Rapid evolution of the COVID-19 pandemic calls for a unified public health response

Saline gargle collection method is comparable to nasopharyngeal/oropharyngeal swabbing for the molecular detection and sequencing of SARS-CoV-2 in Botswana

The coronavirus disease 2019 pandemic has highlighted the importance and challenges of the sample collection component of the diagnostic cycle. Although combined nasopharyngeal and oropharyngeal swabs (NOS) have historically been the gold standard of sampling, the saline gargle (SG) sampling method has been evaluated and implemented in multiple jurisdictions for respiratory pathogen detection. It has proven to be user-acceptable to patients, simple to collect, and highly sensitive to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection by molecular methods when compared to swabs. We performed a prospective cross-sectional study to evaluate the SG collection method against the NOS collection method for molecular detection and next-generation sequencing (NGS) of SARS-CoV-2 in Botswana. Paired SG and NOS samples were collected and underwent nucleic acid extraction prior to molecular detection. The SG had an overall sensitivity of 81.3% (95% CI: 68.8%%-96.0%), while the NOS had an overall sensitivity of 96.9% (95% CI: 84.3-99.4). Paired samples with a mean crossing threshold value of <35 also underwent NGS. SG specimens had a median genome coverage of 94.7% (interquartile range [IQR] 87.0%-99.2%) and NOS specimens had a median genome coverage of 99.6% (IQR 90.0%-99.6%). Bioinformatics analysis showed the 15 successfully matched pairs belong to clades BA.1 and BA.2 indicative of the Omicron variant. Further analysis at the nucleotide level showed a mean similarity of 99.998% ± 0.00465% between NOS and SG. This method has the potential to overcome the challenges that come with swab-based sampling for SARS-CoV-2 testing and may be an alternative in testing for other viral pathogens.

IMPORTANCE

During the coronavirus disease 2019 (COVID-19) pandemic, a major challenge has been inadequate sampling for detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Pediatric patients posed additional challenges with sample collection, and they and others are also at risk of rare complications from swab collection. Saline gargle (SG) sampling method has been evaluated and introduced as an alternative to swab collection in several jurisdictions. Our study affirms the acceptable performance of the saline gargle method for the molecular detection of SARS-CoV-2 and also establishes that SG samples do not pose an obstacle for genomic sequencing of SARS-CoV-2. The SG method may be a reliable alternative for SARS-CoV-2 detection and next-generation sequencing, facilitating COVID-19 surveillance efforts in resource-constraint settings.

Exploring immune evasion of SARS-CoV-2 variants using a pseudotyped system

In the United States, coronavirus disease 2019 (COVID-19) cases have consistently been linked to the prevailing variant XBB.1.5 of SARS-CoV-2 since late 2022. A system has been developed for producing and infecting cells with a pseudovirus (PsV) of SARS-CoV-2 to investigate the infection in a Biosafety Level 2 (BSL-2) laboratory. This system utilizes a lentiviral vector carrying ZsGreen1 and Firefly luciferase (Fluc) dual reporter genes, facilitating the analysis of experimental results. In addition, we have created a panel of PsV variants that depict both previous and presently circulating mutations found in circulating SARS-CoV-2 strains. A series of PsVs includes the prototype SARS-CoV-2, Delta B.1.617.2, BA.5, XBB.1, and XBB.1.5. To facilitate the study of infections caused by different variants of SARS-CoV-2 PsV, we have developed a HEK-293T cell line expressing mCherry and human angiotensin converting enzyme 2 (ACE2). To validate whether different SARS-CoV-2 PsV variants can be used for neutralization assays, we employed serum from rats immunized with the PF-D-Trimer protein vaccine to investigate its inhibitory effect on the infectivity of various SARS-CoV-2 PsV variants. According to our observations, the XBB variant, particularly XBB.1.5, exhibits stronger immune evasion capabilities than the prototype SARS-CoV-2, Delta B.1.617.2, and BA.5 PsV variants. Hence, utilizing the neutralization test, this study has the capability to forecast the effectiveness in preventing future SARS-CoV-2 variants infections.

Next-Generation Vaccines: Nanovaccines in the Fight against SARS-CoV-2 Virus and beyond SARS-CoV-2

The virus responsible for the coronavirus viral pandemic is the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Emerging SARS-CoV-2 variants caused by distinctive mutations within the viral spike glycoprotein of SARS-CoV-2 are considered the cause for the rapid spread of the disease and make it challenging to treat SARS-CoV-2. The manufacturing of appropriate efficient vaccines and therapeutics is the only option to combat this pandemic. Nanomedicine has enabled the delivery of nucleic acids and protein-based vaccines to antigen-presenting cells to produce protective immunity against the coronavirus. Nucleic acid-based vaccines, particularly mRNA nanotechnology vaccines, are the best prevention option against the SARS-CoV-2 pandemic worldwide, and they are effective against the novel coronavirus and its multiple variants. This review will report on progress made thus far with SARS-CoV-2 vaccines and beyond employing nanotechnology-based nucleic acid vaccine approaches.

Perceptions, satisfactions, and performance of undergraduate students during Covid-19 emergency remote teaching

Due to the Covid-19 pandemic, the education system worldwide faced sudden and unforeseen challenges. Many academic institutions closed their doors, forcing both educators and students to transition to Emergency Remote Teaching (ERT) for the remainder of the semester. This transition eliminated hands-on experiences, increased workload, and altered curricula. However, these aspects, as well as students' perceptions, study habits, and performance in response to ERT remain poorly documented. This contribution describes changes in the curriculum of an undergraduate cadaver-based laboratory, and explores students' performance, self-perceived learning, and overall satisfaction during this educational crisis. Online content delivery for this course included both asynchronous instruction and synchronous discussion sessions. While formative assessments remained the same, online spotter examinations included short answer, multiple choice, multiple answer, ordering, and true and false questions. Despite examination grades improving 20% during ERT, students reported lower levels of learning, confidence, and engagement with the course materials when compared to the face-to-face portion of the class. The most prevalent challenges identified by students were those related to the loss of access to cadaver-based learning, including difficulty identifying and visualizing structures in three dimensions, and the loss of context and sensorial cues. Flexibility in taking examinations and learning the material at their own pace were recognized as positive outcomes of the ERT transition. While the resulting student perceptions and performances are unsurprising, they offer insight into the challenges of fostering a productive learning environment in a future threatened by epidemic outbreak and economic uncertainty.