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

Abstract

The COVID-19 pandemic continues to expand globally, with case numbers rising in many areas of the world, including the Eastern Mediterranean Region. Lebanon experienced its largest wave of COVID-19 infections from January to April 2021. Limited genomic surveillance was undertaken, with just 26 SARS-CoV-2 genomes available for this period, nine of which were from travellers from Lebanon detected by other countries. Additional genome sequencing is thus needed to allow surveillance of variants in circulation. In total, 905 SARS-CoV-2 genomes were sequenced using the ARTIC protocol. The genomes were derived from SARS-CoV-2-positive samples, selected retrospectively from the sentinel COVID-19 surveillance network, to capture diversity of location, sampling time, sex, nationality and age. Although 16 PANGO lineages were circulating in Lebanon in January 2021, by February there were just four, with the Alpha variant accounting for 97 % of samples. In the following 2 months, all samples contained the Alpha variant. However, this had changed dramatically by June and July 2021, when all samples belonged to the Delta variant. This study documents a ten-fold increase in the number of SARS-CoV-2 genomes available from Lebanon. The Alpha variant, first detected in the UK, rapidly swept through Lebanon, causing the country's largest wave to date, which peaked in January 2021. The Alpha variant was introduced to Lebanon multiple times despite travel restrictions, but the source of these introductions remains uncertain. The Delta variant was detected in Gambia in travellers from Lebanon in mid-May, suggesting community transmission in Lebanon several weeks before this variant was detected in the country. Prospective sequencing in June/July 2021 showed that the Delta variant had completely replaced the Alpha variant in under 6 weeks.

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

“…In comparison with previous studies [28][29][30] [30], our results showed that the Alpha variant was detected in Akkar province, with a percentage of 6.8% of our sequences.…”

Scalable neighbour search and alignment with uvaia

“…This may affect not only the phylogenetic inference —since likelihood and Bayesian methods can use the ambiguity information— but also in other epidemiological analyses where finding the closest sequences may be challenging. Uvaia has been used successfully in both cases, by improving contact tracing and travel history inferences, and overall evolutionary analyses (Mashe, Takawira, de Oliveira Martins, et al ., 2021; Mashe, Takawira, Gumbo, et al ., 2021; Sarwar et al ., 2021; Aggarwal et al ., 2022; Eales, de Oliveira Martins, et al ., 2022; Merhi et al ., 2022), and here we present further details into the algorithm.…”

“…This program is also multithreaded, works in batches to avoid using up all available memory up, and can read from and write to compressed format. Uvaialign has been used in several SARS-CoV-2 analyses already (Mashe, Takawira, Gumbo, et al ., 2021; Sarwar et al ., 2021; Eales, de Oliveira Martins, et al ., 2022; Eales, Page, et al ., 2022; Merhi et al ., 2022).…”

“…Uvaia has been used for rapidly analysing genomic data to assist pandemic management in multiple countries, including distance based analyses analysing dynamics of the rapid emergence of the Omicron variant of concern in the UK (Eales, de Oliveira Martins, et al ., 2022), for phylogenetic based analyses to understand multiple waves in Zimbabwe (Mashe, Takawira, Gumbo, et al ., 2021), the spread of variants of concern in Pakistan (Sarwar et al ., 2021), the emergence and replacement of multiple variants of concern in Lebanon (Merhi et al ., 2022). Uvaia achieves this by utilising high efficiency compression, efficient parallelisation and combines this with knowledge of the fundamental characteristics and properties found with SARS-CoV-2 genomic datasets.…”

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

“…Prioritizing COVID-19 vaccine doses in Lebanon was in accordance with the recommendations of the WHO Strategic Advisory Group of Experts (SAGE) framework for the allocation and prioritization of COVID-19 vaccination in targeting high-risk groups at different stages of vaccine supply availability [ 32 ]. Our patients were recruited during the circulation of the Alpha (January–April 2021), Delta (June–July 2021), and Omicron (December 2021–May 2022) variants of concern [ 33 , 34 ]. We categorized our study participants into two groups, as previously described [ 35 ].…”