Sequencing identifies predominantly Delta lineages circulating in Syria, Yemen and Lebanon.
Using the Oxford Nanopore midnight protocol, RLID-AD was able to successfully sequence 154/170 samples received (90.5% success rate, Table 1). Of the samples that failed, those that were sent as extracted RNA were more likely to fail, 6 out of 10 extracted RNA failed (60% failure), which is likely due to RNA degradation from the time the samples were extracted in March/April 2021 in Syria, to the time they were sequenced in March/April 2022 in UAE. Of the samples transported in VTM, the majority of failures were in samples with higher Ct (~Ct30) which is not unexpected. Even with the limited number of samples sequenced, it was possible to observe lineage switching over time, with the majority of samples collected in Q1 of 2021 showing the Alpha lineage in both Syria and Yemen, while in Q3 a switch to the Delta lineage was apparent. This was in general agreement with global trends, with Delta becoming the primary lineage in circulation in late 2021 (Figure 2).
Table 1. Total number of samples received from Syria, Yemen and Lebanon and the number of samples sequenced successfully (success rate) with the lineage of SARS-CoV-2 assigned