The Algerian chapter of SARS-CoV-2 pandemic: An evolutionary, genetic, and epidemiological prospect of the first wave.

Zeghbib, S.; Somogyi, B.; Zana, B.; Kemenesi, G.; Herczeg, R.; Derrar, F.; Jakab, F.

To explore the SARS-CoV-2 early pandemic in Algeria, a dataset comprising forty-three genomes originating from SARS-CoV-2 sampled from Algeria and other countries worldwide, from 24 December 2019 through 8 March 2020, of which, were thoroughly examined. While performing a multi-component analysis regarding the Algerian outbreak, the toolkit of phylogenetic, phylodynamic, haplotype analyses and genomic analysis were effectively implemented. We estimated the TMRCA in reference to the Algerian pandemic and highlighted both the introduction of the disease originating in France and the missing data depicted in the transmission loop. Most importantly, we unveiled mutational patterns, recombination events and the relatedness regarding the Algerian sequences to the dataset. Our results revealed the unique amino-acid replacement L129F in the orf3a gene in Algeria_EPI_ISL_418241. Additionally, a connection between Algeria_EPI_ISL_420037 and sequences originating from the USA was observed through a USA characteristic amino-acid replacement T1004I in the nsp3 gene, found in the aforementioned Algerian sequence. Lastly, we assessed the Algerian mitigation measures regarding disease containment using statistical analyses.