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

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.

A Framework for Reconstructing COVID-19 Transmission Network to Inform Betweenness Centrality-Based Control Measures (preprint)

In this paper, we propose a general framework for optimal control measures, which follows the evolution of COVID-19 infection counts collected by Surveillance Units on a country level. We employ an autoregressive model that allows to decompose the mean number of infections into three components that describe: intra-locality infections, inter-locality infections, and infections from other sources such as travelers arriving to a country from abroad. We identify the inter-locality term as a time-evolving network and when it drives the dynamics of the disease we focus on its properties. Tools from network analysis are then employed to get insight into its topology. Building on this, and particularly on the centrality of the nodes of the identified network, a strategy for intervention and disease control is devised.

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

Background On the 11th March, the WHO has declared COVID-19 pandemic. Officially, the virus was introduced in Lebanon on the 21st February 2020. Since then, the national curve has drawn several waves. From July to September 2021, Lebanon has experienced the first delta wave. As part of the investigation, contact tracing was enhanced to limit virus transmission. The objective is to describe close tracing approach and profile of close contacts identified during the first delta wave. Methods COVID-19 surveillance is integrated within the national communicable diseases surveillance. The case definitions are adopted from WHO guides. Laboratories report positive cases on daily basis to the Ministry of Public Health, on DHIS2 platform directly or indirectly via excel files importation. Once reported, case investigation is initiated. It includes contact tracing with: 1) identification of close contacts, 2) advice on quarantine and self-monitoring, 3) contact testing. Referral to field testing is made available free of charge for close contacts. Collected data is updated on DHIS2 platform. Later, data is cleaned and analyzed to generate the daily report including description of close contacts. The report is shared with decision makers, professionals, media and public. Results From week 2021W27 to week 2021W40, 85490 cases were reported. Case investigation rate reached 78.8% of the cases were investigated within 24 hours. 66.5% of investigated cases shared lists of contacts, with 3.6 as average number of contacts per case. We identified a total of 161805 close contacts, 95% were from family members, 71% were not vaccinated and 10 % had prior COVID-19 infection. As for contact testing, 65% had RT-PCR test upon investigation, with 32% positive result. Furthermore, 19205 were referred and tested via field testing, with 25% positivity rate. Of all identified contacts, the reported positive tests reached 56,904 representing 35.2% of all contacts. Conclusion During community transmission and mitigation strategy, contact tracing contributes to increase awareness to the contacts and importance to abide to quarantine measures and thus to slow down the virus circulation. Current close contacts are characterized with new profile of prior infection, vaccination history and testing behavior. There is need to adapt the quarantine measures to close contacts based on their profile, and to ensure easy access to free testing.

Effectiveness of Pfizer-BioNTech Vaccine Against COVID-19 Associated Hospitalizations among Lebanese Adults >=75 years- Lebanon, April-May 2021 (preprint)

Introduction In Lebanon, the nationwide vaccination against COVID-19 was launched in February-2021 using Pfizer-BioNTech vaccine and prioritizing elderly, persons with comorbidities and healthcare workers. Our study aims to estimate the post-introduction vaccine effectiveness (VE) of Pfizer-BioNTech in preventing COVID-19 hospitalization among [≥]75 years in Lebanon. Methods A case-control study design was used. Cases were Lebanese, [≥]75 years and hospitalized with positive PCR result during April-May 2021. Cases were randomly selected from the COVID-19 database of the Epidemiological Surveillance Unit(ESU) at the Ministry of Public Health(MOPH). Each case was matched by age and locality to 2 controls. Controls were hospitalized, non-COVID-19 patients with negative PCR result, randomly selected from the MOPH hospital admission database. VE was calculated for fully and partially vaccinated, using multivariate conditional logistic regression analyses. Results 345 cases and 814 controls were recruited. Half were females, with a mean age of 83 years. 14 cases(5%) and 143 controls(22%) were fully vaccinated. Univariate analysis showed significant association with: gender, month of confirmation/admission, general health, chronic medical conditions, main income source and living arrangement. After adjusting for month of admission and gender, multivariate analysis yielded a VE of 82% (95%CI = 69%-90%) against COVID-19 associated hospitalization for those fully vaccinated and 53% (95%CI = 23%-71%) for those partially vaccinated (<14 days of first or within 14 days of second dose). Conclusions Our study showed that Pfizer-BioNTech vaccine is effective in reducing risk for COVID-19-associated hospitalization in Lebanese elderly([≥]75 years). Additional studies are warranted to explore vaccine effectiveness in reducing hospitalization in younger age groups, as well as in reducing covid-19 infections.

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

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.

Phased Repatriation of Lebanese Expatriates Stranded Abroad During Coronavirus Disease 2019 (COVID-19) Pandemic (preprint)

Background: The coronavirus disease (COVID-19) pandemic represents a serious worldwide threat. Stranded Lebanese citizens abroad appealed to the Lebanese government to embark on citizen repatriation missions. Objectives: We aim to document the Lebanese experience in the repatriation of citizens during COVID-19 which allow us to disclose encountered challenges and lessons learned. Methodology: This is a retrospective description of processes involved in the phased repatriation of Lebanese citizens. The Mission consisted of 4 phases starting, April 5th until June 19th 2020. The prioritization of returnees was based on both medical and social risk assessment. The repatriation team was divided into four groups: the aircraft team, the airport team, the hotel team and the follow up team. On arrival, all returning citizens were tested using Polymerase chain Reaction (PCR) based technique, and were obliged to adhere to a mandatory facility quarantine for 24 to 48 hours. Returning travelers who were tested positive for COVID-19 were transferred to the hospital. Those who were tested negative were urged to strictly comply with home-quarantine for a duration of 14 days. They were followed up on a daily basis by the repatriation team. Results: Overall, 25783 Lebanese citizens have returned home during the phased repatriation. The third phase ranked the uppermost in regard of the number of citizens repatriated. The total number of performed PCR tests at the airport upon arrival was 14893 with an average percentage of around 1% positivity for COVID-19. On the other hand, more than 10687 repatriates underwent external PCR requisite in the third and fourth phases. 272 repatriates were tested positive for COVID-19 upon their arrival. Conclusion: Considering the limited human and financial resources besides the economic and political crisis, the overall repatriation mission could be considered as a successful experience. Such processes would not have been achieved without the professionalism of all involved stakeholders.