSV (22.9%), rhinovirus (21.8%), and adenovirus (14.0%); multi-pathogen co-detections were common. Odds of hospitalization (SARI vs. ILI) varied by sex, age, geographic zone, year of diagnosis, and pathogen identified; hospitalized illnesses were most common among children under the age of 5 years. The greatest number of specimens were submitted for testing during December-April, coinciding with rainy seasons in Tanzania, and several viral pathogens demonstrated seasonal variation (RSV, human metapneumovirus, influenza A and B, and parainfluenza viruses). This study demonstrates that expanding an existing influenza platform to include additional respiratory pathogens can provide valuable insight into the etiology, incidence, severity, and geographic/temporal patterns of respiratory illness. Continued respiratory surveillance in Tanzania, and globally, can provide valuable data, particularly in the context of emerging respiratory pathogens such as SARS-CoV-2, and guide public health interventions to reduce the burden of respiratory illnesses.

Influenza virus and its subtypes circulating during 2018-2019: A hospital-based study from Assam

PURPOSE

Influenza virus can cause serious respiratory illness sometimes resulting in epidemics and pandemics associated with significant morbidity and mortality across the globe. Hence, continuous surveillance of the activity of the influenza virus and its subtypes is necessary to help the policy makers to take effective and appropriate decisions regarding its control. The study aimed to determine distribution of influenza viruses in Assam of north-east India having subtropical climate that may lead to viral subtype divergence.

METHODS

Clinically suspected ninety cases with Influenza like illness (ILI) were included, irrespective of age and sex during the period 1st July 2018 to 30th June 2019. Aseptically collected Nasopharyngeal swabs in viral transport media (VTM) were tested by conventional Reverse Transcriptase Polymerase Chain Reaction (RT PCR) for detection of Influenza A and Influenza B viruses which were further processed for detection of subtypes such as H1N1 pdm09, H3N2 and Influenza B (Yamagata and Victoria lineage). Normally distributed continuous variables were summarised by mean and standard deviation. All categorical variables were summarised as percentages.

RESULTS

Influenza activity was seen in 42.2% of ILI cases with male predominance (57.9%). Influenza A was the predominant type (84.2%). Among the subtypes, A(H1N1) pdm09 was predominant (76.3%) followed by Influenza B (Victoria lineages) (15.8%) and AH3N2 (7.9%). Significant difference was observed between different subtypes with regard to age distribution only. Influenza activity in Assam showed two seasonal peaks; the primary one from May to July and the secondary from November to February.

CONCLUSION

The study described the distribution of different Influenza viruses and its subtypes in Assam along with their seasonal activities. These findings will help to formulate the policy for its prevention and control in Assam as well as to monitor the efficacy of the current influenza vaccine.

Molecular Epidemiology and Evolutionary Dynamics of Human Influenza Type-A Viruses in Africa: A Systematic Review

Genomic characterization of circulating influenza type-A viruses (IAVs) directs the selection of appropriate vaccine formulations and early detection of potentially pandemic virus strains. However, longitudinal data on the genomic evolution and transmission of IAVs in Africa are scarce, limiting Africa's benefits from potential influenza control strategies. We searched seven databases: African Journals Online, Embase, Global Health, Google Scholar, PubMed, Scopus, and Web of Science according to the PRISMA guidelines for studies that sequenced and/or genomically characterized Africa IAVs. Our review highlights the emergence and diversification of IAVs in Africa since 1993. Circulating strains continuously acquired new amino acid substitutions at the major antigenic and potential N-linked glycosylation sites in their hemagglutinin proteins, which dramatically affected vaccine protectiveness. Africa IAVs phylogenetically mixed with global strains forming strong temporal and geographical evolution structures. Phylogeographic analyses confirmed that viral migration into Africa from abroad, especially South Asia, Europe, and North America, and extensive local viral mixing sustained the genomic diversity, antigenic drift, and persistence of IAVs in Africa. However, the role of reassortment and zoonosis remains unknown. Interestingly, we observed substitutions and clades and persistent viral lineages unique to Africa. Therefore, Africa's contribution to the global influenza ecology may be understated. Our results were geographically biased, with data from 63% (34/54) of African countries. Thus, there is a need to expand influenza surveillance across Africa and prioritize routine whole-genome sequencing and genomic analysis to detect new strains early for effective viral control.

