Performance of 22 Rapid Lateral Flow Tests for SARS-CoV-2 Antigen Detection and Influence of "Variants of Concern": Implications for Clinical Use.

Large-scale head-to-head assessment of the performance of lateral-flow tests (LFTs) for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antigen is required in the context of the continuous emergence of new viral variants. The aim of this study was to evaluate the performance of 22 rapid LFTs for the detection of SARS-CoV-2 antigens. The clinical performance of 22 LFTs was evaluated in 1,157 samples collected in the Greater Paris area. The 8 best-performing LFTs were further assessed for their ability to detect 4 variants of concern (VOC), including the alpha, beta, delta, and omicron (BA.1) variants. The specificity of SARS-CoV-2 LFTs was generally high (100% for 15 of them) but was insufficient (<75%) for 3 tests. Sensitivity of the LFTs varied from 30.0% to 79.7% compared to nucleic acid amplification testing (NAAT). Using a cycle threshold (CT) cutoff of ≤25, sensitivity of the assays ranged from 59.7% to 100%. The 8 best-performing assays had a sensitivity of ≥80% for the detection of the 4 VOC when the CT was ≤25. Falsely negative SARS-CoV-2 antigen LFT results were observed with omicron, due to the occurrence of low viral loads (CT > 30 in 32% of samples) during the two first days following symptom onset. Several LFTs exhibited satisfactory sensitivity and specificity, whereas a few others yielded an unacceptable proportion of false-positive results and/or lacked sensitivity. The sensitivity of the best-performing assays was not influenced by VOC, including alpha, beta, delta, and omicron variants. The ability of LFTs to detect the omicron variant could be reduced during the first days following symptom onset due to lower viral loads than with other variants. IMPORTANCE The use of lateral-flow tests (LFTs) to detect SARS-CoV-2 has expanded worldwide. LFTs detect SARS-CoV-2 viral antigen and are less sensitive than nucleic acid amplification testing (NAAT). Their performance must be evaluated independently of the manufacturers. Our study assessed the performance of 22 SARS-CoV-2 antigen LFTs in large panels of well-characterized samples. The majority of LFTs tested exhibited satisfactory sensitivity and specificity, while some assays yielded unacceptable proportions of false-positive results, and others lacked sensitivity for samples containing large amounts of virus. The sensitivity of the best-performing assays did not vary according to the VOC, including the alpha, beta, delta, and omicron variants.

Performance of a high-throughput, automated enzyme immunoassay for the detection of SARS-CoV-2 antigen, including in viral "variants of concern": Implications for clinical use.

Direct detection of SARS-CoV-2 viral antigens could replace RT-PCR, provided that its clinical performance is validated in different epidemiological settings. Here, we evaluated the performance of the VITROS Antigen test, an enzyme immunoassay detecting a SARS-CoV-2 antigen, in NPSs from 3 cohorts of patients. METHODS: Three cohorts including SARS-CoV-2 RNA-positive samples collected during the first and second wave of the French epidemic between March 2020 and February 2021 (including variant B.1.1.7/α and variant B.1.351/ß). RESULTS: Among the 1763 prospectively tested subjects, 8.2% (145/1763) were SARS-CoV-2 RNA-positive by RT-PCR. Using Ct ≤ 30 and Ct ≤ 35 as thresholds, the sensitivities of the antigen assay were 98.8% (93.6-100%) and 93.5% (87.0-97.3%), respectively. The overall specificity of the assay was 100% (1614/1614; 99.8-100%). In a retrospective cohort of subjects infected with variants of concern, 90.4% (47/52) of NPSs containing B. B.1.1.7/α (Ct ≤ 35) and 100% (7/7) of those containing B.1.351/ß were positive with the VITROS EIA SARS-CoV-2 Antigen test. CONCLUSION: The excellent performance of the EIA Antigen test reported here, including in patients infected with viral "variants of concern", support the use of high-throughput, EIA-based SARS-CoV-2 antigen assays as an alternative or complement to nucleic acid testing in order to scale-up laboratory screening and diagnostic capacities.

Novel SARS-CoV-2 Variant Derived from Clade 19B, France.

We report a novel severe acute respiratory syndrome coronavirus 2 variant derived from clade 19B (HMN.19B variant or Henri Mondor variant). This variant is characterized by the presence of 18 amino acid substitutions, including 7-8 substitutions in the spike protein and 2 deletions. These variants actively circulate in different regions of France.

