Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR

Utility of SARS-CoV-2 Subgenomic RNA in Kidney Transplant Recipients Receiving Remdesivir

INTRODUCTION

There is no reliable microbiological marker to guide responses to antiviral treatment in kidney transplant recipients (KTR) with COVID-19. We aimed to evaluate the dynamics of subgenomic RNA (sgRNA) RT-PCR before and after receiving treatment with remdesivir compared with genomic RNA (gRNA) RT-PCR and its use as a surrogate marker of viral replication.

METHODS

We analyzed gRNA and sgRNA at baseline and after remdesivir treatment in KTR who received remdesivir for SARS-CoV-2 infection from November 2021 to February 2022.

RESULTS

Thirty-four KTR received remdesivir for SARS-CoV-2 infection. The median time since transplantation was 80 months (IQR 3-321) and 75% of patients had previously received 3 doses of a mRNA SARS-CoV-2 vaccine. Three patients (8%) were classified with mild, 25 (73%) with moderate, and 6 (17%) with severe SARS-CoV-2 infection. Thirty-two (94%) patients received 5 doses of remdesivir and two patients received 2 doses. The median time between symptom onset to remdesivir treatment was 5 days (IQR 3-8.5). The median days of hospitalization were 6 (IQR 2-112). gRNA was positive in all patients at baseline and after remdesivir. Five (15%) patients had negative sgRNA at baseline and 20 (59%) after receiving remdesivir. Patients presenting with negative sgRNA at baseline were discharged from hospital in ≤ 6 days without complications. Moreover, those with negative sgRNA after remdesivir therapy did not require ICU admission and had favorable outcomes. Nevertheless, patients with positive sgRNA after antiviral treatment presented worse outcomes, with 47% requiring ICU admission and the three (9%) recorded deaths in the study were in this group.

CONCLUSIONS

Based on these data, we hypothesize that sgRNA may have clinical utility to help monitor virologic response more accurately than gRNA in KTR who receive remdesivir. Moreover, patients with negative sgRNA at baseline may not require antiviral treatment and others presenting positive sgRNA at day 5 could benefit from prolonged or combined therapies.

SARS-CoV-2 diagnosis in saliva samples: Usefulness and limitations

Saliva samples are important for diagnosis, because they are noninvasive and easy to acquire. The objective of this cross-sectional study was to investigate the value saliva samples have in detecting SARS-CoV-2 in comparison to nasal swabs and a new system named CovidCheck. A standard methodology identified the virus in 185 nasopharyngeal swabs and saliva samples revealing a sensitivity, specificity and positive and negative predictive values of 82,100,100 and 94.67%, respectively for saliva samples. Viral presence in saliva samples with the standard methodology in comparison to the CovidCheck system was evaluated in 67 samples with sensitivity, specificity and positive and negative predictive values of 68, 81, 68 and 81%, respectively. In conclusion, our results highlight the usefulness saliva samples have in detecting respiratory viral infections. However, presence of viral inhibitors and viral load in saliva, and the patient's clinical status should be considered as they might affect amplifying systems results.

Soft interface confined DNA walker for sensitive and specific detection of SARS-CoV-2 variants

Nucleic acid detection is conducive to preventing the spread of COVID-19 pandemic. In this work, we successfully designed a soft interface confined DNA walker by anchoring hairpin reporter probes on cell membranes for the detection of SARS-CoV-2 variants. In the presence of target RNA, the cyclic self-assembly reaction occurred between hairpin probes H1 and H2, and the continuous walking of target RNA on cell membranes led to the gradual amplification of fluorescence signal. The enrichment of H1 on membranes and the unique fluidity of membranes promoted the collision efficiency between DNA strands in the reaction process, endowing this method with high sensitivity. In addition, the double-blind test of synthetic RNA in 5% normal human serum demonstrated the good stability and anti-interference in complex environment of this method, which exhibited great potential in clinical diagnostics.

Identifying SARS-CoV-2 Variants Using Single-Molecule Conductance Measurements

The global COVID-19 pandemic has highlighted the need for rapid, reliable, and efficient detection of biological agents and the necessity of tracking changes in genetic material as new SARS-CoV-2 variants emerge. Here, we demonstrate that RNA-based, single-molecule conductance experiments can be used to identify specific variants of SARS-CoV-2. To this end, we (i) select target sequences of interest for specific variants, (ii) utilize single-molecule break junction measurements to obtain conductance histograms for each sequence and its potential mutations, and (iii) employ the XGBoost machine learning classifier to rapidly identify the presence of target molecules in solution with a limited number of conductance traces. This approach allows high-specificity and high-sensitivity detection of RNA target sequences less than 20 base pairs in length by utilizing a complementary DNA probe capable of binding to the specific target. We use this approach to directly detect SARS-CoV-2 variants of concerns B.1.1.7 (Alpha), B.1.351 (Beta), B.1.617.2 (Delta), and B.1.1.529 (Omicron) and further demonstrate that the specific sequence conductance is sensitive to nucleotide mismatches, thus broadening the identification capabilities of the system. Thus, our experimental methodology detects specific SARS-CoV-2 variants, as well as recognizes the emergence of new variants as they arise.

Exploring the Potential of Muridae as Sentinels for Human and Zoonotic Viruses

In recent years, the transmission of viruses from wildlife to humans has raised significant public health concerns, exemplified by the COVID-19 pandemic caused by the betacoronavirus SARS-CoV-2. Human activities play a substantial role in increasing the risk of zoonotic virus transmission from wildlife to humans. Rats and mice are prevalent in urban environments and may act as reservoirs for various pathogens. This study aimed to evaluate the presence of zoonotic viruses in wild rats and mice in both urban and rural areas, focusing on well-known zoonotic viruses such as betacoronavirus, hantavirus, arenavirus, kobuvirus, and monkeypox virus, along with other viruses occasionally detected in rats and mice, including rotavirus, norovirus, and astrovirus, which are known to infect humans at a high rate. A total of 128 animals were captured, including 70 brown rats (Rattus norvegicus), 45 black rats (Rattus rattus), and 13 house mice (Mus musculus), and feces, lung, and liver were collected. Among brown rats, one fecal sample tested positive for astrovirus RNA. Nucleotide sequencing revealed high sequence similarity to both human and rat astrovirus, suggesting co-presence of these viruses in the feces. Murine kobuvirus (MuKV) was detected in fecal samples from both black (n = 7) and brown (n = 6) rats, primarily from urban areas, as confirmed by sequence analysis. These findings highlight the importance of surveillance and research to understand and mitigate the risks associated with the potential transmission of pathogens by rodents.

Association of symptomatic upper respiratory tract infections with the alteration of the oropharyngeal microbiome in a cohort of school children in Côte d'Ivoire

Introduction

The oropharyngeal microbiome plays an important role in protection against infectious agents when in balance. Despite use of vaccines and antibiotic therapy to prevent respiratory tract infections, they remain one of the major causes of mortality and morbidity in Low- and middle-income countries. Hence the need to explore other approaches to prevention by identifying microbial biomarkers that could be leveraged to modify the microbiota in order to enhance protection against pathogenic bacteria. The aim of this study was to analyze the oropharyngeal microbiome (OPM) of schoolchildren in Côte d'Ivoire presenting symptoms of upper respiratory tract infections (URTI) for better prevention strategy.

Methods

Primary schools' children in Korhogo (n = 37) and Abidjan (n = 39) were followed for six months with monthly oropharyngeal sampling. Clinical diagnostic of URT infection was performed and nucleic acid extracted from oropharyngeal swabs were used for 16S rRNA metagenomic analysis and RT-PCR.

Results

The clinical examination of children's throat in Abidjan and Korhogo identified respectively 17 (43.59%) and 15 (40.54%) participants with visible symptoms of URTIs, with 26 episodes of infection in Abidjan and 24 in Korhogo. Carriage of Haemophilus influenzae (12%), Streptococcus pneumoniae (6%) and SARS-CoV-2 (6%) was confirmed by PCR. A significant difference in alpha diversity was found between children colonized by S. pneumoniae and those that were not (p = 0.022). There was also a significant difference in alpha diversity between children colonised with H. influenzae and those who were not (p = 0.017). No significant difference was found for SARS-CoV-2. Sphingomonas, Ralstonia and Rothia were significantly enriched in non-carriers of S. pneumoniae; Actinobacillus was significantly enriched in non-carriers of H. influenzae; Actinobacillus and Porphyromonas were significantly enriched in non-carriers of SARS-CoV-2 (p < 0.001).

Discussion

Nearly 40% of children showed clinical symptoms of infection not related to geographical location. The OPM showed an imbalance during H. influenzae and S. pneumoniae carriage. This study provides a baseline understanding of microbiome markers in URTIs in children for future research, to develop targeted interventions aimed at restoring the microbial balance and reducing the symptoms associated with RTIs.

