Increased severity of influenza-associated hospitalizations in resource-limited settings: Results from the Global Influenza Hospital Surveillance Network (GIHSN) (preprint)

Background Influenza disease data remain scarce in middle and lower-income countries. We used data from the Global Influenza Hospital Surveillance Network (GIHSN), a prospective multi-country surveillance system from 2012-2019, to assess differences in the epidemiology and severity of influenza hospitalizations by country income level. Methods We compiled individual-level data on acute respiratory hospitalizations, with standardized clinical reporting and testing for influenza. Adjusted odds ratios (aORs) for influenza-associated intensive care unit (ICU) admission and in-hospital death were estimated with multivariable logistic regression that included country income group (World Bank designation: high-income countries: HIC; upper middle-income countries: UMIC; lower middle-income countries: LMIC), age, sex, number of comorbidities, influenza subtype and lineage, and season as covariates. Findings From 73,121 patients hospitalized with respiratory illness in 22 countries, 15,660 were laboratory-confirmed for influenza. After adjustment for patient-level covariates, there was a two-fold increased risk of ICU admission for patients in UMIC (aOR 2.31; 95% confidence interval (CI) 1.85-2.88, p < 0.001), and a 5-fold increase in LMIC (aOR 5.35; 95% CI 3.98-7.17, p < 0.001), compared to HIC. The risk of in-hospital death in HIC and UMIC was comparable (UMIC: aOR 1.14; 95% 0.87-1.50; p > 0.05), though substantially lower than that in LMIC (aOR 5.05; 95% 3.61-7.03; p < 0.001 relative to HIC). A similar severity increase linked to country income was found in influenza-negative patients. Interpretation We found significant disparities in influenza severity among hospitalized patients in countries with limited resources, supporting global efforts to implement public health interventions. Funding The GIHSN is partially funded by the Foundation for Influenza Epidemiology (France). This analysis was funded by Ready2Respond under Wellcome Trust grant 224690/Z/21/Z. Research in Context Evidence before this study In the past 35 years, fewer than 10% of peer-reviewed articles on influenza burden of disease have reported analyses from lower middle- or lower-income settings. Whereas the impact of influenza in upper middle- and high-income countries – regions where influenza seasonality is well-defined and where high numbers of influenza-related clinic visits, hospital admissions, and deaths are well-documented – has been clearly quantified, data scarcity has challenged our ability to ascertain influenza burden in resource-limited settings. As a result, policy decisions on vaccine use in lower-income countries have been made with limited data, slowing the development of influenza vaccine recommendations in these settings. In this study, we have conducted prospective influenza surveillance in the hospital setting in multiple countries to assess potential geographic differences in the severity of influenza admissions and have shown that influenza is a global concern, and report poorer clinical outcomes among patients admitted to hospitals in resource-limited settings. In these settings, it is especially important to consider the role of preventive measures, such as vaccines, in providing protection against severe disease. Added value of this study Since 2012, in collaboration with over 100 clinical sites worldwide, the Global Influenza Hospital Surveillance Network (GIHSN) has provided patient-level data on severe influenza-like illnesses based on a core protocol and consistent case definitions. To our knowledge, this is the first study to analyze multiple years of global, patient-level data generated by prospective, hospital-based surveillance across a large number of countries to investigate geographic differences in both influenza morbidity and mortality. Our study provides information on influenza burden in under-researched populations, particularly those in lower middle-income countries, and highlights the need for continued global collaboration and unified protocols to better understand the relationships between socio-economic development, healthcare, access to care, and influenza morbidity and mortality. After adjustment for differences in the characteristics of individual patients admitted to the hospital for influenza, we find an increased severity of disease in lower-income settings. In particular, the risk of ICU admissions increases two- and five-fold in upper middle- and lower-middle income countries, compared to high-income countries. The risk of in-hospital death is five-fold higher in lower-middle income countries, compared to more affluent countries. Implications of all the available evidence We find evidence of increased severity in influenza admissions in lower-income countries, which could point at structural differences in access to care between countries (patients arriving at the hospital later in the disease process) and/or differences in care once in the hospital. Understanding the mechanisms responsible for these disparities will be important to improve management of influenza, optimize vaccine allocation, and mitigate global disease burden. The Global Influenza Hospital Surveillance Network serves as an example of a collaborative platform that can be expanded and leveraged to address geographic differences in the epidemiology and severity of influenza, especially in lower and upper middle-income countries.

