Tracking SARS-CoV-2 VOC 202012/01 (lineage B.1.1.7) dissemination in Portugal

The SARS-CoV-2 lineage B.1.1.7, also designated Variant of Concern (VOC) 202012/01, has shown a pronounced frequency increase in the United Kingdom (where it likely emerged by late summer 2020) and is rapidly expanding its geographic range worldwide. Among the several mutations harbored by this variant, the Spike Δ69/70 deletion affects the detection of S-gene by some RT-PCR assays (e.g., TaqPath COVID-19 RT-PCR assay, ThermoFisher), leading to what has been termed “Spike gene target failure (SGTF) or “Spike gene drop out”. In this context, SGTF is being successfully applied as a proxy to indicate carriage of the highly transmissible B.1.1.7 lineage and monitor its geotemporal dissemination.

In this brief report, we present comprehensive data supporting that the proportion of SGTF samples is greatly increasing in Portugal. We used data from 27096 cases confirmed positive by the ThermoFisher TaqPath RT-PCR assay, collected in 287 settings of a large laboratory (Unilabs) distributed throughout the country mainland since December 1st, 2020. We observed that the proportion of SGTF cases increased from ~1% in weeks 49-50 (2020) to 11.4% in week 2 (2021). Unexpectedly, we also detected a considerable proportion of TaqPath positive samples having Cycle threshold (Ct) values for S gene >5 units higher than the maximum Ct value obtained for the other two targets (N and ORF1ab) of the assay. So far, SARS-CoV-2 genome sequencing of samples showing this RT-PCR profile, here tentatively designated as “Spike gene target late amplification” (SGTL), identified the VOC 202012/01 (lineage B.1.1.7) in all of them. SGTL cases present an increasing trend in frequency (about 7-fold increase in relative proportion from week 49/2020 to week 2/2021) similar to that observed for SGTF cases. Also, both SGTF and SGTL samples had median Ct values of ORF1ab and N-gene targets within the same range, and these values were significantly lower than the ones observed for samples where S gene was unbiasedly detected. These results suggests that SGTL observation can constitute an additional proxy to detect and monitor the VOC 202012/01 variant. Current data on age distribution of SGTF+SGTL cases (median=35; IQR=21-48) does not seem to indicate a relevant shift in the age distribution when comparing with non-SGTF/SGTI cases (median=38; IQR=23-53).

In total, SGTF/SGFL cases represented 5.8% of all TaqPath positive cases detected since week 49 (2020), with this proportion reaching 13.3% at end of week 2 (2021). The SGTF/SGTL proportion increased at 70% (63%–76%, CI 95%) rate per week, with our forecast for the next three weeks, assuming no change in the increasing rate, pointing that the proportion of SGTF/SGTL cases can reach up to 60% of TaqPath positive cases by week 5.

In order to facilitate the assessment (and real-time monitoring) of SGTF/SGTL cases, their frequency and geographical dispersion, an interactive dashboard and data cube was developed and shared with the national public health authority. This approach may support timely public-health decisions by enabling early identification of geographical regions with increased incidence and circulation of Δ69-70-bearing SARS-CoV-2, in particular the VOC 202012/01 variant (lineage B.1.1.7).

In the present study, we investigated the proportion of SGTF cases as a mean to get insights on VOC 202012/01 (B.1.1.7 lineage) frequency and geographic spread in Portugal. To achieve this, we took advantage of massive SARS-CoV-2 RT-PCR data comprehensively collected by a large laboratory (Unilabs) in 287 sample collection settings distributed throughout the country. Between week 49 (2020) and week 2 (2021), Unilabs performed more than 134 000 SARS-CoV-2 RT-PCR tests using Thermofisher TaqPath assay (targeting three regions of SARS-CoV-2 genome: ORF1ab, N and S genes), which roughly corresponds to 7% of all SARS-CoV-2 RT-PCR tests done in Portugal during the same period.