The first epidemiological and virological influenza surveillance in the Republic of Guinea revealed the predominance of influenza A/H3N2 and B Victoria viruses

Little is known about respiratory viruses infection in Guinea. Influenza surveillance has not been implemented in Guinea mainly because of the paucity of laboratory infrastructure and capacity. This paper presents the first influenza surveillance data in Guinea.Swabs were obtained from August 2018 through December 2019 at influenza sentinel sites and transported to the Institut National de Santé Publique for testing. Ribonucleic acid was extracted and tested for the presence of influenza A and B by real-time reverse transcription-polymerase chain reaction (RT-PCR). Positive samples were further characterised to determine the subtypes and lineages of influenza viruses.A total of 862 swabs were collected and tested. Twenty-three per cent of samples tested positive for influenza A and B viruses. Characterisation of positive specimens identified influenza A/H1N1pmd09 (2.5%), influenza A/H3N2 (57.3%), influenza B/Victoria lineage (36.7%) and 7 (3.5%) influenza B with undetermined lineage. Influenza B virus activity clustered in August through November while influenza A/H3N2 displayed two clusters of activities that appeared in May through August and November through December.For the first time in Guinea, the epidemiology, diversity and period of circulation of influenza viruses were studied. The results indicate the predominance and the periods of activities of influenza B Victoria lineage and influenza A/H3N2 which are important information for preventive strategies. It is warranted to extend the influenza surveillance to other parts of Guinea to better understand the epidemiology of the viruses and monitor the emergence of influenza strains with pandemic potential.

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.

Aetiology of acute febrile illness in children in a high malaria transmission area in West Africa

OBJECTIVES

Areas with declining malaria transmission in sub-Saharan Africa have recently witnessed important changes in the aetiology of childhood acute febrile illness (AFI). We describe the aetiology of AFI in a high malaria transmission area in rural Burkina Faso.

METHODS

In a prospective hospital-based diagnostic study, children aged 3 months to 15 years with AFI were recruited and assessed using a systematic diagnostic protocol, including blood cultures, whole blood PCR on a selection of bacterial pathogens, malaria diagnostics and a multiplex PCR on nasopharyngeal swabs targeting 21 viral and 4 bacterial respiratory pathogens.

RESULTS

A total of 589 children with AFI were enrolled from whom an infectious disease was considered in 575 cases. Acute respiratory tract infections, malaria and invasive bacterial infections (IBI) accounted for 179 (31.1%), 175 (30.4%) and 75 (13%) of AFI cases respectively; 16 (21.3%) of IBI cases also had malarial parasitaemia. A viral pathogen was demonstrated from the nasopharynx in 157 children (90.7%) with respiratory tract symptoms. Of all children with viral respiratory tract infections, 154 (92.4% received antibiotics, whereas no antibiotic was provided in 13 (17%) of IBI cases.

CONCLUSIONS

Viral respiratory infections are a common cause of childhood AFI in high malaria transmission areas, next to malaria and IBI. These findings highlight the importance of interventions to improve targeted treatment with antimicrobials. Most patients with viral infections received antibiotics unnecessarily, while a considerable number with IBI did not receive antibiotics.

