The Epidemiological and Spatiotemporal Characteristics of the 2019 Novel Coronavirus Disease (COVID-19) in Libya.

COVID-19 is a global pandemic that has affected all aspects of life. Understanding its geographical and epidemiological characteristics has become particularly important in controlling the spread of the pandemic. Such studies are lacking in North African countries, particularly in Libya, which has the second largest area of any country in Africa and the longest coast facing Europe. The objectives of this study are to determine the epidemiological parameters and spatiotemporal patterns of COVID-19 and outline strategies for containing the spread and consequences of the pandemic. This comprehensive study included all the confirmed cases of COVID-19 since its emergence in Libya on March 24, 2020 until July 31, 2020. The epidemiological characteristics of COVID-19 were analyzed and the spatial dynamic trends were explored. Regional counts of weekly reported cases were used to characterize the spatial dynamics of COVID-19. A total of 3,695 confirmed cases of COVID-19 were recorded: 2,515 men (68.1%) and 1,180 women (31.9%), with a male-to-female ratio of 2.1:1. Ages ranged between 2 and 78 years. Older patients infected with COVID-19 were at a risk of higher disease severity and mortality. Broad geographic variability and spatiotemporal spread variation of the COVID-19 pandemic in Libya was observed, indicating a significant increase of COVID-19 spread starting in the middle of July 2020, particularly in the western and southern regions, although it was consistently reported in the central and eastern regions as well. Assessing the spatiotemporal dynamics of COVID-19 in the early stages of the epidemic is particularly important in understanding the pandemic spread. Such assessments are essential for designing effective prevention and control programs aimed at reducing the impact of the COVID- 19 pandemic, particularly in countries with limited resources.

The Impact of Armed Conflict on the Epidemiological Situation of COVID-19 in Libya, Syria and Yemen.

Background: Since the Arab uprising in 2011, Libya, Syria and Yemen have gone through major internal armed conflicts. This resulted in large numbers of deaths, injuries, and population displacements, with collapse of the healthcare systems. Furthermore, the situation was complicated by the emergence of COVID-19 as a global pandemic, which made the populations of these countries struggle under unusual conditions to deal with both the pandemic and the ongoing wars. This study aimed to determine the impact of the armed conflicts on the epidemiology of the novel coronavirus (SARS-CoV-2) within these war-torn countries and highlight the strategies needed to combat the spread of the pandemic and its consequences. Methods: Official and public data concerning the dynamics of the armed conflicts and the spread of SARS-COV-2 in Libya, Syria and Yemen were collected from all available sources, starting from the emergence of COVID-19 in each country until the end of December 2020. Datasets were analyzed by a set of statistical techniques and the weekly resolved data were used to probe the link between the intensity levels of the conflict and the prevalence of COVID-19. Results: The data indicated that there was an increase in the intensity of the violence at an early stage from March to August 2020, when it approximately doubled in the three countries, particularly in Libya. During that period, few cases of COVID-19 were reported, ranging from 5 to 53 cases/day. From September to December 2020, a significant decline in the intensity of the armed conflicts was accompanied by steep upsurges in the rate of COVID-19 cases, which reached up to 500 cases/day. The accumulative cases vary from one country to another during the armed conflict. The highest cumulative number of cases were reported in Libya, Syria and Yemen. Conclusions: Our analysis demonstrates that the armed conflict provided an opportunity for SARS-CoV-2 to spread. The early weeks of the pandemic coincided with the most intense period of the armed conflicts, and few cases were officially reported. This indicates undercounting and hidden spread during the early stage of the pandemic. The pandemic then spread dramatically as the armed conflict declined, reaching its greatest spread by December 2020. Full-blown transmission of the COVID-19 pandemic in these countries is expected. Therefore, urgent national and international strategies should be implemented to combat the pandemic and its consequences.

Epidemiological characterization and geographic distribution of human immunodeficiency virus/acquired immunodeficiency syndrome infection in North African countries.

