Coronavirus: occurrence, surveillance, and persistence in wastewater

Assessment of the clinical and analytical performance of three Seegene Allplex SARS-CoV-2 assays within the VALCOR framework

The coronavirus disease 2019 (COVID-19) pandemic demonstrated the need for accurate diagnostic testing for the early detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Although the pandemic has ended, accurate assays are still needed to monitor viral spread at national levels and beyond through population and wastewater surveillance. To enhance early detection, SARS-CoV-2 assays should have high diagnostic accuracy and should be validated to assure accurate results. Three distinct SARS-CoV-2 assays were evaluated with clinical samples using the VALCOR (VALidation of SARS-CORona Virus-2 assays) framework, with the TaqPath COVID-19 assay (ThermoFisher Scientific, USA) as a comparator. We evaluated clinical sensitivity, specificity, limit of detection (LOD), and overall concordance between comparator and three index Allplex SARS-CoV-2 assays (Seegene, South Korea): Allplex-SC2, Allplex-SC2Fast (Fast PCR), and Allplex-SC2FabR (SARS-CoV-2/FluA/FluB/respiratory syncytial virus). Analytical performance and LOD of index assays were assessed using a dilution series of three synthetic SARS-CoV-2 sequence reference materials (RMs). Ninety SARS-CoV-2 positives and 90 SARS-CoV-2 negatives were tested. All Allplex assays had 100.0% sensitivity (95%CI = 95.9%-100.0%). Allplex-SC2 and Allplex-SC2Fast assays had 97.8% specificity (95%CI = 92.3%-99.7%) and 98.9% overall concordance [κ = 0.978 (95%CI = 0.947-1.000)]. Allplex-SC2FabR assay showed 100.0% specificity (95%CI = 95.9%-100.0%) and 100.0% overall concordance [κ = 1.000 (95%CI = 1.000-1.000)]. LOD assessment of index assays revealed detection down to 2.61 × 102 copies/mL in clinical samples, while the analytical LOD was 9.00 × 102 copies/mL. In conclusion, the evaluation of the three Seegene Allplex SARS-CoV-2 assays showed high sensitivity and specificity and an overall good assay concordance with the comparator. The assays showed low analytical LOD using RM and even a slightly lower LOD in clinical samples. Non-overlapping target gene sequences between SARS-CoV-2 assays and RMs emphasize the need for aligning targeted sequences of diagnostic assays and RMs.IMPORTANCEThe coronavirus disease 2019 pandemic has a significant impact on global public health, economies, and societies. As shown through the first phases of the pandemic, accurate and timely diagnosis is crucial for disease control, prevention, and monitoring. Though the pandemic phase of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has concluded, diagnostic assays remain in demand to monitor SARS-CoV-2 at the individual patient level, regionally, and nationally, as well as to remain an infectious disease preparedness instrument to monitor any new SARS-CoV-2 dissemination across borders using population and wastewater surveillance. The anticipation by WHO and central health care policy entities such as the Center for Disease Control, EMA, and multiple national health authorities is that SARS-CoV-2 will reside as an endemic respiratory disease for years to come. The key strategic consideration is hence shifting from combating a pandemic situation with a high number of patients to instead allowing precise diagnostics of suspected patients with the intention of correct management in a low-prevalence setting.

Predictive models for health outcomes due to SARS-CoV-2, including the effect of vaccination: a systematic review

BACKGROUND

The interaction between modelers and policymakers is becoming more common due to the increase in computing speed seen in recent decades. The recent pandemic caused by the SARS-CoV-2 virus was no exception. Thus, this study aims to identify and assess epidemiological mathematical models of SARS-CoV-2 applied to real-world data, including immunization for coronavirus 2019 (COVID-19).

METHODOLOGY

PubMed, JSTOR, medRxiv, LILACS, EconLit, and other databases were searched for studies employing epidemiological mathematical models of SARS-CoV-2 applied to real-world data. We summarized the information qualitatively, and each article included was assessed for bias risk using the Joanna Briggs Institute (JBI) and PROBAST checklist tool. The PROSPERO registration number is CRD42022344542.

FINDINGS

In total, 5646 articles were retrieved, of which 411 were included. Most of the information was published in 2021. The countries with the highest number of studies were the United States, Canada, China, and the United Kingdom; no studies were found in low-income countries. The SEIR model (susceptible, exposed, infectious, and recovered) was the most frequently used approach, followed by agent-based modeling. Moreover, the most commonly used software were R, Matlab, and Python, with the most recurring health outcomes being death and recovery. According to the JBI assessment, 61.4% of articles were considered to have a low risk of bias.

INTERPRETATION

The utilization of mathematical models increased following the onset of the SARS-CoV-2 pandemic. Stakeholders have begun to incorporate these analytical tools more extensively into public policy, enabling the construction of various scenarios for public health. This contribution adds value to informed decision-making. Therefore, understanding their advancements, strengths, and limitations is essential.

Effectiveness of environmental surveillance of SARS-CoV-2 as an early-warning system: Update of a systematic review during the second year of the pandemic

The aim of this updated systematic review was to offer an overview of the effectiveness of environmental surveillance (ES) of SARS-CoV-2 as a potential early-warning system (EWS) for COVID-19 and new variants of concerns (VOCs) during the second year of the pandemic. An updated literature search was conducted to evaluate the added value of ES of SARS-CoV-2 for public health decisions. The search for studies published between June 2021 and July 2022 resulted in 1,588 publications, identifying 331 articles for full-text screening. A total of 151 publications met our inclusion criteria for the assessment of the effectiveness of ES as an EWS and early detection of SARS-CoV-2 variants. We identified a further 30 publications among the grey literature. ES confirms its usefulness as an EWS for detecting new waves of SARS-CoV-2 infection with an average lead time of 1-2 weeks for most of the publication. ES could function as an EWS for new VOCs in areas with no registered cases or limited clinical capacity. Challenges in data harmonization and variant detection require standardized approaches and innovations for improved public health decision-making. ES confirms its potential to support public health decision-making and resource allocation in future outbreaks.

SARS-CoV-2 Transmission by Arthropod Vectors: A Scoping Review

COVID-19 is a respiratory disease of worldwide importance as it has brought enormous health problems to the world's population. The best-known way of transmission of the virus is through aerosolization. However, research is needed to explore other transmission routes. Researchers hypothesized that arthropods could transmit SARs-CoV-2. This study is aimed at reviewing research on arthropods as possible reservoirs and/or vectors of SARS-CoV-2, the causative agent of COVID-19. Following PRISMA guidelines, we conducted a systematic review using several electronic databases/academic searches with the search terms “arthropods,” “coronavirus,” and “transmission.” A total of 64 unique articles were identified, of which 58 were included in the review. The SARS-CoV-2 virus is tiny and invisible to the naked eye, and its presence in stools, droplets, and surfaces was detected. One doubt is whether insects can transmit the virus from one place to another. Thus, a healthy carrier of the COVID-19 virus can be at the root of the contamination of their community or their family through the transport of the virus by insects from the interior (flies, cockroaches, etc.) from their feces and food surfaces. Hygiene care within communities and families becomes a prime factor. Coronavirus infection is a significant public health problem around the world. The prevention and control of outbreaks remain very important, even with the production of new vaccines. The main option to achieve this is the proper management of the transmission of the virus. The registry of infected people is currently the basis for the transmission of COVID-19. However, questions about the possibility of infection from other sources and its prevention are not receiving adequate attention. Numerous studies have shown the possibility that SARS-COV-2 fragments could have a longer life than shed respiratory droplets. Also, this virus is larger than those of other coronavirus families.