Male fertility in Arabidopsis requires active DNA demethylation of genes that control pollen tube function.

Active DNA demethylation is required for sexual reproduction in plants but the molecular determinants underlying this epigenetic control are not known. Here, we show in Arabidopsis thaliana that the DNA glycosylases DEMETER (DME) and REPRESSOR OF SILENCING 1 (ROS1) act semi-redundantly in the vegetative cell of pollen to demethylate DNA and ensure proper pollen tube progression. Moreover, we identify six pollen-specific genes with increased DNA methylation as well as reduced expression in dme and dme;ros1. We further show that for four of these genes, reinstalling their expression individually in mutant pollen is sufficient to improve male fertility. Our findings demonstrate an essential role of active DNA demethylation in regulating genes involved in pollen function.

tRNA 2'-O-methylation by a duo of TRM7/FTSJ1 proteins modulates small RNA silencing in Drosophila.

2'-O-Methylation (Nm) represents one of the most common RNA modifications. Nm affects RNA structure and function with crucial roles in various RNA-mediated processes ranging from RNA silencing, translation, self versus non-self recognition to viral defense mechanisms. Here, we identify two Nm methyltransferases (Nm-MTases) in Drosophila melanogaster (CG7009 and CG5220) as functional orthologs of yeast TRM7 and human FTSJ1. Genetic knockout studies together with MALDI-TOF mass spectrometry and RiboMethSeq mapping revealed that CG7009 is responsible for methylating the wobble position in tRNAPhe, tRNATrp and tRNALeu, while CG5220 methylates position C32 in the same tRNAs and also targets additional tRNAs. CG7009 or CG5220 mutant animals were viable and fertile but exhibited various phenotypes such as lifespan reduction, small RNA pathways dysfunction and increased sensitivity to RNA virus infections. Our results provide the first detailed characterization of two TRM7 family members in Drosophila and uncover a molecular link between enzymes catalyzing Nm at specific tRNAs and small RNA-induced gene silencing pathways.

The comparative phylogeography of fruit bats of the tribe Scotonycterini (Chiroptera, Pteropodidae) reveals cryptic species diversity related to African Pleistocene forest refugia.

The hypothesis of Pleistocene forest refugia was tested using comparative phylogeography of Scotonycterini, a fruit bat tribe endemic to Africa containing four species: Scotonycteris zenkeri, Casinycteris argynnis, C. campomaanensis, and C. ophiodon. Patterns of genetic structure were assessed using 105 Scotonycterini (including material from three holotypes) collected at 37 localities, and DNA sequences from the mitochondrial cytochrome b gene (1140 nt) and 12 nuclear introns (9641 nt). Phylogenetic trees and molecular dating were inferred by Bayesian methods. Multilocus analyses were performed using supermatrix, SuperTRI, and *BEAST approaches. Mitochondrial analyses reveal strong phylogeographical structure in Scotonycteris, with four divergent haplogroups (4.9-8.7%), from Upper Guinea, Cameroon, western Equatorial Africa, and eastern Democratic Republic of the Congo (DRC). In C. argynnis, we identify two mtDNA haplogroups corresponding to western and eastern Equatorial Africa (1.4-2.1%). In C. ophiodon, the mtDNA haplotypes from Cameroon and Ivory Coast differ by only 1.3%. Nuclear analyses confirm the validity of the recently described C. campomaanensis and indicate that western and eastern populations of C. argynnis are not fully isolated. All mtDNA clusters detected in Scotonycteris are found to be monophyletic based on the nuclear dataset, except in eastern DRC. In the nuclear tree, the clade from western Equatorial Africa is closely related to individuals from eastern DRC, whereas in the mitochondrial tree it appears to be the sister-group of the Cameroon clade. Migrate-n analyses support gene flow from western Equatorial Africa to eastern DRC. Molecular dating indicates that Pleistocene forest refugia have played an important role in shaping the evolution of Scotonycterini, with two phases of allopatric speciation at approximately 2.7 and 1.6 Mya, resulting from isolation in three main forest areas corresponding to Upper Guinea, Cameroon, and Equatorial Africa. Two cryptic species and two subspecies are described herein in the genus Scotonycteris. Female philopatry and male biased dispersal are supported for the smallest taxa, i.e., the three species of Scotonycteris and C. argynnis. The Congo, Ntem, and Sanaga rivers are identified as biogeographic barriers to the dispersal of Scotonycteris during interglacial periods. A greater capacity for long-distance dispersal is inferred for the largest species, C. ophiodon.