BACKGROUND: Human immunodeficiency virus (HIV) infection is a major global public health concern. North African countries carry a disproportionate burden of HIV representing one of the highest rates in Africa. AIM: To characterize the epidemiological and spatial trends of HIV infection in this region. METHODS: A systematic review was carried out on all the published data regarding HIV/acquired immunodeficiency syndrome in North African countries over ten years (2008-2017) following the PRISMA guidelines. We performed a comprehensive literature search using Medline PubMed, Embase, regional and international databases, and country-level reports with no language restriction. The quality, quantity, and geographic coverage of the data were assessed at both the national and regional levels. We used random-effects methods, spatial variables, and stratified results by demographic factors. Only original data on the prevalence of HIV infection were included and independently evaluated by professional epidemiologists. RESULTS: A total of 721 records were identified but only 41 that met the criteria were included in the meta-analysis. There was considerable variability in the prevalence estimates of HIV within the countries of the region. The overall prevalence of HIV ranged from 0.9% [95% confidence interval (CI) 0.8-1.27] to 3.8% (95%CI 1.17-6.53). The highest prevalence was associated with vulnerable groups and particularly drug abusers and sexually promiscuous individuals. The dense HIV clustering noted varied from one country to another. At least 13 HIV subtypes and recombinant forms were prevalent in the region. Subtype B was the most common variant, followed by CRF02_AG. CONCLUSION: This comprehensive review indicates that HIV infection in North African countries is an increasing threat. Effective national and regional strategies are needed to improve monitoring and control of HIV transmission, with particular emphasis on geographic variability and HIV clustering.

Whole Genome Sequence Analysis of the First Vancomycin-Resistant Enterococcus faecium Isolates from a Libyan Hospital in Tripoli.

The purpose of the study was to investigate the molecular characteristics and genetic relatedness of the first reported cases of vancomycin-resistant enterococci (VRE) from the Tripoli Medical Center, Libya. In total, 43 VRE isolates were obtained from various clinical sites throughout the years 2013-2014, including 40 vanA-type and 2 vanB-type vancomycin-resistant Enterococcus faecium isolates and 1 vanC1-type Enterococcus gallinarum. Of the 42 E. faecium, 19 isolates were subjected to whole genome sequencing. Core genome multilocus sequence typing (cgMLST) analysis revealed three sequence clusters (SCs) of clonally related isolates, which were linked to different hospital wards. The first two VRE isolates, isolated early 2013 from patients in the medical intensive care unit, were grouped in SC1 (MLST [ST] 78, vanB) and differed in only 3 of 1423 cgMLST alleles. The SC2 (n = 16, special care baby unit, neonatal intensive care unit, pediatric surgery ward, and oncology ward) and SC3 (n = 1, antenatal ward) were all ST80 vanA-VRE, but the single SC3 isolate differed in 233 alleles compared with SC2. Within SC2, isolates differed in 1-23 alleles. Comparison with a larger database of E. faecium strains indicated that all isolates clustered within the previously defined hospital clade A1. A combination of Resfinder and mlplasmid analysis identified the presence of resistance genes on different plasmid predicted genetic elements among different SCs. In conclusion, this study documents the first isolates causing outbreaks with VRE in the Libyan health care system. Further surveillance efforts using molecular typing methods to monitor spread of multidrug-resistant bacteria in the Libyan health care system are urgently needed.

Spatiotemporal analysis and epidemiological characterization of the human immunodeficiency virus (HIV) in Libya within a twenty five year period: 1993-2017.

