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