Replacement of the Alpha variant of SARS-CoV-2 by the Delta variant in Lebanon between April and June 2021

Scalable neighbour search and alignment with uvaia

Despite millions of SARS-CoV-2 genomes being sequenced and shared globally, manipulating such data sets is still challenging, especially selecting sequences for focused phylogenetic analysis. We present a novel method, uvaia, which is based on partial and exact sequence similarity for quickly extracting database sequences similar to query sequences of interest. Many SARS-CoV-2 phylogenetic analyses rely on very low numbers of ambiguous sites as a measure of quality since ambiguous sites do not contribute to single nucleotide polymorphism (SNP) differences. Uvaia overcomes this limitation by using measures of sequence similarity which consider partially ambiguous sites, allowing for more ambiguous sequences to be included in the analysis if needed. Such fine-grained definition of similarity allows not only for better phylogenetic analyses, but could also lead to improved classification and biogeographical inferences. Uvaia works natively with compressed files, can use multiple cores and efficiently utilises memory, being able to analyse large data sets on a standard desktop.

Clinical Characteristics and Serum Cytokines Profiling in Hospitalized COVID-19 Patients in Lebanon

Since its emergence, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remains a public health threat worldwide. While the majority of patients recover in 3-4 weeks, complications in severely ill patients, including acute respiratory distress syndrome, cardiac injury, thrombosis, and sepsis, can lead to death. Several biomarkers, in addition to cytokine release syndrome (CRS), have been associated with severe and fatal outcomes in coronavirus disease 2019 (COVID-19) patients. The aim of this study is to assess clinical characteristics and cytokines profiles in hospitalized COVID-19 patients in Lebanon. A total of 51 hospitalized COVID-19 patients were recruited between February 2021 and May 2022. Clinical data and sera were collected at two time points: at hospital presentation (T0) and last collected results during hospitalization (T1). Our results showed that 49% of participants were >60 years with males accounting for the majority (72.5%). Hypertension, followed by diabetes and dyslipidemia, were the most frequent comorbid conditions among study participants accounting for 56.9% and 31.4%, respectively. Chronic obstructive pulmonary disease (COPD) was the only significantly different comorbid condition between intensive care unit (ICU) and non-ICU patients. Our results also showed that the median level of D-dimer was significantly elevated among patients in ICU and those who died compared to non-ICU patients and those who survived. Moreover, C-reactive protein (CRP) levels were significantly higher at T0 compared to T1 in ICU and non-ICU patients. The median level of IL-12p70 was significantly higher in patients >60 years compared to those ≤60 years (p = 0.0209). Our data are in agreement with previous reports suggesting the importance of IL-6, CRP, and IL-12p70 in the assessment of risk of severe disease and mortality.

The Role of Lebanon in the COVID-19 Butterfly Effect: The B.1.398 Example

In the present study, we provide a retrospective genomic surveillance of the SARS-CoV-2 pandemic in Lebanon; we newly sequence the viral genomes of 200 nasopharyngeal samples collected between July 2020 and February 2021 from patients in different regions of Lebanon and from travelers crossing the Lebanese-Syrian border, and we also analyze the Lebanese genomic dataset available at GISAID. Our results show that SARS-CoV-2 infections in Lebanon during this period were shaped by the turnovers of four dominant SARS-CoV-2 lineages, with B.1.398 being the first to thoroughly dominate. Lebanon acted as a dispersal center of B.1.398 to other countries, with intercontinental transmissions being more common than within-continent. Within the country, the district of Tripoli, which was the source of 43% of the total B.1.398 sequences in our study, was identified as being an important source of dispersal in the country. In conclusion, our findings exemplify the butterfly effect, by which a lineage that emerges in a small area can be spread around the world, and highlight the potential role of developing countries in the emergence of new variants.

Challenges of coronavirus disease 2019 (COVID-19) in Lebanon in the midst of the economic collapse

Lebanon, one of the smallest countries in the Middle East, has held for decades a reputation for being the premier medical hub for patients from the Arab world as well as neighboring countries and for offering world-class treatment and advanced medical services. However, this once world-renowned healthcare sector is now facing a risk of imminent collapse as overlapping crises have struck the country since October 2019. In this article, we describe the concomitant political, economic, and financial challenges that Lebanon is facing, which have strained the national healthcare system and have undermined its ability to respond to the coronavirus disease 2019 (COVID-19) pandemic. We present an overview of the political instability, the Lebanese revolution with countrywide protests, as well as the devaluation of the Lebanese currency representing one of the worst economic meltdowns since the 19th century. We describe the unprecedented energy crisis the country is facing and the disastrous consequences of the Beirut port explosion of August 2020. We review the efforts and measures taken by different stakeholders to contain the COVID-19 pandemic amid the multifaceted challenges and the large exodus of healthcare personnel.