Biology subjects

Hassanin, A.

Publications and source records attributed to Hassanin, A..

3 recordsLinked to original sources

bioRxiv2021

A novel SARS-CoV-2 related coronavirus in bats from Cambodia

Knowledge of the origin and reservoir of the coronavirus responsible for the ongoing COVID-19 pandemic is still fragmentary. To date, the closest relatives to SARS-CoV-2 have been detected in Rhinolophus bats sampled in the Yunnan province, China. Here we describe the identification of SARS-CoV-2 related coronaviruses in two Rhinolophus shameli bats sampled in Cambodia in 2010. Metagenomic sequencing identified nearly identical viruses sharing 92.6% nucleotide identity with SARS-CoV-2. Most genomic regions are closely related to SARS-CoV-2, with the exception of a small region corresponding to the spike N terminal domain. The discovery of these viruses in a bat species not found in China indicates that SARS-CoV-2 related viruses have a much wider geographic distribution than previously understood, and suggests that Southeast Asia represents a key area to consider in the ongoing search for the origins of SARS-CoV-2, and in future surveillance for coronaviruses.

microbiology↗

bioRxiv2020

Evolutionary history of Carnivora (Mammalia, Laurasiatheria) inferred from mitochondrial genomes

The order Carnivora, which currently includes 296 species classified into 16 families, is distributed across all continents. The phylogeny and the timing of diversifications are still a matter of debate. Here, complete mitochondrial genomes were analysed to reconstruct the phylogenetic relationships and to estimate divergence times among species of Carnivora. We assembled 51 new mitogenomes from 13 families, and aligned them with available mitogenomes by selecting only those showing more than 1% of nucleotide divergence and excluding those suspected to be of low-quality or from misidentified taxa. Our final alignment included 220 taxa representing 2,442 mitogenomes. Our analyses led to a robust resolution of suprafamilial and intrafamilial relationships. We identified 22 fossil calibration points to estimate a molecular timescale for carnivorans. According to our divergence time estimates, crown carnivorans appeared during or just after the Early Eocene Climatic Optimum; all major groups of Caniformia (Cynoidea/Arctoidea; Ursidae; Musteloidea/Pinnipedia) diverged from each other during the Eocene, while all major groups of Feliformia (Nandiniidae; Feloidea; Viverroidea) diversified more recently during the Oligocene, with a basal divergence of Nandinia at the Eocene/Oligocene transition; intrafamilial divergences occurred during the Miocene, except for the Procyonidae, as Potos separated from other genera during the Oligocene.

evolutionary biology↗

bioRxiv2020

The SARS-CoV-2-like virus found in captive pangolins from Guangdong should be better sequenced.

Viruses closely related to SARS-CoV-2, which is the virus responsible of the Covid-19 pandemic, were sequenced in several Sunda pangolins (Manis javanica) seized in the Guangdong and Guangxi provinces of China between 2017 and 20191-3. These viruses belong to two lineages: one from Guangdong (GD/P) and the other from Guangxi (GX/P). The GD/P viruses are particularly intriguing as the amino-acid sequence of the receptor binding domain of the spike protein is very similar to that of the human SARS-CoV-2 virus (97.4%)2. This characteristic suggests that GD/P viruses are capable of binding human ACE2 receptor and may therefore be able to mediate infection of human cells. Whereas all six GX/P genomes were deposited as annotated sequences in GenBank, none of the two GD/P genomes assembled in previous studies2,3 are currently available. To overcome this absence, I assembled these genomes from the Sequence Read Archive (SRA) data available for SARS-CoV-2-like viruses detected in five captive pangolins from Guangdong. I found the genome assemblies of GD/P virus of poor quality, having high levels of missing data. Additionally, unexpected reads in the Illumina sequencing data were identified. The GD/P2S dataset2 contains reads that are identical to SARS-CoV-2, suggesting either the coexistence of two SARS-CoV-2-like viruses in the same pangolin or contamination by the human virus. In the four other GD/P datasets1 many mitochondrial reads from pangolin were identified, as well as from three other species, namely, human, mouse and tiger. Importantly, I only identified three polymorphic nucleotide sites between the five GD/P sequences. Such low levels of polymorphism may reasonably be accounted for by sequencing errors alone, thus raising the possibility that the five pangolins seized in Guangdong in March 2019 were infected by the same virus strain, most probably during their captivity.

bioinformatics↗