Single-cell-resolved interspecies comparison shows a shared inflammatory axis and a dominant neutrophil-endothelial program in severe COVID-19

A key issue for research on COVID-19 pathogenesis is the lack of biopsies from patients and of samples at the onset of infection. To overcome these hurdles, hamsters were shown to be useful models for studying this disease. Here, we further leverage the model to molecularly survey the disease progression from time-resolved single-cell RNA sequencing data collected from healthy and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected Syrian and Roborovski hamster lungs. We compare our data to human COVID-19 studies, including bronchoalveolar lavage, nasal swab, and postmortem lung tissue, and identify a shared axis of inflammation dominated by macrophages, neutrophils, and endothelial cells, which we show to be transient in Syrian and terminal in Roborovski hamsters. Our data suggest that, following SARS-CoV-2 infection, commitment to a type 1- or type 3-biased immunity determines moderate versus severe COVID-19 outcomes, respectively.

Performance of two rapid antigen tests against SARS-CoV-2 in neighborhoods of socioeconomic vulnerability from a middle-income country

BACKGROUND

As new and improved antigen-detecting rapid diagnostic tests for SARS-CoV-2 infection (Ag-RDT) continue to be developed, assessing their diagnostic performance is necessary to increase test options with accurate and rapid diagnostic capacity especially in resource-constrained settings. This study aimed to assess the performance of two Ag-RDTs in a population-based study.

METHODS

We conducted a diagnostic accuracy study in neighborhoods with high socioeconomic vulnerability in Salvador-Brazil, including individuals aged ≥12 years old who attended primary health services, between July and December 2022, with COVID-19 symptoms or who had been in contact with a confirmed case. Two Ag-RDTs were compared in parallel using reverse transcription polymerase chain reaction (RT-PCR) as reference standard, the PanbioTM COVID-19 Ag test (Abbott®) and Immuno-Rapid COVID-19 Ag (WAMA Diagnostic®). Sensitivity, specificity, positive (PPV) and negative predictive values (NPV) were calculated.

RESULTS

For the Abbott test the sensitivity was 52.7% (95% CI: 44.3% - 61.0%), specificity 100% (95% CI: 98.7% - 100%), PPV 100% (95% CI: 95.4% - 100%) and NPV 80.4% (95% CI: 75.9% - 84.4%). For the WAMA test, the sensitivity was 53.4% (95% CI: 45.0% - 61.6%), specificity 100% (95% CI: 98.7% - 100%), PPV 100% (95% CI: 95.4% - 100%) and NPV 80.7% (95% CI: 76.2% - 84.6%). Sensitivity for the group with Cycle Threshold (CT) <24 was 82.3% (95%CI: 72.1-90.0, n = 83) for PanbioTM COVID-19 Ag test and 87.3% (95%CI: 77.9-93.8, n = 83) for Immuno-Rapid COVID-19 Ag test.

CONCLUSION

Sensitivity for both Ag-RDT was lower than reported by manufacturers. In the stratified analysis, sensitivity was higher among those with lower CT values <24. Specificity was high for both rapid antigen tests. Both Ag-RDT showed to be useful for rapid diagnostic of potential cases of COVID-19. Negative results must be assessed carefully according to clinical and epidemiological information.

Lung Disease Detection Using U-Net Feature Extractor Cascaded by Graph Convolutional Network

Computed tomography (CT) scans have recently emerged as a major technique for the fast diagnosis of lung diseases via image classification techniques. In this study, we propose a method for the diagnosis of COVID-19 disease with improved accuracy by utilizing graph convolutional networks (GCN) at various layer formations and kernel sizes to extract features from CT scan images. We apply a U-Net model to aid in segmentation and feature extraction. In contrast with previous research retrieving deep features from convolutional filters and pooling layers, which fail to fully consider the spatial connectivity of the nodes, we employ GCNs for classification and prediction to capture spatial connectivity patterns, which provides a significant association benefit. We handle the extracted deep features to form an adjacency matrix that contains a graph structure and pass it to a GCN along with the original image graph and the largest kernel graph. We combine these graphs to form one block of the graph input and then pass it through a GCN with an additional dropout layer to avoid overfitting. Our findings show that the suggested framework, called the feature-extracted graph convolutional network (FGCN), performs better in identifying lung diseases compared to recently proposed deep learning architectures that are not based on graph representations. The proposed model also outperforms a variety of transfer learning models commonly used for medical diagnosis tasks, highlighting the abstraction potential of the graph representation over traditional methods.

Detection of co-infection and recombination cases with Omicron and local Delta variants of SARS-CoV-2 in Vietnam

The first nationwide outbreak of COVID-19 in Vietnam started in late April 2021 and was caused almost exclusively by a single Delta lineage, AY.57. In early 2022, multiple Omicron variants co-circulated with Delta variants and quickly became dominant. The co-circulation of Delta and Omicron happened leading to possibility of co-infection and recombination events which can be revealed by viral genomic data. From January to October 2022, a total of 1028 viral RNA samples out of 4852 positive samples (Ct < 30) were sequenced by the long pooled amplicons method on Illumina platforms. All sequencing data was analysed by the workflow for SARS-CoV-2 on CLC genomics workbench and Illumina Dragen Covid application. Among those sequenced samples, we detected a case of Delta AY.57/Omicron BA.1 co-infection and two cases of infection with Delta AY.57/Omicron BA.2 recombinants which were nearly identical and had different epidemiological characteristics. Since the AY.57 lineage circulated almost exclusively in Vietnam, these results strongly suggest domestic events of co-infection and recombination. These findings highlight the strengths of genomic surveillance in monitoring the circulating variants in the community enabling rapid identification of viral changes that may affect viral properties and evolutionary events.

KCL TEST: an open-source inspired asymptomatic SARS-CoV-2 surveillance programme in an academic institution

Rapid and accessible testing was paramount in the management of the COVID-19 pandemic. Our university established KCL TEST: a SARS-CoV-2 asymptomatic testing programme that enabled sensitive and accessible PCR testing of SARS-CoV-2 RNA in saliva. Here, we describe our learnings and provide our blueprint for launching diagnostic laboratories, particularly in low-resource settings. Between December 2020 and July 2022, we performed 158277 PCRs for our staff, students, and their household contacts, free of charge. Our average turnaround time was 16 h and 37 min from user registration to result delivery. KCL TEST combined open-source automation and in-house non-commercial reagents, which allows for rapid implementation and repurposing. Importantly, our data parallel those of the UK Office for National Statistics, though we detected a lower positive rate and virtually no delta wave. Our observations strongly support regular asymptomatic community testing as an important measure for decreasing outbreaks and providing safe working spaces. Universities can therefore provide agile, resilient, and accurate testing that reflects the infection rate and trend of the general population. Our findings call for the early integration of academic institutions in pandemic preparedness, with capabilities to rapidly deploy highly skilled staff, as well as develop, test, and accommodate efficient low-cost pipelines.

Comparison of the diagnostic accuracy of the Pluslife Mini Dock RHAM technology with Abbott ID Now and Cepheid GenXpert: A retrospective evaluation study

Rapid and sensitive detection of pathogens is critical in interrupting the transmission chain of infectious diseases. Currently, real-time (RT-)PCR represents the gold standard for the detection of SARS-CoV-2. RNase HII-assisted amplification (RHAM) is a promising technology, enabling reliable point-of-care (PoC) testing; however, its diagnostic accuracy has not yet been investigated. The present study compared the Pluslife Mini Dock (RHAM technology), with Abbott ID Now and Cepheid GeneXpert IV. The positive percent agreement (PPA) and negative percent agreement (NPA) were determined in 100 SARS-CoV-2 positive and 210 SARS-CoV-2 negative samples. Further, the reliability of the Pluslife Mini Dock was investigated in different SARS-CoV-2 variants (Delta and Omicron subvariants). The PPA was 99.00% for Pluslife, 100.00% for Abbott ID Now, and 99.00% for Cepheid GeneXpert, with an NPA of 100.00%, 98.90%, and 93.72%, respectively. Abbott ID Now demonstrated the highest rate of invalid results. All SARS-CoV-2 analysed variants were detected by the Pluslife device. Altogether, the Pluslife Mini Dock demonstrated a PPA of 99.16% (235/237) for CT < 36 and an NPA of 100.00% (313/313), respectively. In conclusion, the Pluslife Mini Dock demonstrated better analytical performance than Abbott ID Now and Cepheid GeneXpert IV, representing a highly accurate and rapid PoC alternative to RT-PCR.

Prevalence of mental health symptoms and associated risk factors among healthcare workers in specialized COVID-19 hospitals in Anyang, China: A cross-sectional survey

Background

The novel coronavirus disease 2019 (COVID-19) pandemic spread worldwide and brought unprecedented challenges to healthcare systems. Healthcare workers experienced tremendous pressure and psychological issues.

Methods

A cross-sectional online survey was conducted from January 2022 to April 2022 among healthcare workers in Anyang, Henan Province, China. Insomnia, anxiety, depression, post-traumatic stress disorder (PTSD), and problematic internet use (PIU) were evaluated. Logistic regression analyses were used to explore the factors that were associated with mental health problems.

