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

Abstract

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.

Tracking SARS-CoV-2 Variants During the 2023 Flu Season and Beyond in Lebanon

“…The largest scale sequencing attempt however was the one reported by Merhi et al [22] which was the transition period (December 2020 and June 2021) marked by the worldwide gradual replacement of the Alpha variant and the dominance of the Delta. Other sporadic studies were also conducted with different focus groups such as the one by Al Kalamouni et al [23] which revealed the prevalence of BA.1, BA.1.1, and BA.2, Omicron lineages in healthcare workers, between December 2021 and January 2022.…”

Immunogenicity and Effectiveness of Primary and Booster Vaccine Combination Strategies during Periods of SARS-CoV-2 Delta and Omicron Variants

“…In Lebanon, the pandemic was defined by the dominance of four SARS-CoV-2 lineages, upon analyzing the whole Lebanese dataset in GISAID [ 20 , 21 ].The genomes available in GISAID show that, by July of 2021, the variant of concern, Delta (B.1.617.2), had already completely substituted Alpha and was, in turn, completely replaced by Omicron (sublineages BA.1 and BA.1.1) by the end of December 2021 [ 20 , 21 ]. Coincidently, the appearances of both lineages (Delta and Omicron) were followed by new surges in the number of cases in Lebanon [ 20 , 21 ].…”

“…In Lebanon, the pandemic was defined by the dominance of four SARS-CoV-2 lineages, upon analyzing the whole Lebanese dataset in GISAID [ 20 , 21 ].The genomes available in GISAID show that, by July of 2021, the variant of concern, Delta (B.1.617.2), had already completely substituted Alpha and was, in turn, completely replaced by Omicron (sublineages BA.1 and BA.1.1) by the end of December 2021 [ 20 , 21 ]. Coincidently, the appearances of both lineages (Delta and Omicron) were followed by new surges in the number of cases in Lebanon [ 20 , 21 ]. Accordingly, employees were referred to as SARS-CoV-2 Delta cases if they first tested positive between 1 August 2021, and 20 December 2021, as the majority of the cases in Lebanon were predominantly attributable to the circulating Delta variant during that time [ 20 , 21 ].…”

“…Coincidently, the appearances of both lineages (Delta and Omicron) were followed by new surges in the number of cases in Lebanon [ 20 , 21 ]. Accordingly, employees were referred to as SARS-CoV-2 Delta cases if they first tested positive between 1 August 2021, and 20 December 2021, as the majority of the cases in Lebanon were predominantly attributable to the circulating Delta variant during that time [ 20 , 21 ]. Employees were referred to as SARS-CoV-2 Omicron (B.1.1.529) cases if they first tested positive between 1 January 2022, and 28 February 2022, as the Omicron variant was the predominant circulating variant during that period [ 20 ].…”