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

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.

Comparison of four automated SARS-CoV-2 serological immunoassays in Lebanon.

Automated immunoassays have been introduced to complement real time PCR (RT-PCR) in the battle against SARS-CoV-2. This study compares four serological automated immunoassays by different manufacturers (Abbott, Euroimmun, Roche and Snibe) that are available in Lebanon with regards to specificities, sensitivities, inter-agreement and positive/negative distinction abilities. One hundred and fifty-seven samples (73 with a positive RT-PCR and 84 controls) were analyzed. The 73 study samples were divided into 3 time categories: ≤ 7 days, 8-13 days and ≥ 14 days based on time since first positive RT-PCR or first symptoms. The category "total days" was studied as the average of all the three time categories. All assays had 100% specificity and their sensitivities in the "total days" category ranged from 75.3% to 20.6% (Snibe IgM). The sensitivity was low for all at ≤ 7 days and increased gradually in the other time categories. The IgG assays by different manufacturers showed high inter-agreement. The assays also showed good positive/negative discriminative abilities after 14 days. The four studied automated immunoassays (except for Snibe IgM) show an adequate diagnostic performance when used 14 days after first positive PCR or first symptom onset.