Results

A total of 242 participants (mean [SD] age, 34.7 [6.6] years, 187 female [77.3 %]) were included in the study. The prevalence of symptoms of insomnia, anxiety, depression, PTSD and PIU during the COVID-19 pandemic in China was 53.7 %, 100.0 %, 7.0 %, 20.3 %, and 19.4 %, respectively. Participants who smoked, used sedative-hypnotic drugs and may need psychological assistance were at a higher risk for mental health problems. Respondents who were older than 45 years and were married displayed a lower risk of insomnia and PTSD, respectively.

Conclusions

Mental health symptoms are pervasive among healthcare workers in specialized COVID-19 hospitals during the outbreak. Risk factors include smoking, sedative-hypnotic drug use, and the need for psychological assistance, while protective factors include age and marital status. Developing social media platforms and providing psychological assistance may be effective interventions for healthcare workers.

An alternative method for SARS-CoV-2 detection with use modified fluorescent in situ hybridization

The real-time reverse-transcriptase polymerase-chain-reaction (rRT-PCR) tests are the gold standard in detecting SARS-CoV-2 virus infection. However, despite high sensitivity and specificity, they have limitations that in some cases may result in false negative results. Therefore, it is reasonable to search for additional tools that could support microbiological diagnosis of SARS-CoV-2. The aim of the study was to develop a highly specific molecular test capable of detecting and visualizing SARS-CoV-2 infection. A universal probe and a set of 18 specific oligonucleotides with a FLAP sequence attached to them on both sides were designed to visualize SARS-CoV-2 virus infection based on the fluorescence in situ hybridization method (FISH). FISH conditions using the developed kit were standardized on the Vero CCL-81 cell line infected by SARS-CoV-2 virus. The method was tested on 290 nasopharyngeal swabs (collected in a doublet) from patients with clinical symptoms of SARS-CoV-2. Each one swab from the doublet was subjected to RNA isolation and amplification by rRT-PCR. From the second swab, a microscopic preparation was performed for FISH. The use of the rRT-PCR allowed obtaining 200 positive and 90 negative results, while our FISH method allowed for 220 positive results and 70 negative results. The differences obtained using both methods were statistically significant (p = 0.008). The obtained results support the use of FISH as an additional method in microbiological diagnostics of SARS-CoV-2.

Back to the future: the novel art of digital auscultation applied in a prospective observational study of critically ill Covid-19 patients

BACKGROUND

The Covid-19 pandemic has caused immense pressure on Intensive Care Units (ICU). In patients with severe ARDS due to Covid-19, respiratory mechanics are important for determining the severity of lung damage. Lung auscultation could not be used during the pandemic despite its merit. The main objective of this study was to investigate associations between lung auscultatory sound features and lung mechanical properties, length of stay (LOS) and survival, in adults with severe Covid-19 ARDS.

METHODS

Consecutive patients admitted to a large ICU between 2020 and 2021 (n = 173) were included. Digital stethoscopes obtained auscultatory sounds and stored them in an on-line database for replay and further processing using advanced AI techniques. Correlation and regression analysis explored relationships between digital auscultation findings and lung mechanics or the ICU outcome. The resulting annotated lung sounds database is also publicly available as supplementary material.

RESULTS

The presence of squawks was associated with the ICU LOS, outcome and 90-day mortality. Other features (age, SOFA score & oxygenation index upon admission, minimum crackle entropy) had significant impact on outcome. Additional features affecting the 90-d survival were age and mean crackle entropy. Multivariate logistic regression showed that survival was affected by age, baseline SOFA, baseline oxygenation index and minimum crackle entropy.

CONCLUSIONS

Respiratory mechanics were associated with various adventitious sounds, whereas the lung sound analytics and the presence of certain adventitious sounds correlated with the ICU outcome and the 90-d survival. Spectral features of crackles sounds can serve as prognostic factors for survival, highlighting the importance of digital auscultation.

Screening for SARS-CoV-2 and Other Coronaviruses in Urban Pigeons (Columbiformes) from the North of Spain under a 'One Health' Perspective

Coronaviruses have a major impact on human and animal health. The SARS-CoV-2, a beta coronavirus responsible for the COVID-19 pandemic, is a clear example. It continues circulating and causes human deaths, and its high replication rate results in numerous variants. Coronaviruses adapt to birds and mammals and constitute a serious threat, and new viruses are likely to emerge. Urban pigeons (Columbiformes) are synanthropic birds of great interest from a 'One Health' perspective, due to their interaction with humans and other animals. Aware that they may act as viral reservoirs and contribute to their spread, we aimed to investigate the possible presence of SARS-CoV-2 and other coronaviruses in Columbiformes in the city of Logroño, Spain. Oropharyngeal and cloacal swabs were tested using real-time (N1 and E genes from SARS-CoV-2) and conventional PCR assays (RdRp gene from all coronaviruses). SARS-CoV-2 was not detected. A total of 13.3% of pigeons harbored coronaviruses closely related to Gamma coronavirus (Igacovirus) from Columbiformes in Finland, Poland and China. Monitoring the emergence of a new variant of SARS-CoV-2 capable of infecting Columbiformes should continue. SARS-CoV-2 is still circulating, the viral RNA of this virus has been detected in avian species (Phasianidae and Anatidae), and other coronaviruses are associated with animals that are in close contact with humans. The presence of Gamma coronavirus in urban pigeons must be considered for the risk of surveillance of human infections.

Rapid Determination of SARS-CoV-2 Integrity and Infectivity by Using Propidium Monoazide Coupled with Digital Droplet PCR

SARS-CoV-2 is a highly infectious virus responsible for the COVID-19 pandemic. Therefore, it is important to assess the risk of SARS-CoV-2 infection, especially in persistently positive patients. Rapid discrimination between infectious and non-infectious viruses aids in determining whether prevention, control, and treatment measures are necessary. For this purpose, a method was developed and utilized involving a pre-treatment with 50 µM of propidium monoazide (PMAxx, a DNA intercalant) combined with a digital droplet PCR (ddPCR). The ddPCR method was performed on 40 nasopharyngeal swabs (NPSs) both before and after treatment with PMAxx, revealing a reduction in the viral load at a mean of 0.9 Log copies/mL (SD ± 0.6 Log copies/mL). Furthermore, six samples were stratified based on the Ct values of SARS-CoV-2 RNA (Ct < 20, 20 < Ct < 30, Ct > 30) and analyzed to compare the results obtained via a ddPCR with viral isolation and a negative-chain PCR. Of the five samples found positive via a ddPCR after the PMAxx treatment, two of the samples showed the highest post-treatment SARS-CoV-2 loads. The virus was isolated in vitro from both samples and the negative strand chains were detected. In three NPS samples, SARS CoV-2 was present post-treatment at a low level; it was not isolated in vitro, and, when detected, the strand was negative. Our results indicate that the established method is useful for determining whether the SARS-CoV-2 within positive NPS samples is intact and capable of causing infection.

Genetic diversity and spread dynamics of SARS-CoV-2 variants present in African populations

The dynamics of coronavirus disease-19 (COVID-19) have been extensively researched in many settings around the world, but little is known about these patterns in Africa. A total of 7540 complete nucleotide genomes from 51 African nations were obtained and analysed using the National Center for Biotechnology Information and Global Initiative on Sharing Influenza Data databases to examine the genetic diversity and spread dynamics of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineages circulating in Africa. Using various clade and lineage nomenclature schemes, we examined their diversity and used maximum parsimony inference methods to reconstruct the evolutionary hypotheses about the spread of the virus in Africa. According to this study, only 465 of the 2610 Pango lineages found to have existed in the world circulated in Africa three years after the COVID-19 pandemic, with five different lineages dominating at various points during the outbreak. We identified South Africa, Kenya and Nigeria as key sources of viral transmission among sub-Saharan African nations. These findings provide insights into the viral strains that circulate in Africa and their evolutionary patterns.

SARS-CoV-2 in Captive Nonhuman Primates, Spain, 2020-2023

We conducted a serologic and molecular study to assess exposure of captive nonhuman primates (NHPs) to SARS-CoV-2 in Spain during the 2020-2023 COVID-19 pandemic. We found limited exposure of NHPs to SARS-CoV-2. Biosafety measures must be strictly maintained to avoid SARS-CoV-2 reverse-zoonotic transmission in the human-NHP interface.

Zoom in: factors affecting vocal habits during online meetings, a prospective trial on 40 subjects

PURPOSE

To identify factors that influence vocal habits during online meetings (OMs).

METHODS

A prospective trial of forty participants without any known hearing or vocal cord disorders. Subjects participated in an OM divided into six randomly ordered sections, with alterations in audio/speaking equipment and language: the computer's speaker-microphone, a single earbud, two-earbuds or headphones; with/without video, native-language-speaking (Hebrew) versus second language-speaking (English). Each section included free speech, sustained phonation, and a standardized passage. Participants ranked their vocal-effort for each section. Three blinded raters independently scored the voice using the GRBAS scale, and acoustic analyses were performed.