BACKGROUND: Infection with the human immunodeficiency virus (HIV) is an alarming problem in North African countries, but few studies have analyzed the geographical distribution of the epidemic. Libya, the second largest country in Africa and with the longest coast on the Mediterranean basin facing Europe, has experienced major outbreaks of HIV infection. Since then, no studies have followed up on the burden of HIV infections. To plan interventions and allocate resources, spatial analysis of HIV/AIDS clusters are required in order to identify epidemic foci and trends in the country. The objective of this study was to assess HIV infection clustering and trends in Libya. METHODS: Information on all recorded HIV/AIDS cases during 1993-2017 were extracted from the National Reporting System. A total of 8015 newly diagnosed HIV cases with address information were included. Spatial autocorrelation and spatial-temporal analysis were used to identify HIV clusters. Spatial correlations between cases and socio-demographic factors were determined using spatial regression. RESULTS: HIV cases steadily increased within the Libyan population, particularly among those aged < 27 years. Spatiotemporal analysis showed marked geographic and temporal variation of HIV infection, particularly during 2005-2012. The risk factors varied from one region to another, and the contribution of injection drug use to infection increased with time. Four clusters in three time periods were identified, three on the Mediterranean coast and one in the south. CONCLUSION: HIV is an emerging problem in Libya, particularly among young adults. The infection rate varies greatly among the regions and districts, particularly within certain definable geographical areas. Effective intervention strategies are needed to contain HIV infections, especially within the endemic areas.

Trends and patterns of deaths, injuries and intentional disabilities within the Libyan armed conflict: 2012-2017.

BACKGROUND: The consequences of armed conflicts impose considerable burdens on the economy and health care services, particularly in countries that are not equipped to deal with them, such as in the Middle-East, and North African countries. Little is known about the burden of mortality and injury resulting from the Libyan armed conflict. This study aimed to determine the trends and patterns of mortality, injury and disabilities directly associated with the Libyan armed conflict and analyze the geographic variation within the country during 2012-2107. METHODS: Data on conflict-related deaths, injuries, and disabilities were obtained from the national registry offices. The information included date, place, and demographic information. A questionnaire was also used to obtain information from the affected individuals and their families. National and regional trends of mortality, injury and disabilities were calculated. Spatial analysis was performed using geographic data available on all documented cases to analyze clustering of mortality and injury. RESULTS: A total of 16,126 deaths and 42,633 injuries were recorded with complete information during the Libyan conflict from 2012 till 2017. The overall mortality rate was 2.7/1000 population and injury rate was 7.1/1000. The overall male-to-female ratio of mortality and injury was 4.4:1; 42.3% were single and aged 20-30 years old, and 26.4% were aged 31-40 years. Moreover, injuries resulted in death in 20.1% of cases and disability in 33.5% of the cases. Most of the disabilities were caused by blasts, while gun shots resulted in more deaths. The overall mortality and injury rates were highest during 2015-2017. These rates were highest in the eastern region. Injuries were most concentrated in Benghazi and Derna in the east, followed by Sert and Musrata in the central region. CONCLUSIONS: Conflict-related mortality, injury and disability has inflicted a heavy burden on the Libyan society that may persist for a long time. The rates of these casualties varied in time and place. National, well-planned efforts are needed to address this serious situation and its consequences.

The geographic variation and spatiotemporal distribution of hepatitis C virus infection in Libya: 2007-2016.

BACKGROUND: Hepatitis C Virus infection has been considered an important hidden pandemic in developing countries, particularly in Africa. It varies greatly from one region to another and even within districts of the same region. Macroscopic geospatial analysis has become an important scientific tool for identifying the density and clustering of HCV infection and provides epidemiological information for planning interventions and control strategies. The application of these parameters provides a better knowledge of the hepatitis C virus infection prevalence at the national level and can help to implement pertinent strategies to address the HCV-related burdens. This study aims to determine the geographical variability of HCV infection in Libya and to identify the hot spots within regions and districts of the country, and to analyze the population-based demographic determinants involved and outline the intervention programs needed. METHODS: Disease mapping and spatial analysis were conducted using geographic information data available on all documented cases of HCV infections in Libya between 2007 and 2016. Spatial autocorrelation was tested using Moran's Index, which determines and measures the degree of clustering and dispersion of HCV infection in a country. RESULTS: A total 114,928 HCV infection cases during a ten-year period with accurate geographic information were studied. Ages ranged between 16 and 50 years and the male to female ratio was 2:1. HCV infection was unevenly distributed in Libya, and its incidence increased steadily over the study period. Several hot spots and cold spots were found mainly in the southern and eastern regions of the country. CONCLUSION: HCV infection in Libya was geographically variable, with several hot spots particularly in eastern and southern Libya associated with different demographic determinants. Future intervention planning should consider the geospatial variability and risk factors involved.

