Abstract
The pandemic caused by SARS-CoV-2 has prompted a collaborative global effort to contain viral spread and improve health outcomes for those infected. The tracking of SARS-CoV-2 variants since the first sequence was published in January 2020 is an important part understanding the pandemic. There is limited data regarding SARS-CoV-2 circulation in Jordan. In this study we determined the prevalence of genetic variants of SARS-CoV-2 during June-September 2021 by sequencing the full genome of 213 viral samples from Jordanian Royal Medical Services military hospitals. Our analysis revealed the presence of 33 variants, with (B.1.617.2.AY.106) as the predominate strain. Six variants were present at a prevalence greater than 2%((B.1.617.2.AY.106), 52.8%; Delta (B.1.617.2), 7.0%; (B.1.617.2.AY.34.1), 5.6%;(B.1.617.2.AY.44), 2.8%; (B.1.617.2.AY.121), 2.33%; (B.1.617.2.AY.102), 2.33%). Variant prevalence varied significantly by region and (B.1.617.2.AY.106) variant tended to be associated with mild to moderate symptoms, on the other hand other variants were asymptomatic. We did not find significant associations of variants with other factors such as age, gender or vaccination status. These data help us to understand the occurrence of new variants in Jordan, their geographic distribution, and associations with demographic variables, vaccination status, and symptom severity. The sustained circulation of SARS-CoV-2 continues to lead to novel variant emergence. These findings highlight the need to continue tracking new variants, monitor the dynamics of variant prevalence, and future efforts will guide prevention, vaccination, and control strategies.