RESULTS

No significant difference in self-reported vocal effort was demonstrated between sections. Second-language speaking resulted in significantly increased intensity (p < 0.0001), frequency (p = 0.015), GRBAS (p = 0.008), and strain (p < 0.0001) scores. Using the computer's speaker/microphone resulted in significantly higher strain (p < 0.0001). Using headphones, single or two earbuds resulted in lower intensity and a lower strain score. No differences were detected between OMs with or without video.

CONCLUSIONS

Using the computer's microphone/speaker or speaking in a second language during OMs, may result in vocal habits associated with vocal trauma.

Dynamic of SARS-CoV-2 variants circulation in Tunisian pediatric population, during successive waves, from March 2020 to September 2022

The emergence of SARS-CoV-2 variants has led to several cases among children. However, limited information is available from North African countries. This study describes the SARS-CoV-2 strains circulating in Tunisian pediatric population during successive waves. A total of 447 complete sequences were obtained from individuals aged from 13 days to 18 years, between March 2020 and September 2022: 369 sequences generated during this study and 78 ones, available in GISAID, previously obtained from Tunisian pediatric patients. These sequences were compared with 354 and 274 ones obtained from Tunisian adults and a global dataset, respectively. The variant circulation dynamics of predominant variants were investigated during the study period using maximum-likelihood phylogenetic analysis. Among the studied population, adolescents were the predominant age group, comprising 55.26% of cases. Twenty-three lineages were identified; seven of which were not previously reported in Tunisia. Phylogenetic analysis showed a close relationship between the sequences from Tunisian adults and children. The connections of sequences from other countries were variable according to variants: close relationships were observed for Alpha, B1.160 and Omicron variants, while independent Tunisian clusters were observed for Delta and B.1.177 lineages. These findings highlight the pivotal role of children in virus transmission and underscore the impact of vaccination on virus spread. Vaccination of children, with booster doses, may be considered for better management of future emergences.

Rapid and accurate SERS assay of disease-related nucleic acids based on isothermal cascade signal amplifications of CRISPR/Cas13a system and catalytic hairpin assembly

Developing rapid, accurate and convenient nucleic acid diagnostic techniques is essential for the prevention and control of contagious diseases that are prone to gene mutations and may have homologous sequences, especially emerging infectious diseases such as the SARS-CoV-2 pandemic. Herein, a one-pot SERS assay integrating isothermal cascade signal amplification strategy (i.e., CRISPR/Cas13a system (Cas13a) and catalytic hairpin assembly (CHA), Cas13a-CHA) and SERS-active silver nanorods (AgNRs) sensing chips was proposed for rapid and accurate detection of disease-related nucleic acids. Taking SARS-CoV-2 RNA assay as a model, the Cas13a-CHA based SERS sensing strategy can achieve ultra-high sensitivity low to 5.18 × 102 copies·mL-1 within 60 min, and excellent specificity, i.e., not only the ability to identify SARS-CoV-2 RNA from gene mutations, but also incompatibility with coronaviruses such as severe acute respiratory syndrome (SARS-CoV), Middle East respiratory syndrome (MERS-CoV), and other respiratory viruses. The proposed Cas13a-CHA based SERS assay for SARS-CoV-2 RNA has satisfactory sensitivity, specificity, uniformity, and repeatability, and can be easily expanded and universalized for screening different viruses, which is expected to promise as a crucial role for diagnosis of disease-related nucleic acids in various medical application scenarios.

RT-qPCR investigation of post-mortem tissues during COVID-19

In 2020, there were numerous cases in Kazakhstan with clinical symptoms of COVID-19 but negative PCR results in nasopharyngeal and oropharyngeal swabs. The diagnosis was confirmed clinically and by CT scans (computed tomography). The problem with such negative PCR results for SARS-CoV-2 infection confirmation still exists and indicates the need to confirm the diagnosis in the bronchoalveolar lavage in such cases. There is also a lack of information about confirmation of SARS-CoV-2 infection in deceased patients. In this study, various tissue materials, including lungs, bronchi, and trachea, were examined from eight patients who died, presumably from SARS-CoV-2 infection, between 2020 and 2022. Naso/oropharyngeal swabs taken from these patients in hospitals tested PCR negative for SARS-CoV-2. This study presents a modified RNA isolation method based on a comparison of the most used methods for RNA isolation in laboratories: QIAamp Viral RNA Mini Kit and TRIzol-based method. This modified nucleic acid extraction protocol can be used to confirm SARS-CoV-2 infection by RT-qPCR in the tissues of deceased patients in disputed cases. RT-qPCR with RNA of SARS-CoV-2 re-extracted with such method from post-mortem tissues that were stored at -80 °C for more than 32 months still demonstrated high-yielding positive results.

Development of a highly stable, active small interfering RNA with broad activity against SARS-CoV viruses

Treatment options for COVID-19 remain limited. Here, we report the optimization of an siRNA targeting the highly conserved leader region of SARS-CoV-2. The siRNA was rendered nuclease resistant by the introduction of modified nucleotides without loss of activity. Importantly, the siRNA also retained its inhibitory activity against the emerged omicron sublineage variant BA.2, which occurred after the siRNA was designed and is resistant to other antiviral agents such as antibodies. In addition, we show that a second highly active siRNA designed against the viral 5'-UTR can be applied as a rescue molecule, to minimize the spread of escape mutations. We therefore consider our siRNA-based molecules to be promising broadly active candidates for the treatment of current and future SARS-CoV-2 variants.

Digital Sort-Enabled Counting Allows Absolute Electrical Quantification of Target Nucleic Acid

Quantitative nucleic acid amplification tests are of great importance for diagnostics, but current approaches require complex and costly optical setups that limit their nonlaboratory applications. Herein we describe the implementation of a microfluidics platform that can perform binary DNA-amplification-activated droplet sorting. The digital sort-enabled counting (DISCO) platform enables label-free absolute quantification of the nucleic acid. This is achieved by provoking a pH change in droplets through a loop-mediated isothermal amplification (LAMP) reaction, followed by using sorting by interfacial tension (SIFT) to direct positive and negative droplets to different outlets. With the use of on-chip electrodes at both outlets, we demonstrate that the digital electrical counting of target DNA and RNA can be realized. DISCO is a promising approach for realizing sensitive nucleic acid quantification in point-of-care settings.

Assessment of handwashing impact on detection of SARS-CoV-2, Staphylococcus aureus, Escherichia coli on hands in rural and urban settings of Côte d'Ivoire during COVID-19 pandemic

BACKGROUND

Handwashing is the first line of hygiene measures and one of the oldest methods of preventing the spread of infectious diseases. Despite its efficacy in the health system, handwashing is often inadequately practiced by populations. This study aimed to assess the presence of SARS-CoV-2, Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus) on hands as indicators of lack of hand hygiene during COVID 19 pandemic.

METHODS

A cross-sectional study was conducted in rural Taabo and urban Abidjan (Côte d'Ivoire) from January to September 2021. A total of 384 participants from 384 households were included in the study. The total households were distributed proportionally within various municipalities in the two study areas according to the number of households in each municipality, based on data of the National Institute of Statistics from the 2014 general population census. Hand swabbing of the 384 participants within households (320 in Abidjan and 64 in Taabo) was performed for the enumeration of E. coli and S aureus, using laboratory standard method and for the detection of SARS-CoV-2 by RT-qPCR. A binary logistic regression model was built with the outcome variable presence of Staphylococcus spp. on hands of respondents that was categorized into binary variables, Staphylococcus spp. (1 = presence, 0 = absence) for the Risk Ratio estimation. Place of living, sex, handwashing, education and age group were used to adjust the model to observe the effects of these explanatory variables.

RESULTS

No presence of SARS-CoV-2 virus was detected on the hands of respondents in both sites. However, in urban Abidjan, only Staphylococcus spp. (Coagulase Negative Staphylococci) was found on the hands of 233 (72.8%, 95%CI: 67.7-77.4) respondents with the average load of 0.56 CFU/ Cm2 (95% CI, 0.52-0.60). Meanwhile, in rural Taabo, Staphylococcus spp. (Coagulase Negative Staphylococci) and E. coli were found on the hands of 40 (62.5%, 95%CI: 50.3-73.3) and 7 (10.9%, 95%CI: 5.4-20.9) respondents with the respective average load of 0.49 CFU/ Cm2 (95% CI, 0.39-0.59) and 0.08 CFU/ Cm2 (95% CI, 0.03-0.18). Participants living in rural Taabo were less likely to have Staphylococcus spp. on their hands (RR = 0.811; 95%IC: 0.661-0.995) compared to those living in urban Abidjan.