Systematic Review of Important Viral Diseases in Africa in Light of the 'One Health' Concept

Emerging and re-emerging viral diseases are of great public health concern. The recent emergence of Severe Acute Respiratory Syndrome (SARS) related coronavirus (SARS-CoV-2) in December 2019 in China, which causes COVID-19 disease in humans, and its current spread to several countries, leading to the first pandemic in history to be caused by a coronavirus, highlights the significance of zoonotic viral diseases. Rift Valley fever, rabies, West Nile, chikungunya, dengue, yellow fever, Crimean-Congo hemorrhagic fever, Ebola, and influenza viruses among many other viruses have been reported from different African countries. The paucity of information, lack of knowledge, limited resources, and climate change, coupled with cultural traditions make the African continent a hotspot for vector-borne and zoonotic viral diseases, which may spread globally. Currently, there is no information available on the status of virus diseases in Africa. This systematic review highlights the available information about viral diseases, including zoonotic and vector-borne diseases, reported in Africa. The findings will help us understand the trend of emerging and re-emerging virus diseases within the African continent. The findings recommend active surveillance of viral diseases and strict implementation of One Health measures in Africa to improve human public health and reduce the possibility of potential pandemics due to zoonotic viruses.

Silent Infection of B and CD8+ T Lymphocytes by Influenza A Virus in Children with Tonsillar Hypertrophy

Influenza A viruses (IAVs) cause more than 2 million annual episodes of seasonal acute respiratory infections (ARI) and approximately 500,000 deaths worldwide. Depending on virus strain and host immune status, acute infections by IAV may reach sites other than the respiratory tract. In the present study, IAV RNA and antigens were searched for in tissues of palatine tonsils and adenoids removed from patients without ARI symptoms. A real-time reverse transcriptase PCR (RT-PCR) screening revealed that 8 tissue samples from 7 patients out of 103 were positive for IAV. Positive samples were subjected to next-generation sequencing (NGS) and 3 of 8 tissues yielded complete IAV pH1N1 genomes, whereas in 5 samples, the PB1 gene was not fully assembled. Phylogenetic analysis placed tonsil-derived IAV in clusters clearly segregated from contemporaneous Brazilian viruses. Flow cytometry of dispersed tissue fragments and serial immunohistochemistry of paraffin-embedded sections of naturally infected biopsies indicated that CD20⁺ B lymphocytes, CD8⁺ T lymphocytes, and CD11c⁺ cells are susceptible to IAV infection. We sought to investigate whether these lymphoid tissues could be sites of viral replication and sources of viable virus particles. MDCK cells were inoculated with tissue lysates, enabling recovery of one IAV isolate confirmed by immunofluorescence, reverse transcriptase quantitative PCR (RT-qPCR), and NGS. The data indicate that lymphoid tissues not only harbor expression of IAV proteins but also contain infectious virus. Asymptomatic long-term infection raises the possibility of IAV shedding from tonsils, which may have an impact on host-to-host transmission.IMPORTANCE Influenza A virus (IAV) infections are important threats to human health worldwide. Although extensively studied, some aspects of virus pathogenesis and tissue tropism remain unclear. Here, by different strategies, we describe the asymptomatic infection of human lymphoid organs by IAV in children. Our results indicate that IAV was not only detected and isolated from human tonsils but displayed unique genetic features in comparison with those of contemporaneous IAVs circulating in Brazil and detected in swabs and nasal washes. Inside the tissue microenvironment, immune cells were shown to be carrying IAV antigens, especially B and T CD8⁺ lymphocytes. Taken together, these results suggest that human lymphoid tissues can be sites of silent IAV infections with possible impact on virus shedding to the population.

Serological evidence of swine exposure to pandemic H1N1/2009 influenza A virus in Burkina Faso

Despite improvement of human and avian influenza surveillance, swine influenza surveillance in sub-Saharan Africa is scarce and pandemic preparedness is still deemed inadequate, including in Burkina Faso. This cross-sectional study therefore aimed to investigate the (past) exposure of pigs to influenza A viruses. Practices of people with occupational contacts with pigs and their knowledge on influenza A were investigated in order to formulate future prevention guidelines. In 2016-2017, pig nasopharyngeal swabs and sera were collected and screened for the presence of influenza virus by RT-PCR or of anti-influenza antibodies by competitive ELISA. Seropositive samples were further characterized in virus microneutralization assays against human and swine H1N1 virus strains. Nasopharyngeal swabs were obtained from people with occupational contact with pigs and screened similarly. Demographic data as well as practices related to their profession were recorded. No influenza A virus was detected in nasopharyngeal swabs in humans (n = 358) or in pigs (n = 600). Seroprevalence in pigs reached 6.8 % (41/600) and seropositive animals were found in 50.0 % of extensive settings (10/20) and 19.0 % of (semi-)intensive farms (4/21). All positive sera reacted against the pandemic H1N1/2009 strain, while seropositivity against two Eurasian avian-like and one American swine H1N1 strains and individual titers were lower. These results suggested exposure to pandemic H1N1/2009 virus and cross-reactivity to other H1N1 strains. Farmers with higher frequency of contact to pigs, absence of protective equipment and lack of knowledge on zoonoses are likely key players in driving human-to-swine virus transmission.

