Biology subjects

Allam, L.

Publications and source records attributed to Allam, L..

3 recordsLinked to original sources

bioRxiv2020

Genetic analysis of SARS-CoV-2 strains collected from North Africa: viral origins and mutational spectrum

The SARS-CoV-2 identified as coronavirus species associated with severe acute respiratory syndrome. At the time of writing, the genetic diversity of Moroccan strains of SARS-CoV-2 is poorly documented. The present study aims to analyze and identify the genetic variants of fortyeight Moroccan strains of SARS-CoV-2 collected from mid-March to the end of May and the prediction of their possible sources. Our results revealed 108 mutations in Moroccan SARS-CoV-2, 50% were non-synonymous were present in seven genes (S, M, N, E, ORF1ab, ORF3a, and ORF8) with variable frequencies. Remarkably, eight non-synonymous mutations were predicted to have a deleterious effect for (ORF1ab, ORF3a, and the N protein. The analysis of the haplotype network of Moroccan strains suggests different sources of SARS-CoV-2 infection in Morocco. Likewise, the phylogenetic analysis revealed that these Moroccan strains were closely related to those belonging to the five continents, indicating no specific strain dominating in Morocco. These findings have the potential to lead to new comprehensive investigations combining genomic data, epidemiological information, and clinical characteristics of SARS-CoV-2 patients in Morocco and could indicate that the developed vaccines are likely to be effective against Moroccan strains.

genomics↗

bioRxiv2020

Genomic diversity and hotspot mutations in 30,983 SARS-CoV-2 genomes: moving toward a universal vaccine for the "confined virus"?

The COVID-19 pandemic has been ongoing since its onset in late November 2019 in Wuhan, China. Understanding and monitoring the genetic evolution of the virus, its geographical characteristics, and its stability are particularly important for controlling the spread of the disease and especially for the development of a universal vaccine covering all circulating strains. From this perspective, we analyzed 30,983 complete SARS-CoV-2 genomes from 79 countries located in the six continents and collected from December 24, 2019, to May 13, 2020, according to the GISAID database. Our analysis revealed the presence of 3,206 variant sites, with a uniform distribution of mutation types in different geographic areas. Remarkably, a low frequency of recurrent mutations has been observed; only 169 mutations (5.27%) had a prevalence greater than 1% of genomes. Nevertheless, fourteen non-synonymous hotspot mutations (> 10%) have been identified at different locations along the viral genome; eight in ORF1ab polyprotein (in nsp2, nsp3, transmembrane domain, RdRp, helicase, exonuclease, and endoribonuclease), three in nucleocapsid protein and one in each of three proteins: spike, ORF3a, and ORF8. Moreover, 36 non-synonymous mutations were identified in the RBD of the spike protein with a low prevalence (<1%) across all genomes, of which only four could potentially enhance the binding of the SARS-CoV-2 spike protein to the human ACE2 receptor. These results along with mutational frequency dissimilarity and intra-genomic divergence of SARS-CoV-2 could indicate that the SARS-CoV-2 is not yet adapted to its host. Unlike the influenza virus or HIV viruses, the low mutation rate of SARS-CoV-2 makes the development of an effective global vaccine very likely.

genomics↗

bioRxiv2020

Serological evidence of Rift Valley fever infection and risk factors among one humped camels (Camelus dromedarius) in Northern Nigeria.

BackgroundRift Valley fever (RVF) is a zoonotic disease that has become emerging and re-emerging in some regions of the world, infecting livestock and humans. One-humped camels are important economic livestock species in Africa used for traction, transportation, and food. Regional and international trade has continued to increase the risk of this disease, spreading widely and causing severe economic and public health catastrophes in affected regions. In spite of these risks, there is a dearth of information about the status of RVF in camels in Nigeria. This study was carried out to determine the prevalence of the RVF virus in one-humped camels in Nigeria and identify the risk factors associated with the disease. MethodsA cross-sectional study with simple random sampling was carried out in seven local government areas of Jigawa and Katsina States. The sera from camels were tested for anti-RVFV IgG. Camel owners were administered a structured questionnaire to ascertain their knowledge, attitude, and practice. ResultsAn overall prevalence of 19.9% (95% CI; 17.07-22.90) was recorded. Based on age groups, the highest prevalence of 20.9% (95% CI; 17.00-25.31) was obtained among older camels (6-10 years), while female camels recorded a high prevalence of 20.4% (95%CI; 15.71-25.80). Sule Tankar-kar recorded the highest prevalence with 33% (95%CI; 1.31-4.72, p= 0.007) and OR 2.47 in Jigawa State while Maiadua had 24.7% (95%CI; 0.97-2.73, p=0.030) with OR 1.62 in Katsina State respectively. From the risk map, local government areas bordering Niger Republic were at a high risk of RVF. Only high rainfall was not significantly linked with RVF occurrence among nomadic camel pastoralists (95%CI 0.93-5.20; p=0.070). ConclusionThere is a need for the country to have quarantine units across borders for screening animals coming from neighbouring countries for transboundary infectious diseases such as RVF. Author SummaryRift Valley fever is a viral haemorrhagic fever that affects animals and humans with high mortality. Recently there has been increased demand in camel meat and products for food and therapeutic purposes. Climate change, coupled with insecurity in the Sahel, has had a significant impact on transhumance activities where camels and their owners move to different countries in search of pasture for their animals. Though Nigeria has not reported an outbreak of Rift Valley fever despite serological evidence in various animal species, there is a need to assess RVF in camels, which is a critical animal species, involved in transhumance with the potential of introducing transboundary diseases into new areas. The study assessed the presence of antibodies in camels, identified risk factors associated with the disease in camels and areas at risk for the disease. Our study found a seroprevalence of 19.9% in camels in two northern states of Nigeria, which shares a boundary with the Niger Republic that recently reported an outbreak. Our findings suggest that areas in proximity to Niger Republic are at a high risk to the disease and camels belonging to transhumance pastoralists are highly likely to contract Rift Valley fever since they are exposed to various ecological and environmental factors that precipitate the disease.

microbiology↗