CONCLUSIONS

No SARS-CoV-2 was detected on the hands of participants in both sites, suggesting that our study did not show direct transmission through hands. No E. coli was found in urban Abidjan while E. coli was found on the hands of participants in rural Taabo indicating poor hand washing and disinfection practices in rural Taabo. Living in urban Abidjan is statistically associated to having Staphylococcus spp. on hands. Further studies are necessary especially to understand to what extent the presence of Staphylococcus spp. on hands indicates a higher infection or fecal colonization rates in the case of E. coli.

Correlation between unproven therapies and delayed return-to-work for COVID-19-infected healthcare workers

The objective of this study is to investigate factors influencing the time to return to work (RTW) of HealthCare Workers (HCW) infected with COVID-19 during the initial wave of the pandemic in a southern French university hospital. Data collection of 170 HCW (between March 16 to June 1, 2020) included demographic and professional information, clinical profiles, comorbidities, medical management, therapies and RT-PCR results. The mean time to RTW was 15.6 days. Multivariate analyses revealed that the time to RTW was shorter among laboratory and emergency workers, while it was longer for HCW aged 40 to 49 years, at higher risk of severe illness, with a delayed negative SARS-CoV-2 PCR or those treated with azithromycin and/or hydroxychloroquine. This study highlights diverse factors affecting HCW RTW post-COVID-19 infection, underscoring the importance of exercising caution in administering unproven therapies to HCW during the early stages of a novel infectious pandemic.

Kinetics of SARS-CoV-2 Viral Load in Hospitalized Patients

The rapid and accurate detection of infectious people is crucial in controlling outbreaks. The aim of this study was to evaluate the kinetics of the viral load expressed as Ct in COVID-19 hospitalized patients. Nasopharyngeal swab specimens were collected for RT-PCR testing. Forty-one subjects were recruited, of which 48.8% developed severe symptoms and 51.2% showed milder symptoms. The distribution of Ct values measured from the symptom onset showed that the kinetics of the viral load decreased with increasing time. A Ct of 25 (high viral load) was reached after a mean of 9.9 ± 4.8 days from the symptom onset, without a significant difference between patients with severe (10.9 ± 5.7 days) and milder (9.0 ± 3.9 days) symptoms. In 65.8% of cases, a high viral load was maintained for more than 7 days from the symptom onset, especially in patients with severe symptoms (70.6%). A Ct of 30 (moderate viral load) and of 38 (low viral load) were reached after a mean of 16.1 ± 8.1 and 28.5 ± 22.4 days from the symptom onset, respectively, with a significant difference between patients with severe (Ct = 30:17.9 ± 9.8 days; Ct = 38:34.6 ± 29.6 days) and milder (Ct = 30:14.3 ± 5.8 days; Ct = 38:22.7 ± 9.9 days) symptoms. These results provide an understanding of the viral kinetics of SARS-CoV-2 and have implications for pandemic control strategies and practices.

Genomic Context of SARS-CoV-2 Outbreaks in Farmed Mink in Spain during Pandemic: Unveiling Host Adaptation Mechanisms

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infects various mammalian species, with farmed minks experiencing the highest number of outbreaks. In Spain, we analyzed 67 whole genome sequences and eight spike sequences from 18 outbreaks, identifying four distinct lineages: B.1, B.1.177, B.1.1.7, and AY.98.1. The potential risk of transmission to humans raises crucial questions about mutation accumulation and its impact on viral fitness. Sequencing revealed numerous not-lineage-defining mutations, suggesting a cumulative mutation process during the outbreaks. We observed that the outbreaks were predominantly associated with different groups of mutations rather than specific lineages. This clustering pattern by the outbreaks could be attributed to the rapid accumulation of mutations, particularly in the ORF1a polyprotein and in the spike protein. Notably, the mutations G37E in NSP9, a potential host marker, and S486L in NSP13 were detected. Spike protein mutations may enhance SARS-CoV-2 adaptability by influencing trimer stability and binding to mink receptors. These findings provide valuable insights into mink coronavirus genetics, highlighting both host markers and viral transmission dynamics within communities.

Multiplexed detection of eight respiratory viruses based on nanozyme colorimetric microfluidic immunoassay

Pandemics caused by respiratory viruses, such as the SARS-CoV-1/2, influenza virus, and respiratory syncytial virus, have resulted in serious consequences to humans and a large number of deaths. The detection of such respiratory viruses in the early stages of infection can help control diseases by preventing the spread of viruses. However, the diversity of respiratory virus species and subtypes, their rapid antigenic mutations, and the limited viral release during the early stages of infection pose challenges to their detection. This work reports a multiplexed microfluidic immunoassay chip for simultaneous detection of eight respiratory viruses with noticeable infection population, namely, influenza A virus, influenza B virus, respiratory syncytial virus, SARS-CoV-2, human bocavirus, human metapneumovirus, adenovirus, and human parainfluenza viruses. The nanomaterial of the nanozyme (Au@Pt nanoparticles) was optimized to improve labeling efficiency and enhance the detection sensitivity significantly. Nanozyme-binding antibodies were used to detect viral proteins with a limit of detection of 0.1 pg/mL with the naked eye and a microplate reader within 40 min. Furthermore, specific antibodies were screened against the conserved proteins of each virus in the immunoassay, and the clinical sample detection showed high specificity without cross reactivity among the eight pathogens. In addition, the microfluidic chip immunoassay showed high accuracy, as compared with the RT-PCR assay for clinical sample detection, with 97.2%/94.3% positive/negative coincidence rates. This proposed approach thus provides a convenient, rapid, and sensitive method for simultaneous detection of eight respiratory viruses, which is meaningful for the early diagnosis of viral infections. Significantly, it can be widely used to detect pathogens and biomarkers by replacing only the antigen-specific antibodies.

Accelerated diagnosis: a crosslinking catalytic hairpin assembly system for rapid and sensitive SARS-CoV-2 RNA detection

The COVID-19 pandemic has underscored the urgent need for rapid and reliable strategies for early detection of SARS-CoV-2. In this study, we propose a DNA nanosphere-based crosslinking catalytic hairpin assembly (CCHA) system for the rapid and sensitive SARS-CoV-2 RNA detection. The CCHA system employs two DNA nanospheres functionalized with catalytic hairpin assembly (CHA) hairpins. The presence of target SARS-CoV-2 RNA initiated the crosslinking of DNA nanospheres via CHA process, leading to the amplification of fluorescence signals. As a result, the speed of SARS-CoV-2 diagnosis was enhanced by significantly increasing the local concentration of the reagents in a crosslinked DNA product, leading to a detection limit of 363 fM within 5 min. The robustness of this system has been validated in complex environments, such as fetal bovine serum and saliva. Hence, the proposed CCHA system offers an efficient and simple approach for rapid detection of SARS-CoV-2 RNA, holding substantial promise for enhancing COVID-19 diagnosis.

Exposure to urban particulate matter alters responses of olfactory mucosal cells to SARS-CoV-2 infection

Respiratory viruses have a significant impact on health, as highlighted by the COVID-19 pandemic. Exposure to air pollution can contribute to viral susceptibility and be associated with severe outcomes, as suggested by recent epidemiological studies. Furthermore, exposure to particulate matter (PM), an important constituent of air pollution, is linked to adverse effects on the brain, including cognitive decline and Alzheimer's disease (AD). The olfactory mucosa (OM), a tissue located at the rooftop of the nasal cavity, is directly exposed to inhaled air and in direct contact with the brain. Increasing evidence of OM dysfunction related to neuropathogenesis and viral infection demonstrates the importance of elucidating the interplay between viruses and air pollutants at the OM. This study examined the effects of subacute exposure to urban PM 0.2 and PM 10-2.5 on SARS-CoV-2 infection using primary human OM cells obtained from cognitively healthy individuals and individuals diagnosed with AD. OM cells were exposed to PM and subsequently infected with the SARS-CoV-2 virus in the presence of pollutants. SARS-CoV-2 entry receptors and replication, toxicological endpoints, cytokine release, oxidative stress markers, and amyloid beta levels were measured. Exposure to PM did not enhance the expression of viral entry receptors or cellular viral load in human OM cells. However, PM-exposed and SARS-CoV-2-infected cells showed alterations in cellular and immune responses when compared to cells infected only with the virus or pollutants. These changes are highly pronounced in AD OM cells. These results suggest that exposure of human OM cells to PM does not increase susceptibility to SARS-CoV-2 infection in vitro, but it can alter cellular immune responses to the virus, particularly in AD. Understanding the interplay of air pollutants and COVID-19 can provide important insight for the development of public health policies and interventions to reduce the negative influences of air pollution exposure.

