Genetic diversity and genomic epidemiology of SARS-CoV-2 in Morocco

Coronavirus disease 2019 (COVID-19) is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), declared as a pandemic due to its rapid spread worldwide. In this study, we investigate the genetic diversity and genomic epidemiology of SARS-CoV-2, using 22 virus genome sequences reported by three different laboratories in Morocco till June 7,2020, as well as 40,366 virus genomes from all around the world. The SARS-CoV-2 genomes from Moroccan patients revealed 62 mutations, of which 30 were mis-sense mutations. The mutations Spike_D614G and NSP12_P323L were present in all the 22 analyzed sequences, followed by N_G204R and N_R203K, which occurred in 9 among the 22 sequences. The mutations NSP10_R134S, NSP15_D335N, NSP16_I169L, NSP3_L431H, NSP3_P1292L and Spike_V6F occurred once in Moroccan sequences, with no record in other sequences worldwide. Phylogenetic analyses revealed that Moroccan SARS-CoV-2 genomes included 9 viruses belonging to Clade 20A, 9 to Clade 20B and 2 to Clade 20C, suggesting that the epidemic spread in Morocco did not display a predominant SARS-CoV-2 route. Therefore, multiple and unrelated introductions of SARS-CoV-2 into Morocco through different routes have occurred, giving rise to the diversity of virus genomes in the country. Further, in all probability, the SARS-CoV-2 circulated in a cryptic way in Morocco, starting from January 15, 2020 before the first case was officially discovered on March 2, 2020. •This study investigated the diversity and genomic epidemiology of SARS-CoV-2 in Morocco.•To apply such approach for investigating the evolution of SARS-CoV-2 in Morocco, we collected from GISAID (https://www.gisaid.org/) 40390 genome sequences of SARS-CoV-2, of which 22 were from Moroccan patients.•The genetic analysis of the SARS-CoV-2 genomes from Moroccan patients revealed some new mutations with no aforementioned record in other sequences worldwide.•Genomic Epidemiology analyses revealed that the COVID-19 spread occurred through multiple and unrelated introductions of COVID-19 into Morocco via different routes.•Deep genomic surveillance of SARS-CoV-2 reveals the circulating lineages of the virus, their changes over time and, in case of extensive sampling, could be a good way to evaluate how the interventions are affecting virus evolution