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.

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

Soon after detection of the first COVID-19 case in Lebanon, a testing strategy was developed aiming to early detect new cases and identify close contacts in order to implement isolation and quarantine measures, thus limiting disease transmission. Field-testing activities were initiated in March 2020, focusing on suspected cases and close contacts. The objective of this paper is to present data collected between the 1st and the 35th week of 2021 and discuss challenges and lessons learned. During the study period, testing activities were conducted in field sites covering all Lebanese districts and following a fixed schedule. Testing was provided free of charge for suspected/probable patients with COVID-19 and close contacts of positive cases. Nasopharyngeal specimens were collected and sent to designated laboratories for reverse transcription polymerase chain reaction testing. Results were received on a timely manner, within 48 hours. From the 1st to the 35th week of 2021, 1244 field-testing activities were conducted with an average of 37 testing activities per week. During this period, 71 542 samples were collected with an average of 2104 specimens per week. On average, activities covered 78% of the Lebanese districts. The average positivity rate for this period was 24% (15%-33%) in line with the virus circulation levels in the country. Timely development and implementation of a testing strategy is crucial during epidemics. The success of Lebanon's field-testing experience was mainly due to the timely adapted approach that covered all national territories, targeting all residents as well as high-risk groups in suburbs and remote areas.

Calculating the serial interval of SARS-CoV-2 in Lebanon using 2020 contact-tracing data.

INTRODUCTION: The first detected case in Lebanon on 21 February 2020 engendered implementation of a nationwide lockdown alongside timely contact-tracing and testing. OBJECTIVES: Our study aims to calculate the serial interval of SARS-CoV-2 using contact tracing data collected 21 February to 30 June 2020 in Lebanon to guide testing strategies. METHODS: rRT-PCR positive COVID-19 cases reported to the Ministry of Public Health Epidemiological Surveillance Program (ESU-MOH) are rapidly investigated and identified contacts tested. Positive cases and contacts assigned into chains of transmission during the study time-period were verified to identify those symptomatic, with non-missing date-of-onset and reported source of exposure. Selected cases were classified in infector-infectee pairs. We calculated mean and standard deviation for the serial interval and best distribution fit using AIC criterion. RESULTS: Of a total 1788 positive cases reported, we included 103 pairs belonging to 24 chains of transmissions. Most cases were Lebanese (98%) and male (63%). All infectees acquired infection locally. Mean serial interval was 5.24 days, with a standard deviation of 3.96 and a range of - 4 to 16 days. Normal distribution was an acceptable fit for our non-truncated data. CONCLUSION: Timely investigation and social restriction measures limited recall and reporting biases. Pre-symptomatic transmission up to 4 days prior to symptoms onset was documented among close contacts. Our SI estimates, in line with international literature, provided crucial information that fed into national contact tracing measures. Our study, demonstrating the value of contact-tracing data for evidence-based response planning, can help inform national responses in other countries.

Risk estimates for hip fracture from clinical and densitometric variables and impact of database selection in Lebanese subjects.

Bone mineral density (BMD) and fracture incidence vary greatly worldwide. The data, if any, on clinical and densitometric characteristics of patients with hip fractures from the Middle East are scarce. The objective of the study was to define risk estimates from clinical and densitometric variables and the impact of database selection on such estimates. Clinical and densitometric information were obtained in 60 hip fracture patients and 90 controls. Hip fracture subjects were 74 yr (9.4) old, were significantly taller, lighter, and more likely to be taking anxiolytics and sleeping pills than controls. National Health and Nutrition Examination Survey (NHANES) database selection resulted in a higher sensitivity and almost equal specificity in identifying patients with a hip fracture compared with the Lebanese database. The odds ratio (OR) and its confidence interval (CI) for hip fracture per standard deviation (SD) decrease in total hip BMD was 2.1 (1.45-3.05) with the NHANES database, and 2.11 (1.36-2.37) when adjusted for age and body mass index (BMI). Risk estimates were higher in male compared with female subjects. In Lebanese subjects, BMD- and BMI-derived hip fracture risk estimates are comparable to western standards. The study validates the universal use of the NHANES database, and the applicability of BMD- and BMI-derived risk fracture estimates in the World Health Organization (WHO) global fracture risk model, to the Lebanese.