A measles-vectored vaccine candidate expressing prefusion-stabilized SARS-CoV-2 spike protein brought to phase I/II clinical trials: candidate selection in a preclinical murine model

In the early COVID-19 pandemic with urgent need for countermeasures, we aimed at developing a replicating viral vaccine using the highly efficacious measles vaccine as vector, a promising technology with prior clinical proof of concept. Building on our successful pre-clinical development of a measles virus (MV)-based vaccine candidate against the related SARS-CoV, we evaluated several recombinant MV expressing codon-optimized SARS-CoV-2 spike glycoprotein. Candidate V591 expressing a prefusion-stabilized spike through introduction of two proline residues in HR1 hinge loop, together with deleted S1/S2 furin cleavage site and additional inactivation of the endoplasmic reticulum retrieval signal, was the most potent in eliciting neutralizing antibodies in mice. After single immunization, V591 induced similar neutralization titers as observed in sera of convalescent patients. The cellular immune response was confirmed to be Th1 skewed. V591 conferred long-lasting protection against SARS-CoV-2 challenge in a murine model with marked decrease in viral RNA load, absence of detectable infectious virus loads, and reduced lesions in the lungs. V591 was furthermore efficacious in an established non-human primate model of disease (see companion article [S. Nambulli, N. Escriou, L. J. Rennick, M. J. Demers, N. L. Tilston-Lunel et al., J Virol 98:e01762-23, 2024, https://doi.org/10.1128/jvi.01762-23]). Thus, V591 was taken forward into phase I/II clinical trials in August 2020. Unexpected low immunogenicity in humans (O. Launay, C. Artaud, M. Lachâtre, M. Ait-Ahmed, J. Klein et al., eBioMedicine 75:103810, 2022, https://doi.org/10.1016/j.ebiom.2021.103810) revealed that the underlying mechanisms for resistance or sensitivity to pre-existing anti-measles immunity are not yet understood. Different hypotheses are discussed here, which will be important to investigate for further development of the measles-vectored vaccine platform.IMPORTANCESARS-CoV-2 emerged at the end of 2019 and rapidly spread worldwide causing the COVID-19 pandemic that urgently called for vaccines. We developed a vaccine candidate using the highly efficacious measles vaccine as vector, a technology which has proved highly promising in clinical trials for other pathogens. We report here and in the companion article by Nambulli et al. (J Virol 98:e01762-23, 2024, https://doi.org/10.1128/jvi.01762-23) the design, selection, and preclinical efficacy of the V591 vaccine candidate that was moved into clinical development in August 2020, 7 months after the identification of SARS-CoV-2 in Wuhan. These unique in-human trials of a measles vector-based COVID-19 vaccine revealed insufficient immunogenicity, which may be the consequence of previous exposure to the pediatric measles vaccine. The three studies together in mice, primates, and humans provide a unique insight into the measles-vectored vaccine platform, raising potential limitations of surrogate preclinical models and calling for further refinement of the platform.

Evaluations of modes of pooling specimens for COVID-19 screened by quantitative PCR and droplet digital PCR

Though pooling samples for SARS-CoV-2 detection has effectively met the need for rapid diagnostic and screening tests, many factors can influence the sensitivity of a pooled test. In this study, we conducted a simulation experiment to evaluate modes of pooling specimens and aimed at formulating an optimal pooling strategy. We focussed on the type of swab, their solvent adsorption ability, pool size, pooling volume, and different factors affecting the quality of preserving RNA by different virus solutions. Both quantitative PCR and digital PCR were used to evaluate the sampling performance. In addition, we determined the detection limit by sampling which is simulated from the virus of different titers and evaluated the effect of sample-storage conditions by determining the viral load after storage. We found that flocked swabs were better than fibre swabs. The RNA-preserving ability of the non-inactivating virus solution was slightly better than that of the inactivating virus solution. The optimal pooling strategy was a pool size of 10 samples in a total volume of 9 mL. Storing the collected samples at 4 °C or 25 °C for up to 48 h had little effect on the detection sensitivity. Further, we observed that our optimal pooling strategy performed equally well as the single-tube test did. In clinical applications, we recommend adopting this pooling strategy for low-risk populations to improve screening efficiency and shape future strategies for detecting and managing other respiratory pathogens, thus contributing to preparedness for future public health challenges.

The potential of tailed amplicons for SARS-CoV-2 detection in Nucleic Acid Lateral Flow Assays

Nucleic Acid Lateral Flow Assays (NALFAs) are a promising solution for the point-of-care detection of viruses like SARS-CoV-2. However, they show some drawbacks, such as the great dependency on the use of antibodies and the need for post-amplification protocols that enable the preparation of amplicons for effective readings, as well as low sensitivity. Here, we developed amplicons of a specific SARS-CoV-2 gene tailed with single-strand DNA (ssDNA) sequences to hybridize with DNA probes immobilized on the NALFA strips, thus overcoming the aforementioned problems. Results have shown that tailed primers have not compromised the amplification efficiency and allowed the correct detection of the amplicons in the lateral flow strip. This approach has presented a limit of detection (LOD) of 25 RNA copies /reaction mix (1 copy/μL) and the test of cross-reactivity with other related viruses has not shown any cross-reactivity. Twenty clinical samples were evaluated by NALFA and simultaneously compared with the gold standard RT-qPCR protocol, originating equal results. Although the number of clinical specimens tested being relatively small, this indicates a sensitivity and specificity both of 100%. In short, an alternative NALFA was successfully implemented, rendering an accurate route for SARS-CoV-2 diagnosis, compatible with low-resource settings.

Development and evaluation of a lyophilization protocol for colorimetric RT-LAMP diagnostic assay for COVID-19

Molecular diagnostics involving nucleic acids (DNA and RNA) are regarded as extremely functional tools. During the 2020 global health crisis, efforts intensified to optimize the production and delivery of molecular diagnostic kits for detecting SARS-CoV-2. During this period, RT-LAMP emerged as a significant focus. However, the thermolability of the reagents used in this technique necessitates special low-temperature infrastructure for transport, storage, and conservation. These requirements limit distribution capacity and necessitate cost-increasing adaptations. Consequently, this report details the development of a lyophilization protocol for reagents in a colorimetric RT-LAMP diagnostic kit to detect SARS-CoV-2, facilitating room-temperature transport and storage. We conducted tests to identify the ideal excipients that maintain the molecular integrity of the reagents and ensure their stability during room-temperature storage and transport. The optimal condition identified involved adding 5% PEG 8000 and 75 mM trehalose to the RT-LAMP reaction, which enabled stability at room temperature for up to 28 days and yielded an analytical and diagnostic sensitivity and specificity of 83.33% and 90%, respectively, for detecting SARS-CoV-2. This study presents the results of a lyophilized colorimetric RT-LAMP COVID-19 detection assay with diagnostic sensitivity and specificity comparable to RT-qPCR, particularly in samples with high viral load.

Droplet Digital RT-PCR (dd RT-PCR) Detection of SARS-CoV-2 in Honey Bees and Honey Collected in Apiaries across the Campania Region

Coronaviruses (CoVs), a subfamily of Orthocoronavirinae, are viruses that sometimes present a zoonotic character. Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is responsible for the recent outbreak of COVID-19, which, since its outbreak in 2019, has caused about 774,593,066 confirmed cases and 7,028,881 deaths. Aereosols are the main route of transmission among people; however, viral droplets can contaminate surfaces and fomites as well as particulate matter (PM) in suspensions of natural and human origin. Honey bees are well known bioindicators of the presence of pollutants and PMs in the environment as they can collect a great variety of substances during their foraging activities. The aim of this study was to evaluate the possible role of honey bees as bioindicators of the prevalence SARS-CoV-2. In this regard, 91 samples of honey bees and 6 of honey were collected from different apiaries of Campania region (Southern Italy) in four time periods from September 2020 to June 2022 and were analyzed with Droplet Digital RT-PCR for SARS-CoV-2 target genes Orf1b and N. The screening revealed the presence of SARS-CoV-2 in 12/91 in honey bee samples and in 2/6 honey samples. These results suggest that honey bees could also be used as indicators of outbreaks of airborne pathogens such as SARS-CoV-2.

Quality assurance of SARS-CoV-2 testing laboratories during the pandemic period in India - An experience from a designated provider laboratory

PURPOSE

Indian Council of Medical Research (ICMR) initiated an Inter-Laboratory Quality Control testing (ILQC) program for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) testing. Under this program, SARS-CoV-2 testing laboratories across the country submit specimens to the assigned State Quality Control (SQCs) laboratories for ILQC testing. This study aimed to investigate the performance of public and private SARS-CoV-2 testing laboratories in Delhi and highlights the country's effort in ramping up testing facility with close monitoring of the quality of Covid-19 testing results.

METHODS

In the present study, two-years of SARS-CoV-2 testing data is included. During July 2020 through February 2022, a total of 1791 anonymised specimens were received from 56 public and private laboratories. These specimens were processed by reverse transcriptase - polymerase chain reaction (RT-PCR) tests as per National Institute of Virology (NIV) protocol and the results were uploaded on the ICMR quality control/quality assurance (QC/QA) portal without directly conveying the results to respective participating laboratories. This portal generated a final report stating concordance and intimate results to individual laboratories.

