A framework for reconstructing transmission networks in infectious diseases.

In this paper, we propose a general framework for the reconstruction of the underlying cross-regional transmission network contributing to the spread of an infectious disease. 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. This model is commonly used in the identification of spatiotemporal patterns in seasonal infectious diseases and thus in forecasting infection counts. However, our contribution lies in identifying the inter-locality term as a time-evolving network, and rather than using the model for forecasting, we focus on the network properties without any assumption on seasonality or recurrence of the disease. The topology of the network is then studied to get insight into the disease dynamics. 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 mortality surveillance in Lebanon.

Since the beginning of the COVID-19 pandemic, the Epidemiological surveillance program of the Lebanese Ministry of Public Health has launched a rapid surveillance system for collecting COVID-19-related mortality data. In this study, we document the Lebanese experience of COVID-19 mortality surveillance and provide an analysis of the epidemiological characteristics of confirmed deaths. The implementation of the rapid COVID-19 mortality surveillance system, data sources, and data collection were described. A retrospective descriptive analysis of the epidemiological characteristics of confirmed cases occurring in Lebanon between February 20, 2020, and September 15, 2021, was performed. Epidemiological curves of Covid-19 confirmed cases and deaths as well as the geographic distribution map of mortality rates were generated. Between February 21, 2020, and September 15, 2021, a total of 8163 COVID-19-related deaths were reported with a predominance of males (60.4%). More than 60% were aged 70 years or above. Of all deaths, 84% occurred at hospitals and 16% at home. The overall cumulative mortality rate was 119.6 per 100,000. The overall case fatality ratio (CRF) was 1.3%. Of the total deaths, 82.2% had at least one underlying medical condition. The top reported COVID-19 comorbidities associated with COVID-19-related deaths are cardiovascular diseases including hypertension (59.1%), diabetes (37.2%), kidney diseases including dialysis (11%), cancer (6.7%), and lung diseases (6.3%). The CFR was 30.9% for kidney diseases, 20.2% for cancer, 20.2% for lung diseases, 18.1% for liver diseases, 14% for diabetes, and 12.2% for cardiovascular diseases. Considering the limited human and financial resources in Lebanon due to the economic and political crisis, the rapid mortality surveillance system can be considered successful. Improving this system is important and would contribute to better detection of deaths from emerging and re-emerging diseases during health crises.

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.