Crowded Probabilities in Tests for the Presence of Infection

In the presentation, problems have been addressed in perception and popular delusions in the interpretation of information related to the level of confidence / uncertainty of tests by which the presence or absence of contamination is verified. The theoretical essence of the probabilities of a false positive and false negative result, as well as the level of confidence / uncertainty of the test results and on this basis there are assumptions about the perception of such information and possible misconceptions in its interpretation by society. Assumptions made are checked on the information based on a non-reporting survey. The results obtained reveal user difficulties in rationalizing and interpreting the data provided as well as when detecting logical links characteristic of such information.

Emergence and fast spread of B.1.1.7 lineage in Lebanon

ABSTRACTThe severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remains a rapid spread emerging disease. Recently, a new variant of this virus called SARS-CoV-2 VOC 202012/01 (or B.1.1.7 lineage), described in the United Kingdom (UK), has become highly prevalent in several countries. Its rate of transmission has been estimated to be greatly higher. B.1.1.7 lineage harbors 23 mutations co-existed for the first time in the same variant. Herein, we are interested only by the deletion mutation ΔH69/ΔV70 in the spike protein.In the UK they were able to identify the increase of this new variant through the increase in the false negative result for the spike target of a three-target RT-PCR assay from Thermo Fisher Scientific (TaqPath kit). Later, the manufacturer announced that this false negative result is because of the deletion ΔH69/ΔV70 in the area targeted by the TaqPath Kit. Furthermore, The European CDC recommended that the use of this kit help to track the new variant.Genome sequencing is the gold method to confirm the new variant, but observational studies provide also stronger evidence if similar models are observed in multiple countries, especially when randomized studies are not possible. In Lebanon, the highest number of confirmed cases were reported in first week of 2021. In the present study, we show the emergence and the fast spreading of the new variant in Lebanon and a relationship between SARS-CoV-2 transmission intensity and the frequency of the new variant during the first twelve days of January.

Two-step strategy for the identification of SARS-CoV-2 variants co-occurring with spike deletion H69-V70, Lyon, France, August to December 2020

The spike deletion H69-V70 (ΔH69/ΔV70) has been recently detected in a SARS-CoV-2 variant under investigation in England (VUI 202012/01) as well as in cluter-5 variant detected both in minks and humans in Denmark. Herein we report the implementation of a two-step strategy enabling to detect SARS-CoV-2 variants carrying H69-V70 deletion. We found that this deletion resulted in a false negative result for the spike target of a three-target RT-PCR assay (TaqPath kit). From August 3rd to December 20th, 59/9,266 (0.6%) of positive tests displayed a S negative profile (negative for S target and positive for N & ORF1ab targets). Among the 59 samples without detection of the S target, 36 were available for whole genome sequencing (WGS). The most frequent S mutations co-occurring with ΔH69/ΔV70 were S477N & D614G (21/36 samples). The co-occurrence of N439K and D614G mutations was found in 10/36 samples. The complete combination of S mutations detected in VUI 202012/01 or in cluster-5 variant was not found. The data presented herein emphasize that the TaqPath RT-PCR assay enables a rapid, large-scale screening of ΔH69/ΔV70 variants. Samples with S negative profiles should be further addressed to national referral laboratories for SARS-CoV-2 WGS. This 2-step strategy is currently being reinforced in France as national diagnostic platforms have mainly implemented the TaqPath RT-PCR kit.