Analytical Performances of the COVISTIXTM Antigen Rapid Test for SARS-CoV-2 Detection in an Unselected Population (All-Comers).

The performance and validity of the COVISTIXTM rapid antigen test for the detection of SARS-CoV-2 were evaluated in an unselected population. Additionally, we assessed the influence of the Omicron SARS-CoV-2 variant in the performance of this antigen rapid test. Swab samples were collected at two point-of-care facilities in Mexico City from individuals that were probable COVID-19 cases, as they were either symptomatic or asymptomatic persons at risk of infection due to close contact with SARS-CoV-2 positive cases. Detection of the Omicron SARS-CoV-2 variant was performed in 91 positive cases by Illumina sequencing. Specificity and sensitivity of the COVISTIXTM rapid antigen test was 96% (CI 95% 94-98) and 81% (CI 95% 76-85), respectively. The accuracy parameters were not affected in samples collected after 7 days of symptom onset, and it was possible to detect almost 65% of samples with a Ct-value between 30 and 34. The COVISTIXTM antigen rapid test is highly sensitive (93%; CI 95% 88-98) and specific (98%; CI 95% 97-99) for detecting Omicron SARS-CoV-2 variant carriers. The COVISTIXTM rapid antigen test is adequate for examining asymptomatic and symptomatic individuals, including those who have passed the peak of viral shedding, as well as carriers of the highly prevalent Omicron SARS-CoV-2 variant.

The Evolutionary Landscape of SARS-CoV-2 Variant B.1.1.519 and Its Clinical Impact in Mexico City.

The SARS-CoV-2 pandemic is one of the most concerning health problems around the globe. We reported the emergence of SARS-CoV-2 variant B.1.1.519 in Mexico City. We reported the effective reproduction number (Rt) of B.1.1.519 and presented evidence of its geographical origin based on phylogenetic analysis. We also studied its evolution via haplotype analysis and identified the most recurrent haplotypes. Finally, we studied the clinical impact of B.1.1.519. The B.1.1.519 variant was predominant between November 2020 and May 2021, reaching 90% of all cases sequenced in February 2021. It is characterized by three amino acid changes in the spike protein: T478K, P681H, and T732A. Its Rt varies between 0.5 and 2.9. Its geographical origin remain to be investigated. Patients infected with variant B.1.1.519 showed a highly significant adjusted odds ratio (aOR) increase of 1.85 over non-B.1.1.519 patients for developing a severe/critical outcome (p = 0.000296, 1.33-2.6 95% CI) and a 2.35-fold increase for hospitalization (p = 0.005, 1.32-4.34 95% CI). The continuous monitoring of this and other variants will be required to control the ongoing pandemic as it evolves.

Saliva is a reliable and accessible source for the detection of SARS-CoV-2.

OBJECTIVES: The aim of this study was to investigate the feasibility of saliva sampling as a non-invasive and safer tool to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and to compare its reproducibility and sensitivity with nasopharyngeal swab samples (NPS). The use of sample pools was also investigated. METHODS: A total of 2107 paired samples were collected from asymptomatic healthcare and office workers in Mexico City. Sixty of these samples were also analyzed in two other independent laboratories for concordance analysis. Sample processing and analysis of virus genetic material were performed according to standard protocols described elsewhere. A pooling analysis was performed by analyzing the saliva pool and the individual pool components. RESULTS: The concordance between NPS and saliva results was 95.2% (kappa 0.727, p = 0.0001) and 97.9% without considering inconclusive results (kappa 0.852, p = 0.0001). Saliva had a lower number of inconclusive results than NPS (0.9% vs 1.9%). Furthermore, saliva showed a significantly higher concentration of both total RNA and viral copies than NPS. Comparison of our results with those of the other two laboratories showed 100% and 97% concordance. Saliva samples are stable without the use of any preservative, and a positive SARS-CoV-2 sample can be detected 5, 10, and 15 days after collection when the sample is stored at 4 °C. CONCLUSIONS: The study results indicate that saliva is as effective as NPS for the identification of SARS-CoV-2-infected asymptomatic patients. Sample pooling facilitates the analysis of a larger number of samples, with the benefit of cost reduction.

A draft genome sequence of the elusive giant squid, Architeuthis dux.

BACKGROUND: The giant squid (Architeuthis dux; Steenstrup, 1857) is an enigmatic giant mollusc with a circumglobal distribution in the deep ocean, except in the high Arctic and Antarctic waters. The elusiveness of the species makes it difficult to study. Thus, having a genome assembled for this deep-sea-dwelling species will allow several pending evolutionary questions to be unlocked. FINDINGS: We present a draft genome assembly that includes 200 Gb of Illumina reads, 4 Gb of Moleculo synthetic long reads, and 108 Gb of Chicago libraries, with a final size matching the estimated genome size of 2.7 Gb, and a scaffold N50 of 4.8 Mb. We also present an alternative assembly including 27 Gb raw reads generated using the Pacific Biosciences platform. In addition, we sequenced the proteome of the same individual and RNA from 3 different tissue types from 3 other species of squid (Onychoteuthis banksii, Dosidicus gigas, and Sthenoteuthis oualaniensis) to assist genome annotation. We annotated 33,406 protein-coding genes supported by evidence, and the genome completeness estimated by BUSCO reached 92%. Repetitive regions cover 49.17% of the genome. CONCLUSIONS: This annotated draft genome of A. dux provides a critical resource to investigate the unique traits of this species, including its gigantism and key adaptations to deep-sea environments.

Characterized Bioelectric Signals by Means of Neural Networks and Wavelets to Remotely Control a Human-Machine Interface.

