SARS-CoV-2 testing of aircraft wastewater shows that mandatory tests and vaccination pass before boarding did not prevent massive importation of Omicron variant in Europe

BackgroundMost new SARS-CoV-2 epidemics in France occurred following importation from abroad of emerging viral variants. Currently, the control of such risk of new variant importation is based on the negativity of a screening test (PCR or antigenic) and on an up-to-date vaccine status, such as International Air Transport Association travel pass. MethodsWastewater of 2 planes arriving in Marseille (France) from Addis-Ababa (Ethiopia) on December 2021 were i) tested by RT-PCR for SARS-CoV2 detection, and variants screening; these tests were carried out between landing and custom clearance, ii)sequenced by MiSeq Illumina. Antigenic tests and sequencing by NovaSeq were carried out on respiratory samples collected from the 56 passengers of the second flight. ResultsSARS-CoV-2 RNA suspected of being from the Omicron BA.1 variant was detected on the aircrafts wastewater., SARS-CoV2 RNA was detected for 11 (20%) passengers and the Omicron BA.1 variant was identified. ConclusionOur work shows the efficiency of aircraft wastewater testing to detect SARS-CoV-2 cases among travelers and identify the viral genotype. It also highlights the low performance for incoming flights from outside Europe to France of the current filter strategy that combines requirement for a vaccine pass and a negative testing before boarding.

High speed large scale automated isolation of SARS-CoV-2 from clinical samples using miniaturized co-culture coupled with high content screening

SARS-CoV-2, a novel coronavirus infecting humans, is responsible for the current COVID-19 global pandemic. If several strains could be isolated worldwide, especially for in-vitro drug susceptibility testing and vaccine development, few laboratories routinely isolate SARS-CoV-2. This is due to the fact that the current co-culture strategy is highly time consuming and requires working in a biosafety level 3 laboratory. In this work, we present a new strategy based on high content screening automated microscopy (HCS) allowing large scale isolation of SARS-CoV-2 from clinical samples in 1 week. A randomized panel of 104 samples, including 72 tested positive by RT-PCR and 32 tested negative, were processed with our HCS procedure and were compared to the classical isolation procedure. Isolation rate was 43 % with both strategies on RT-PCR positive samples, and was correlated with the initial RNA viral load in the samples, where we obtained a positivity threshold of 27 Ct. Co-culture delays were shorter with HCS strategy, where 80 % of the positive samples were recovered by the third day of co-culture, as compared to only 25 % with the classic strategy. Moreover, only the HCS strategy allowed us to recover all the positive elements after 1 week of co-culture. This system allows rapid and automated screening of clinical samples with minimal operator work load, thus reducing the risks of contamination.