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

Abstract

Background: 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 twenty six 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. Methods: Nine hundred and five 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, gender, nationality and age. Results: Although sixteen 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 two months, all samples contained the Alpha variant. However, this had changed dramatically by June and July, when all samples belonged to the Delta variant. Discussion: This study provides 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 six weeks.

COVID-19 contact tracing during first delta wave, Lebanon, 2021

“…The wave is called first delta wave as genomic surveillance showed introduction and dominance of delta and delta variant (8, 16).…”

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

“…Between February 2020 and January 2021, the most frequently reported SARS-CoV-2 lineage among 58 analyzed samples was B.1.398 followed by B.1.1.7 and B.1 [34]. Moreover, an analysis of 905 samples showed the rapid emergence and dominance of the B.1.1.7 Alpha variant between January and April 2021 followed by the replacement of Alpha with Delta variant between June and July [24]. Our study reveals that Omicron BA.1.1 followed by BA.1 predominated during January 2022.…”

“…Genomic surveillance of SARS-CoV-2 was first initiated in Lebanon back in 2020 with direct support from the WHO [24]. Lebanon was the first in the Eastern Mediterranean Region (EMR) to identify the Delta variant in a timely manner.…”

Experience of field testing in Lebanon during the COVID-19 pandemic, January to August 2021

“…For the latter wave, genomic surveillance identified delta and delta-like variants in positive samples. 4 The observed increase in the number of field activities and collected specimens were concomitant with the COVID-19 waves. This highlights the importance of the collected field-testing data during the different stages of the COVID-19 outbreak in the country.…”

“…As per genomic surveillance findings, the dominant variant was alpha during this period. 4 Between June and mid-July 2021, the number of cases decreased and maintained stable levels. Starting mid-July, a new wave emerged, with 53 807 reported cases and 179 deaths (up to 31 August 2021).…”