Everyday, people interact with different types of human machine interfaces, and the use of them is increasing, thus, it is necessary to design interfaces which are capable of responding in an intelligent, natural, inexpensive, and accessible way, regardless of social, cultural, economic, or physical features of a user. In this sense, it has been sought out the development of small interfaces to avoid any type of user annoyance. In this paper, bioelectric signals have been analyzed and characterized in order to propose a more natural human-machine interaction system. The proposed scheme is controlled by electromyographic signals that a person can create through arm movements. Such arm signals have been analyzed and characterized by a back-propagation neural network, and by a wavelet analysis, in this way control commands were obtained from such arm electromyographic signals. The developed interface, uses Extensible Messaging and Presence Protocol (XMPP) to send control commands remotely. In the experiment, it manipulated a vehicle that was approximately 52 km away from the user, with which it can be showed that a characterized electromyographic signal can be sufficient for controlling embedded devices such as a Raspberri Pi, and in this way we can use the neural network and the wavelet analysis to generate control words which can be used inside the Internet of Things too. A Tiva-C board has been used to acquire data instead of more popular development boards, with an adequate response. One of the most important aspects related to the proposed interface is that it can be used by almost anyone, including people with different abilities and even illiterate people. Due to the existence of individual efforts to characterize different types of bioelectric signals, we propose the generation of free access Bioelectric Control Dictionary, to define and consult each characterized biosignal.

Population genomic footprints of environmental pollution pressure in natural populations of the Mediterranean mussel.

Bivalve molluscs of the genus Mytilus are considered a model organism in ecotoxicology and are known to be well adapted to marine ecosystems affected by multiple anthropogenic factors, including pollution. In order to assess whether pollution interferes with the reproductive success of Mytilus and affects the diversity within and between populations, we sequenced the transcriptomes of 72 individuals from 9 populations of Mytilus galloprovincialis collected along a ca. 130-km north-south transect on the Western coast of the Iberian Peninsula. We found that polluted areas are acting as a barrier to gene flow, potentially because of the detrimental effect of anthropogenic chemicals on larvae carried from more pristine environments. Furthermore, we observed an increase in genetic diversity in populations from polluted site, which could be indicative of higher mutagenicity driven by the environment. We propose that a microevolutionary perspective is essential for a full characterization of human activities on the dispersal of M. galloprovincialis and that it should be incorporated into management, and conservation plans and policies in the context of the effects of pollution on populations.

An expanded mammal mitogenome dataset from Southeast Asia.

Southeast (SE) Asia is 1 of the most biodiverse regions in the world, and it holds approximately 20% of all mammal species. Despite this, the majority of SE Asia's genetic diversity is still poorly characterized. The growing interest in using environmental DNA to assess and monitor SE Asian species, in particular threatened mammals-has created the urgent need to expand the available reference database of mitochondrial barcode and complete mitogenome sequences. We have partially addressed this need by generating 72 new mitogenome sequences reconstructed from DNA isolated from a range of historical and modern tissue samples. Approximately 55 gigabases of raw sequence were generated. From this data, we assembled 72 complete mitogenome sequences, with an average depth of coverage of ×102.9 and ×55.2 for modern samples and historical samples, respectively. This dataset represents 52 species, of which 30 species had no previous mitogenome data available. The mitogenomes were geotagged to their sampling location, where known, to display a detailed geographical distribution of the species. Our new database of 52 taxa will strongly enhance the utility of environmental DNA approaches for monitoring mammals in SE Asia as it greatly increases the likelihoods that identification of metabarcoding sequencing reads can be assigned to reference sequences. This magnifies the confidence in species detections and thus allows more robust surveys and monitoring programmes of SE Asia's threatened mammal biodiversity. The extensive collections of historical samples from SE Asia in western and SE Asian museums should serve as additional valuable material to further enrich this reference database.

Genome Evolution in Three Species of Cactophilic Drosophila.

We report genomes of two species of cactophilic Drosophila: Drosophila arizonae and D. navojoa These two are the closest relatives of D. mojavensis, forming the D. mojavensis cluster. D. mojavensis and D. arizonae diverged from D. navojoa ∼5.8 Mya, while the split between D. arizonae and D. mojavensis is more recent, at 1.5 Mya. Together the three genomes provide opportunities to examine genomic changes associated with speciation and host shifts in this ecologically defined group of flies. The three species are also separated by fixed inversion differences in three of their six chromosomes. While the levels of nucleotide divergence in the colinear chromosomes are significantly lower than in the inverted chromosomes, consistent with a past role of the inversions in preventing gene flow, the patterns differ among the inverted chromosomes when the locations of nucleotides inside or outside of the inversions are considered. For Muller element E, there is greater divergence external to the inversion breakpoints. For Muller A, the divergence is slightly higher inside the inversions, while for Muller B, the breakpoints and hence the difference in substitutions in relation to the inversions could not be determined. The differences among the inverted chromosomes, especially once the breakpoints are clearly established, could aid in dating the origins of the inversions.

Complete mitochondrial genomes of the Laotian Rock Rat (Laonastes aenigmamus) confirm deep divergence within the species.

Mitochondrial genomes of five Laotian Rock Rat (Laonastes aenigmamus) samples from Vietnam and Laos were sequenced using an Illumina platform. After de novo assembly, 13 protein-coding genes and two rRNA (12S and 16S) of the five genomes were aligned and analyzed with those from other related species under maximum likelihood and Bayesian inferences. Both methods revealed congruent tree topologies, which support two independently evolving clades of L. aenigmamus from Laos and Vietnam. The relaxed time calibration analysis showed that the two major lineages of the Laotian Rock Rat split about 8 million years ago, which was consistent with the results from previous studies using only cytochrome b sequences. Such a deep divergence time suggests the recognition of two rock rat species, but further nuclear DNA and morphological data are needed to solve the taxonomy of this taxon.