RESULTS

Among the 1791 specimens, 25 were rejected and the remaining 1766 were tested. Among these specimens 1691 (95.75%) revealed concordance, and 75 (4.24%) were discordant. A total of 29 laboratories had 100% concordance, 21 laboratories had over 90% concordance and six laboratories had over 80% concordance.

CONCLUSIONS

The study demonstrates that the establishment of an inter-laboratory comparison program for SARS-CoV-2 testing helped in monitoring quality of SARS-CoV-2 testing in the country.

Non-canonical CRISPR/Cas12a-based technology: A novel horizon for biosensing in nucleic acid detection

Nucleic acids are essential biomarkers in molecular diagnostics. The CRISPR/Cas system has been widely used for nucleic acid detection. Moreover, canonical CRISPR/Cas12a based biosensors can specifically recognize and cleave target DNA, as well as single-strand DNA serving as reporter probe, which have become a super star in recent years in the field of nucleic acid detection due to its high specificity, universal programmability and simple operation. However, canonical CRISPR/Cas12a based biosensors are hard to meet the requirements of higher sensitivity, higher specificity, higher efficiency, larger target scope, easier operation, multiplexing, low cost and diversified signal reading. Then, advanced non-canonical CRISPR/Cas12a based biosensors emerge. In this review, applications of non-canonical CRISPR/Cas12a-based biosensors in nucleic acid detection are summarized. And the principles, peculiarities, performances and perspectives of these non-canonical CRISPR/Cas12a based biosensors are also discussed.

SARS-CoV-2 wastewater surveillance at two university campuses: lessons learned and insights on intervention strategies for public health guidance

Wastewater surveillance has been a tool for public health officials throughout the COVID-19 pandemic. Universities established pandemic response committees to facilitate safe learning for students, faculty, and staff. These committees met to analyze both wastewater and clinical data to propose mitigation strategies to limit the spread of COVID-19. This paper reviews the initial efforts of utilizing campus data inclusive of wastewater surveillance for SARS-CoV-2 RNA concentrations, clinical case data from university response teams, and mitigation strategies from Grand Valley State University in West Michigan (population 21,648 students) and Oakland University in East Michigan (population 18,552 students) from November 2020 to April 2022. Wastewater positivity rates for both universities ranged from 32.8 to 46.8%. Peak viral signals for both universities directly corresponded to variant points of entry within the campus populations from 2021 to 2022. It was found that the organization of clinical case data and variability of wastewater testing data were large barriers for both universities to effectively understand disease dynamics within the university population. We review the initial efforts of onboarding wastewater surveillance and provide direction for structuring ongoing surveillance workflows and future epidemic response strategies based on those that led to reduced viral signals in campus wastewater.

Viral epidemic preparedness: a perspective from five clinical microbiology laboratories in Europe

BACKGROUND

Pandemic preparedness is critical to respond effectively to existing and emerging/new viral pathogens. Important lessons have been learned during the last pandemic at various levels. This revision discusses some of the major challenges and potential ways to address them in the likely event of future pandemics.

OBJECTIVES

To identify critical points of readiness that may help us accelerate the response to future pandemics from a clinical microbiology laboratory perspective with a focus on viral diagnostics and genomic sequencing. The potential areas of improvement identified are discussed from the sample collection to information reporting.

SOURCES

Microbiologists and researchers from five countries reflect on challenges encountered during the COVID-19 pandemic, review published literature on prior and current pandemics, and suggest potential solutions in preparation for future outbreaks.

CONTENT

Major challenges identified in the pre-analytic and post-analytic phases from sample collection to result reporting are discussed. From the perspective of clinical microbiology laboratories, the preparedness for a new pandemic should focus on zoonotic viruses. Laboratory readiness for scalability is critical and should include elements related to material procurement, training personnel, specific funding programmes, and regulatory issues to rapidly implement "in-house" tests. Laboratories across various countries should establish (or re-use) operational networks to communicate to respond effectively, ensuring the presence of agile circuits with full traceability of samples.

IMPLICATIONS

Laboratory preparedness is paramount to respond effectively to emerging and re-emerging viral infections and to limit the clinical and societal impact of new potential pandemics. Agile and fully traceable methods for sample collection to report are the cornerstone of a successful response. Expert group communication and early involvement of information technology personnel are critical for preparedness. A specific budget for pandemic preparedness should be ring-fenced and added to the national health budgets.

Brain exposure to SARS-CoV-2 virions perturbs synaptic homeostasis

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is associated with short- and long-term neurological complications. The variety of symptoms makes it difficult to unravel molecular mechanisms underlying neurological sequalae after coronavirus disease 2019 (COVID-19). Here we show that SARS-CoV-2 triggers the up-regulation of synaptic components and perturbs local electrical field potential. Using cerebral organoids, organotypic culture of human brain explants from individuals without COVID-19 and post-mortem brain samples from individuals with COVID-19, we find that neural cells are permissive to SARS-CoV-2 to a low extent. SARS-CoV-2 induces aberrant presynaptic morphology and increases expression of the synaptic components Bassoon, latrophilin-3 (LPHN3) and fibronectin leucine-rich transmembrane protein-3 (FLRT3). Furthermore, we find that LPHN3-agonist treatment with Stachel partially restored organoid electrical activity and reverted SARS-CoV-2-induced aberrant presynaptic morphology. Finally, we observe accumulation of relatively static virions at LPHN3-FLRT3 synapses, suggesting that local hindrance can contribute to synaptic perturbations. Together, our study provides molecular insights into SARS-CoV-2-brain interactions, which may contribute to COVID-19-related neurological disorders.

Culturing of SARS-CoV-2 from patient samples: Protocol for optimal virus recovery and assessment of infectious viral load

Optimal sampling, preservation, and culturing of SARS-CoV-2 from COVID-19 patients are critical for successful recovery of virus isolates and to accurately estimate contagiousness of the patient. In this study, we investigated the influence of the type of sampling media, storage time, freezing conditions, sterile filtration, and combinations of these to determine the optimal pre-analytic conditions for virus recovery and estimation of infectious viral load in COVID-19 patients. Further, we investigated the viral shedding kinetics and mucosal antibody response in 38 COVID-19 hospitalized patients. We found Universal Transport Medium (Copan) to be the most optimal medium for preservation of SARS-CoV-2 infectivity. Our data showed that the probability of a positive viral culture was strongly correlated to Ct values, however some samples did not follow the general trend. We found a significant correlation between plaque forming units and levels of mucosal antibodies and found that high levels of mucosal antibodies correlated with reduced chance of isolating the virus. Our data reveals essential parameters to consider from specimen collection over storage to culturing technique for optimal chance of isolating SARS-CoV-2 and accurately estimating patient contagiousness.

Epidemiology and Clinical Features of COVID-19 among 4,015 Neonates in Iran: Results of the National Study from the Iranian Maternal and Neonatal Network

OBJECTIVE

The coronavirus disease 2019 (COVID-19) pandemic had a significant impact on pregnant women and neonates in Iran. This retrospective study describes the national experience among neonates having suspected and confirmed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection following hospital admission to examine the epidemiology, demographic, and clinical features.

STUDY DESIGN

All nationwide cases of suspected and confirmed neonatal SARS-CoV-2 infection were drawn from the Iranian Maternal and Neonatal Network (IMaN) between February 2020 and February 2021. IMaN registers demographic, maternal, and neonatal health data throughout Iran. Statistical analysis of demographic, epidemiological, and clinical data were performed.

RESULTS

There were 4,015 liveborn neonates having suspected or confirmed SARS-CoV-2 infection that fulfilled the study inclusion criteria identified in the IMaN registry from 187 hospitals throughout Iran. There were 1,392 (34.6%) neonates that were preterm, including 304 (7.6%) less than 32 weeks' gestation. Among the 2,567 newborns admitted to the hospital immediately after birth, the most common clinical problems were respiratory distress (1,095 cases; 42.6%), sepsis-like syndrome (355; 13.8%), and cyanosis (300 cases; 11.6%). Of 683 neonates transferred from another hospital, the most frequent problems were respiratory distress (388; 56.8%), sepsis-like syndrome (152; 22.2%), and cyanosis (134; 19.6%). Among 765 neonates discharged home after birth and subsequently admitted to the hospital, sepsis-like syndrome (244 cases; 31.8%), fever (210; 27.4%), and respiratory distress (185; 24.1%) were most frequent. A total of 2,331 (58%) of neonates required respiratory care, with 2,044 surviving and 287 having a neonatal death. Approximately 55% of surviving neonates received respiratory support, compared with 97% of neonates who expired. Laboratory abnormalities included elevations of white blood cell count, creatine phosphokinase, liver enzymes, and C-reactive protein.

CONCLUSION

This report adds the national experience of Iran to the list of reports from multiple countries describing their experience with COVID-19 in neonates, demonstrating that newborns are not exempt from COVID-19-morbidity and mortality.