Molecular characterization of influenza A(H1N1)pdm09 in Cameroon during the 2014-2016 influenza seasons

In 2009, Influenza A(H1N1)pdm09 caused the first influenza pandemic of the 21st century with high mortality rates of about 284 500 deaths. This virus, however, continues to circulate as a seasonal influenza virus and to cause illness and deaths worldwide. In this study, we describe the genetic diversity of A(H1N1)pdm09 viruses collected between 2014 and 2016 in Cameroon. Three gene segments (HA, NA and M) of Cameroon strains were studied. The phylogenetic tree of the coding nucleotide sequences was generated by MEGA version 6.0 using a Maximum Likelihood method. The NA and M protein coding sequences were analyzed for the reported genetic markers of resistance against neuraminidase inhibitors and adamantanes, while predicted vaccine efficacy was estimated using the P_epitope method. Overall 39 strains were obtained. Phylogenetic analysis of the HA gene of influenza A(H1N1)pdm09 showed that Cameroon strains belonged to two major clades. The 2014 Cameroon sequences belonged to clade 6C while all sequences collected between 2015 and 2016 belonged to clade 6B. Majority of the samples had some mutations in the NA gene notably: I117M, N248D, and N369K while the amantadine-resistant M mutant, S31N, was found to be absent only in the two sequences collected in 2014. Overall, A/California/07/2009 vaccine strain showed a predicted vaccine efficacy of 24.55% to 35.77% against Cameroon A(H1N1)pdm09 strains circulating between 2014 and 2016. Our findings confirms the fast evolution of A(H1N1)pdm09 since its first introduction and highlights on the importance of influenza vaccine in reducing the burden caused by influenza in the community.

Epidemiology and molecular characterization of influenza viruses in Burkina Faso, sub-Saharan Africa

Background

The importance of influenza viruses in respiratory infections in sub‐Saharan Africa has been historically overlooked, including in Burkina Faso.

Objectives

This study therefore aimed at evaluating the prevalence and seasonal occurrence of influenza viruses in children under 5 years old, at risk of influenza‐related complications, presenting with influenza‐like illness (ILI) or severe acute respiratory infection (SARI). The study also aimed at identifying the periods with increased influenza transmission for vaccination recommendations in Burkina Faso.

Methods

From January 2014 to December 2015, ILI and SARI (2015 only) patients were recruited in six healthcare centers in Burkina Faso. Influenza A and B molecular detection and subtyping were performed. Clade clustering of a subset of A(H1N1)pdm09 and A(H3N2) strains was deduced by performing phylogenetic analyses on hemagglutinin gene sequences. Weekly surveillance data from FluNet (2011‐2013; 2016) and this study (2014‐2015) were used to identify periods of increased influenza activity.

Results

Influenza A and B viruses were detected in 15.1% (112 of 743) of ILI and 6.6% (12 of 181) of SARI patients. Overall, influenza A viruses were largely predominant (81 of 124, 65.3%), with 69.1% of A(H3N2) and 30.9% of A(H1N1)pdm09 strains. Four waves of increased transmission were identified in 2014‐2015, each dominated by different influenza subtypes and clades. Between 2011 and 2016, periods of increased influenza activity varied in their frequency, duration, and timing.

Conclusion

Influenza A and B viruses were detected in a substantial number of ILI and SARI cases in Burkina Faso. Vaccination in September‐October would likely protect the highest number of patients.