Distinct SARS-CoV-2 lineages, discovered through various genomic surveillance initiatives, have emerged during the pandemic following unprecedented reductions in worldwide human mobility. We here describe a SARS-CoV-2 lineage - designated B.1.620 - discovered in Lithuania and carrying many mutations and deletions in the spike protein shared with widespread variants of concern (VOCs), including E484K, S477N and deletions HV69Δ, Y144Δ, and LLA241/243Δ. As well as documenting the suite of mutations this lineage carries, we also describe its potential to be resistant to neutralising antibodies, accompanying travel histories for a subset of European cases, evidence of local B.1.620 transmission in Europe with a focus on Lithuania, and significance of its prevalence in Central Africa owing to recent genome sequencing efforts there. We make a case for its likely Central African origin using advanced phylogeographic inference methodologies incorporating recorded travel histories of infected travellers.

Many high-income countries have met the SARS-CoV-2 pandemic with overwhelming sequencing resources and have identified numerous distinct lineages, including some with notably altered biology. Over a year into the pandemic following unprecedented reductions in worldwide human mobility, distinct introduced lineages of SARS-CoV-2 without sequenced antecedents are increasingly discovered in high-income countries as a result of ongoing SARS-CoV-2 genomic surveillance initiatives. We here describe one such SARS-CoV-2 lineage, carrying many mutations and deletions in the spike protein shared with widespread variants of concern (VOCs), including E484K, S477N and deletions HV69del, Y144del, and LLA241/243del. This lineage - designated B.1.620 - is known to circulate in Lithuania and has now been found in several European states, but also in increasing numbers in central Africa owing to important recent increases in genome sequencing efforts on the continent. We provide evidence of likely ongoing local transmission of B.1.620 in Lithuania, France, Germany, Spain, Belgium and the Central African Republic. We describe the suite of mutations this lineage carries, its potential to be resistant to neutralising antibodies, travel histories for a subset of the European cases, and evidence of local B.1.620 transmission in Europe. We make a case for the likely Central African origin of this lineage by providing travel records as well as the outcomes of carefully crafted phylogenetic and phylogeographic inference methodologies, the latter of which is able to exploit individual travel histories recorded for infected travellers having entered different European countries.

No abstract

Quantitative reverse transcription polymerase chain reaction (RT-qPCR) is regarded as the gold-standard for diagnostic testing. However, the detection of residual viral RNA genome fragments is affecting several percent of recovered patients, which unnecessarily pro-longs quarantines or delays clinical procedures. To minimize the detection of such fragments, we introduced a single modification in the COVID-19 RT-qPCR to distinguish between infectious and non-infectious viral RNA. After validation of the assay using UVC inactivation of infectious virus, we analyzed positive COVID-19 clinical samples from two different countries. We find that after 15 days of the onset of symptoms, the modified RT-qPCR protocol leads to significantly fewer positive diagnoses in persistently positive samples compared to the standard RT-qPCR test, without compromising diagnoses within 5 days of the onset of symptoms. The method may improve test-to-release protocols and expand the tools available for clinical diagnosis.ImportanceMolecular tests can be used to detect RNA virus infections. The RT-qPCR test is currently regarded as the gold-standard, but its sensitivity to residual viral RNA genome fragments can lead to “incorrectly-positive” RT-qPCR results. Such results are different from false-positive RT-qPCR results, which can be generated due to in vitro cross-reactivity or contaminations. However, the detection of RNA fragments leads to similar incorrect conclusions about the presence of infectious virus long after a patient has recovered from a viral infection and thus false-positive diagnoses. We here modified a commercial RT-qPCR kit to make it less sensitive to residual viral RNA genome fragments, reducing the likelihood for such results in recovered COVID-19 patients. The method may improve test-to-release protocols, expand the tools available for clinical testing, and help reduce hospital encumbrance.