Genomic Surveillance of SARS CoV2 in COVID-19 vaccinated healthcare workers in Lebanon (preprint)

The emergence of SARS-CoV-2 variants including the Delta and Omicron along with waning of vaccine-induced immunity over time contributed to increased rates of breakthrough infection specifically among healthcare workers (HCWs). SARS-CoV-2 genomic surveillance is an important tool for timely detection and characterization of circulating variants as well as monitoring the emergence of new strains. Our study is the first national SARS-CoV-2 genomic surveillance among HCWs in Lebanon. We collected 250 samples from five hospitals across Lebanon between December 2021 and January 2022. We extracted viral RNA and performed whole genome sequencing using the Illumina NextSeq 500 platform. A total of 133 (57.1%) samples belonging to the Omicron (BA.1.1) sub-lineage were identified, as well as 44 (18.9%) samples belonging to the BA.1 sub-lineage, 28 (12%) belonging to the BA.2 sub-lineage, and only 15 (6.6%) samples belonging to the Delta variant sub-lineage B.1.617.2. These results show that Lebanon followed the global trend in terms of circulating SARS-CoV-2 variants with Delta rapidly replaced by the Omicron variant. This study underscores the importance of continuous genomic surveillance programs in Lebanon for the timely detection and characterization of circulating variants. The latter is critical to guide public health policy making and to timely implement public health interventions.

Integrative Transcriptome Analyses Empower the Anti-COVID-19 Drug Arsenal (preprint)

The beginning of the twenty-first century has been marked by three distinct waves of zoonotic coronavirus outbreaks into the human population. The current pandemic COVID-19 (Coronavirus disease 2019) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). With a rapid infection rate, it is a global threat endangering the livelihoods of millions worldwide. Currently, and despite the collaborative efforts of governments, researchers, and the pharmaceutical industries, there are no substantially significant treatment protocols for the disease. To address the need for such an immediate call of action, we leveraged the largest dataset of drug- induced transcriptomic perturbations, public SARS-CoV-2 transcriptomic datasets, and expression profiles from normal lung transcriptomes. Our unbiased systems biology approach not only shed light on previously unexplored molecular details of SARS-CoV-2 infection (e.g., interferon signaling, inflammation and ACE2 co-expression hallmarks in normal and infected lungs) but most importantly prioritized more than 50 repurposable drug candidates (e.g., Corticosteroids, Janus kinase and Bruton kinase inhibitors). Further clinical investigation of these FDA approved candidates as monotherapy or in combination with an antiviral regimen (e.g., Remdesivir) could lead to promising outcomes in COVID-19 patients.Funding: This work is partially supported by a Discovery Grant from the National Sciences and Engineering Research Council of Canada (RGPIN/06101-2014) and an operating grant from the Cancer Research Society (OG24054). M.R holds a Fonds de la Recherche en Santé du Québec Junior II Award.Conflict of Interest: All authors declare no conflict of interest.

Integrative transcriptome analyses empower the anti-COVID-19 drug arsenal (preprint)

The beginning of the twenty-first century has been marked by three distinct waves of zoonotic coronavirus outbreaks into the human population. The current pandemic COVID-19 (Coronavirus disease 2019) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). With a rapid infection rate, it is a global threat endangering the livelihoods of millions worldwide. Currently, and despite the collaborative efforts of governments, researchers, and the pharmaceutical industries, there are no substantially significant treatment protocols for the disease. To address the need for such an immediate call of action, we leveraged the largest dataset of drug-induced transcriptomic perturbations, public SARS-CoV-2 transcriptomic datasets, and expression profiles from normal lung transcriptomes. Our unbiased systems biology approach not only shed light on previously unexplored molecular details of SARS-CoV-2 infection (e.g., interferon signaling, inflammation and ACE2 co-expression hallmarks in normal and infected lungs) but most importantly prioritized more than 50 repurposable drug candidates (e.g., Corticosteroids, Janus kinase and Bruton kinase inhibitors). Further clinical investigation of these FDA approved candidates as monotherapy or in combination with an antiviral regimen (e.g., Remdesivir) could lead to promising outcomes in COVID-19 patients.