Comparative analysis of SARS-CoV-2 variants with two high-throughput sequencing platforms

Whole-genome sequencing of upper respiratory tract specimens from patients with confirmed COVID-19 in Henan Province was performed to compare the performance of the Illumina and Oxford Nanopore sequencing platforms, thus providing a reference for whole-genome monitoring of the novel coronavirus (SARS-CoV-2). Ten samples from COVID-19 cases in Henan Province from June 2021 to January 2022 were collected and sequenced with Illumina and Nanopore high-through-put sequencing technology to obtain full genome sequences of the novel coronavirus, which were compared with the Wuhan reference sequence (Wuhan-Hu-1). Bioinformatics software (CLC) was used for sequence alignment analysis. Three of the ten samples were Omicron (BA.1) variants with 55,61 nucleotide variation sites. One sample was an Alpha (B.1.1.7) variant with 41 nucleotide variation sites. Six samples were Delta (8.1.617.2) variants with 35,42,47 nucleotide variation sites. The sequence identity of mutation sites in six samples was 100%, and the mutation sites in the S genome segment of seven samples were consistent. For samples with a Ct value < 33, both next-generation and third-generation sequencing achieved high genome coverage and sequencing depth. A significant difference in coverage was observed between second-generation sequencing and third-generation sequencing (t=-2.037, P < 0.06). However, the coverage at different time points of the third-generation sequencing did not significantly differ (F=2.498, P > 0.05). The needs for SARS-CoV-2 mutant detection could be met through use of either high-throughput sequencing platform. The identification of mutations in the novel coronavirus through Illumina high-throughput sequencing was more accurate, whereas Nanopore high-throughput sequencing technology could be used for rapid detection and typing of different novel coronaviruses.

Recent Advances in the Use of Mesoporous Silica Nanoparticles for the Diagnosis of Bacterial Infections.

Public awareness of infectious diseases has increased in recent months, not only due to the current COVID-19 outbreak but also because of antimicrobial resistance (AMR) being declared a top-10 global health threat by the World Health Organization (WHO) in 2019. These global issues have spiked the realization that new and more efficient methods and approaches are urgently required to efficiently combat and overcome the failures in the diagnosis and therapy of infectious disease. This holds true not only for current diseases, but we should also have enough readiness to fight the unforeseen diseases so as to avoid future pandemics. A paradigm shift is needed, not only in infection treatment, but also diagnostic practices, to overcome the potential failures associated with early diagnosis stages, leading to unnecessary and inefficient treatments, while simultaneously promoting AMR. With the development of nanotechnology, nanomaterials fabricated as multifunctional nano-platforms for antibacterial therapeutics, diagnostics, or both (known as "theranostics") have attracted increasing attention. In the research field of nanomedicine, mesoporous silica nanoparticles (MSN) with a tailored structure, large surface area, high loading capacity, abundant chemical versatility, and acceptable biocompatibility, have shown great potential to integrate the desired functions for diagnosis of bacterial infections. The focus of this review is to present the advances in mesoporous materials in the form of nanoparticles (NPs) or composites that can easily and flexibly accommodate dual or multifunctional capabilities of separation, identification and tracking performed during the diagnosis of infectious diseases together with the inspiring NP designs in diagnosis of bacterial infections.

Anxiety and depression and the related factors in nurses of Guilan University of Medical Sciences hospitals during COVID-19: A web-based cross-sectional study.

BACKGROUND: The outbreak of COVID-19 is an unprecedented challenge to the health systems in Iran. We aimed to assess the psychological impact of this outbreak on nurses in the hospitals of Guilan University of Medical Sciences that is one of the top provinces of incidence of COVID-19. METHODS: In a web-based cross-sectional study, 441 nurses working were selected from the hospitals, from 7 to 12 April 2020. Anxiety and depression were measured using the Generalized Anxiety Disorder-7 and the Patient Health Questionnaire-9, respectively. Simple and multiple logistic regression models were used to identify the factors related to anxiety and depression. RESULTS: The majority were in contact with suspected or confirmed COVID-19 cases (93.4%) and their relatives had been infected with COVID-19 (42%). The mean of anxiety-7 and depression total scores were 8.64 ± 5.60 and 8.48 ± 6.19, respectively. Female (OR = 3.27, 95% CI = 1.01-10.64), working in COVID-19 designated hospital (OR = 1.82, 95% CI = 1.13-2.93), being suspected with COVID-19 infection (OR = 2.01, 95% CI = 1.25-3.26), and insufficient personal protective equipment (OR = 2.61, 95% CI = 1.68-4.06) were associated with anxiety. Depression was significantly associated with female sex (OR = 4.62, %95 CI = 1.24-17.16), having chronic disease (OR = 2.12, 95% CI = 1.20-3.74), being suspected or confirmed with COVID-19 infection (OR = 3.44, 95% CI = 2.11-5.59, and OR = 2.21, 95% CI = 1.04-4.70, respectively), and insufficient personal protective equipment (OR = 1.86, 95% CI = 1.19-2.91). CONCLUSION: The finding declares healthcare workers are at high risk for mental illness. Continuous supervision of the psychological consequences following infectious diseases outbreaks should be a part of the preparedness efforts of health care systems.