The Epidemiology of Hepatitis D Virus in North Africa: A Systematic Review and Meta-Analysis.

BACKGROUND: Hepatitis D virus (HDV) infection has been considered a serious neglected pandemic, particularly in developing countries. The virus causes a more severe disease than mono infection with hepatitis B virus (HBV). The epidemiology of HDV is not well documented in North Africa, which is known to be endemic for HBV. In this study, we explored the prevalence of HDV infection and also attempted to identify factors associated with hepatitis D positive status among chronic hepatitis B patients in North Africa. METHODS: The electronic databases PubMed, Embase, Scopus, Science Direct, Web of Science, and Google Scholar were comprehensively searched for all papers published between January 1, 1998, and December 31, 2017, using appropriate strategies containing all related keywords, including North Africa, names of countries in the region, and all permutations of hepatitis D virus. The estimated prevalence of HDV in North Africa was calculated as an average of the pooled infection prevalence in each country weighted by the ratio of the country's hepatitis D virus population to the study's sample size in the survey data analysis. FINDINGS: A total of 312 studies were identified and 32 were included in this study, with a total sample of 4907 individuals screened for HDV. There was considerable variability in the prevalence estimates of HDV within the countries of the region. The overall prevalence of HDV in the general population of North Africa was 5·01% (95% CI: 1·25-8·27) and in liver disease patients it was 20.7% (95% CI:9.87-44.53). Genotype-1 was the most prominent genotype reported in five published studies. Ten studies reported on HDV RNA in participants who were seropositive for HDV, and four studies highlighted the impact of demographic factors (sex and age). No study showed the impact of risk factors on the prevalence of HDV in North Africa. INTERPRETATION: This review provides a comprehensive assessment of the burden of HDV in Northern Africa. There were significant differences in seroprevalence, study population, and diagnostic testing between the countries in the region. The results presented here will alert health professionals to implement clear policies based on evidence to diminish the burden of HDV infection. Such measures may include but are not restricted to improving the laboratory diagnostic tests and initiating patient data registries and blood screening. Further epidemiological and research studies are needed to explore the risk factors, coinfections, and approaches to increase testing for HDV, particularly in high-risk subpopulations, such as intravenous drug users and immigrants, and to define the consequences of HDV infection in North Africa.

Spa typing and identification of pvl genes of meticillin-resistant Staphylococcus aureus isolated from a Libyan hospital in Tripoli.

OBJECTIVES: The purpose of the study was to investigate the molecular characteristics of meticillin-resistant Staphylococcus aureus (MRSA) isolated from clinical sources in Tripoli, Libya. METHODS: A total of 95 MRSA strains collected at the Tripoli medical Centre were investigated by spa typing and identification of the Panton-Valentine Leukocidin (pvl) genes. RESULTS: A total of 26 spa types were characterized and distributed among nine clonal complexes; CC5 (n=32), CC80 (n=18), CC8 (n=17) and CC22 (n=12) were the most prevalent clonal complexes. In total, 34% of the isolates were positive for PVL. CONCLUSIONS: This study demonstrated the presence of CA-MRSA and pvl positive strains in hospital settings and underlines the importance of using molecular typing to investigate the epidemiology of MRSA. Preventative measures and surveillance systems are needed to control and minimize the spread of MRSA in the Libyan health care system.