KEY POINTS

· Most common clinical problem was respiratory distress.. · Sepsis-like syndrome was also frequently present.. · A total of 58% of all neonates required respiratory care..

Detection accuracy and clinical applications of DP-TOF mass spectrometry

OBJECTIVE

Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is currently used in clinical microbiology laboratories. This study aimed to determine whether dual-polarity time-of-flight mass spectrometry (DP-TOF MS) could be applied to clinical nucleotide detection.

METHODS

This prospective study included 40 healthy individuals and 110 patients diagnosed with cardiovascular diseases. We used DP-TOF MS and Sanger sequencing to evaluate 17 loci across 11 genes associated with cardiovascular drug responses. In addition, we used DP-TOF MS to test 998 retrospectively collected clinical DNA samples with known results.

RESULTS

A, T, and G nucleotide detection by DP-TOF MS and Sanger sequencing revealed 100% concordance, whereas the C nucleotide concordance was 99.86%. Genotyping based on the results of the two methods showed 99.96% concordance. Regarding clinical applications, DP-TOF MS yielded a 99.91% concordance rate for known loci. The minimum detection limit for DNA was 0.4 ng; the inter-assay and intra-assay precision rates were both 100%. Anti-interference analysis showed that aerosol contamination greater than 1013 copies/µL in the laboratory environment could influence the results of DP-TOF MS.

CONCLUSIONS

The DP-TOF MS platform displayed good detection performance, as demonstrated by its 99.96% concordance rate with Sanger sequencing. Thus, it may be applied to clinical nucleotide detection.

Machine Learning-based Voice Assessment for the Detection of Positive and Recovered COVID-19 Patients

Many virological tests have been implemented during the Coronavirus Disease 2019 (COVID-19) pandemic for diagnostic purposes, but they appear unsuitable for screening purposes. Furthermore, current screening strategies are not accurate enough to effectively curb the spread of the disease. Therefore, the present study was conducted within a controlled clinical environment to determine eventual detectable variations in the voice of COVID-19 patients, recovered and healthy subjects, and also to determine whether machine learning-based voice assessment (MLVA) can accurately discriminate between them, thus potentially serving as a more effective mass-screening tool. Three different subpopulations were consecutively recruited: positive COVID-19 patients, recovered COVID-19 patients and healthy individuals as controls. Positive patients were recruited within 10 days from nasal swab positivity. Recovery from COVID-19 was established clinically, virologically and radiologically. Healthy individuals reported no COVID-19 symptoms and yielded negative results at serological testing. All study participants provided three trials for multiple vocal tasks (sustained vowel phonation, speech, cough). All recordings were initially divided into three different binary classifications with a feature selection, ranking and cross-validated RBF-SVM pipeline. This brough a mean accuracy of 90.24%, a mean sensitivity of 91.15%, a mean specificity of 89.13% and a mean AUC of 0.94 across all tasks and all comparisons, and outlined the sustained vowel as the most effective vocal task for COVID discrimination. Moreover, a three-way classification was carried out on an external test set comprised of 30 subjects, 10 per class, with a mean accuracy of 80% and an accuracy of 100% for the detection of positive subjects. Within this assessment, recovered individuals proved to be the most difficult class to identify, and all the misclassified subjects were declared positive; this might be related to mid and short-term vocal traces of COVID-19, even after the clinical resolution of the infection. In conclusion, MLVA may accurately discriminate between positive COVID-19 patients, recovered COVID-19 patients and healthy individuals. Further studies should test MLVA among larger populations and asymptomatic positive COVID-19 patients to validate this novel screening technology and test its potential application as a potentially more effective surveillance strategy for COVID-19.

High-Affinity-Mediated Viral Entry Triggers Innate Affinity Escape Resulting in Type I IFN Resistance and Impaired T Cell Immunity

Increased receptor binding affinity may allow viruses to escape from Ab-mediated inhibition. However, how high-affinity receptor binding affects innate immune escape and T cell function is poorly understood. In this study, we used the lymphocytic choriomeningitis virus (LCMV) murine infection model system to create a mutated LCMV exhibiting higher affinity for the entry receptor α-dystroglycan (LCMV-GPH155Y). We show that high-affinity receptor binding results in increased viral entry, which is associated with type I IFN (IFN-I) resistance, whereas initial innate immune activation was not impaired during high-affinity virus infection in mice. Consequently, IFN-I resistance led to defective antiviral T cell immunity, reduced type II IFN, and prolonged viral replication in this murine model system. Taken together, we show that high-affinity receptor binding of viruses can trigger innate affinity escape including resistance to IFN-I resulting in prolonged viral replication.

Integrating socio-economic vulnerability factors improves neighborhood-scale wastewater-based epidemiology for public health applications

Wastewater Based Epidemiology (WBE) of COVID-19 is a low-cost, non-invasive, and inclusive early warning tool for disease spread. Previously studied WBE focused on sampling at wastewater treatment plant scale, limiting the level at which demographic and geographic variations in disease dynamics can be incorporated into the analysis of certain neighborhoods. This study demonstrates the integration of demographic mapping to improve the WBE of COVID-19 and associated post-COVID disease prediction (here kidney disease) at the neighborhood level using machine learning. WBE was conducted at six neighborhoods in Seattle during October 2020 - February 2022. Wastewater processing and RT-qPCR were performed to obtain SARS-CoV-2 RNA concentration. Census data, clinical data of COVID-19, as well as patient data of acute kidney injury (AKI) cases reported during the study period were collected and the distribution across the city was studied using Geographic Information System (GIS) mapping. Further, we analyzed the data set to better understand socioeconomic impacts on disease prevalence of COVID-19 and AKI per neighborhood. The heterogeneity of eleven demographic factors (such as education and age among others) was observed within neighborhoods across the city of Seattle. Dynamics of COVID-19 clinical cases and wastewater SARS-CoV-2 varied across neighborhood with different levels of demographics. Machine learning models trained with data from the earlier stages of the pandemic were able to predict both COVID-19 and AKI incidence in the later stages of the pandemic (Spearman correlation coefficient of 0·546 - 0·904), with the most predictive model trained on the combination of wastewater data and demographics. The integration of demographics strengthened machine learning models' capabilities to predict prevalence of COVID-19, and of AKI as a marker for post-COVID sequelae. Demographic-based WBE presents an effective tool to monitor and manage public health beyond COVID-19 at the neighborhood level.

Detection of SARS-CoV-2 B.1.1.529 (Omicron) variant by SYBR Green-based RT-qPCR

The coronavirus disease 2019 (COVID-19) pandemic is unceasingly spreading across the globe, and recently a highly transmissible Omicron SARS-CoV-2 variant (B.1.1.529) has been discovered in South Africa and Botswana. Rapid identification of this variant is essential for pandemic assessment and containment. However, variant identification is mainly being performed using expensive and time-consuming genomic sequencing. In this study, we propose an alternative RT-qPCR approach for the detection of the Omicron BA.1 variant using a low-cost and rapid SYBR Green method. We have designed specific primers to confirm the deletion mutations in the spike (S Δ143-145) and the nucleocapsid (N Δ31-33) which are characteristics of this variant. For the evaluation, we used 120 clinical samples from patients with PCR-confirmed SARS-CoV-2 infections, and displaying an S-gene target failure (SGTF) when using TaqPath COVID-19 kit (Thermo Fisher Scientific, Waltham, USA) that included the ORF1ab, S, and N gene targets. Our results showed that all the 120 samples harbored S Δ143-145 and N Δ31-33, which was further confirmed by whole-genome sequencing of 10 samples, thereby validating our SYBR Green-based protocol. This protocol can be easily implemented to rapidly confirm the diagnosis of the Omicron BA.1 variant in COVID-19 patients and prevent its spread among populations, especially in countries with high prevalence of SGTF profile.

Mucosal prime-boost immunization with live murine pneumonia virus-vectored SARS-CoV-2 vaccine is protective in macaques

Immunization via the respiratory route is predicted to increase the effectiveness of a SARS-CoV-2 vaccine. Here, we evaluate the immunogenicity and protective efficacy of one or two doses of a live-attenuated murine pneumonia virus vector expressing SARS-CoV-2 prefusion-stabilized spike protein (MPV/S-2P), delivered intranasally/intratracheally to male rhesus macaques. A single dose of MPV/S-2P is highly immunogenic, and a second dose increases the magnitude and breadth of the mucosal and systemic anti-S antibody responses and increases levels of dimeric anti-S IgA in the airways. MPV/S-2P also induces S-specific CD4+ and CD8+ T-cells in the airways that differentiate into large populations of tissue-resident memory cells within a month after the boost. One dose induces substantial protection against SARS-CoV-2 challenge, and two doses of MPV/S-2P are fully protective against SARS-CoV-2 challenge virus replication in the airways. A prime/boost immunization with a mucosally-administered live-attenuated MPV vector could thus be highly effective in preventing SARS-CoV-2 infection and replication.