Detection of environmental SARS-CoV-2 RNA in a high prevalence setting in Spain

Evaluation of wastewater percent positive for assessing epidemic trends - A case study of COVID-19 in Shangrao, China

Objective

This study aims to assess the feasibility of evaluating the COVID-19 epidemic trend through monitoring the positive percentage of SARS-CoV-19 RNA in wastewater.

Method

The study collected data from January to August 2023, including the number of reported cases, the positive ratio of nucleic acid samples in sentinel hospitals, the incidence rate of influenza-like symptoms in students, and the positive ratio of wastewater samples in different counties and districts in Shangrao City. Wastewater samples were obtained through grabbing and laboratory testing was completed within 24 h. The data were then normalized using Z-score normalization and analyzed for lag time and correlation using the xcorr function and Spearman correlation coefficient.

Results

A total of 2797 wastewater samples were collected. The wastewater monitoring study, based on sampling point distribution, was divided into two phases. Wuyuan County consistently showed high levels of positive ratio in wastewater samples in both phases, reaching peak values of 91.67% and 100% respectively. The lag time analysis results indicated that the peak positive ratio in all wastewater samples in Shangrao City appeared around 2 weeks later compared to the other three indicators. The correlation analysis revealed a strong linear correlation across all four types of data, with Spearman correlation coefficients ranging from 0.783 to 0.977, all of which were statistically significant.

Conclusion

The positive ratio of all wastewater samples in Shangrao City accurately reflected the COVID-19 epidemic trend from January to August 2023. This study confirmed the lag effect of wastewater percent positive and its strong correlation with the reported incidence rate and the positive ratio of nucleic acid samples in sentinel hospitals, supporting the use of wastewater percent positive monitoring as a supplementary tool for infectious disease surveillance in the regions with limited resources.

Wastewater Surveillance of SARS-CoV-2 in Zambia: An Early Warning Tool

Wastewater-based surveillance has emerged as an important method for monitoring the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). This study investigated the presence of SARS-CoV-2 in wastewater in Zambia. We conducted a longitudinal study in the Copperbelt and Eastern provinces of Zambia from October 2023 to December 2023 during which 155 wastewater samples were collected. The samples were subjected to three different concentration methods, namely bag-mediated filtration, skimmed milk flocculation, and polythene glycol-based concentration assays. Molecular detection of SARS-CoV-2 nucleic acid was conducted using real-time Polymerase Chain Reaction (PCR). Whole genome sequencing was conducted using Illumina COVIDSEQ assay. Of the 155 wastewater samples, 62 (40%) tested positive for SARS-CoV-2. Of these, 13 sequences of sufficient length to determine SARS-CoV-2 lineages were obtained and 2 sequences were phylogenetically analyzed. Various Omicron subvariants were detected in wastewater including BA.5, XBB.1.45, BA.2.86, and JN.1. Some of these subvariants have been detected in clinical cases in Zambia. Interestingly, phylogenetic analysis positioned a sequence from the Copperbelt Province in the B.1.1.529 clade, suggesting that earlier Omicron variants detected in late 2021 could still be circulating and may not have been wholly replaced by newer subvariants. This study stresses the need for integrating wastewater surveillance of SARS-CoV-2 into mainstream strategies for monitoring SARS-CoV-2 circulation in Zambia.

Efficacy of Three Antimicrobials Against two SARS-COV-2 Surrogates, Bovine Coronavirus and Human Coronavirus OC43, on Hard or Soft Nonporous Materials

The efficacy of three antimicrobials was evaluated against two severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) surrogates - bovine coronavirus (BCoV) and human coronavirus (HCoV) OC43 - on hard and soft nonporous materials. Three antimicrobials with three different active ingredients (chlorine, hydrogen peroxide, and quaternary ammonium compound + alcohol) were studied. Initially, a neutralization method was optimized for each antimicrobial. Then, we determined their efficacy against BCoV and HCoV OC43 in both suspension and on surfaces made with polyethylene terephthalate (PET) plastic and vinyl upholstery fabric. All tests were conducted under ambient environmental conditions with a soil load of 5% fetal bovine serum. After a 2-min exposure, all three antimicrobials achieved a >3.0 log10 reduction in viral titers in suspension. All three also reduced virus infectivity on both surface materials below the detection limit (0.6 log10 TCID50/carrier). Treatments in which the reduction in virus titer was <3.0 log10 were attributed to a decreased dynamic range on the carrier during drying prior to disinfection. The carrier data revealed that both surrogates were inactivated more rapidly (p <0.05) on vinyl or under conditions of high relative humidity. Three classes of antimicrobials were efficacious against both SARS-CoV-2 surrogate viruses, with BCoV demonstrating slightly less sensitivity compared to HCoV OC43. These findings also illustrate the importance of (1) optimizing the neutralization method and (2) considering relative humidity as a key factor for efficacy testing.

First Molecular Detection of SARS-CoV-2 in Sewage and Wastewater in Ghana

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is shed in the stool of infected individuals and can be detected in sewage and wastewater contaminated with infected stool. This study is aimed at detecting the virus and its potential survival in sewage and wastewater in Ghana. The cross-sectional study included samples from 16 validated environmental surveillance sites in 7 regions of Ghana. A total of 354 samples composed of wastewater (280) and sewage (74) were collected from November 2020 to November 2022. Overall, 17% of the samples were positive for SARS-CoV-2 by real-time PCR, with 6% in sewage and 11% in wastewater. The highest number of positive samples was collected from the Greater Accra Region (7.3%) with the least recorded in the Bono East Region (0.6%). Further characterization of the positive samples using the next-generation sequencing (NGS) approach yielded two variants: Alpha (B.1.1.7) and Delta (AY.36). Attempts to isolate SARS-CoV-2 in the Vero cell line were not successful probably due to the low viral load concentrations (Ct values > 35) or prolonged exposure to high temperatures rendering the virus noninfectious. Our findings suggest that SARS-CoV-2 RNA in sewage and wastewater may not be infectious, but the prevalence shows that the virus persists in the communities within Ghana.

Sampling and recovery of infectious SARS-CoV-2 from high-touch surfaces by sponge stick and macrofoam swab

Effective sampling for severe acute respiratory syndrome 2 (SARS-CoV-2) is a common approach for monitoring disinfection efficacy and effective environmental surveillance. This study evaluated sampling efficiency and limits of detection (LODs) of macrofoam swab and sponge stick sampling methods for recovering infectious SARS-CoV-2 and viral RNA (vRNA) from surfaces. Macrofoam swab and sponge stick methods were evaluated for collection of SARS-CoV-2 suspended in a soil load from 6-in2 coupons composed of four materials: stainless steel (SS), acrylonitrile butadiene styrene (ABS) plastic, bus seat fabric, and Formica. Recovery of infectious SARS-CoV-2 was more efficient than vRNA recovery on all materials except Formica (macrofoam swab sampling) and ABS (sponge stick sampling). Macrofoam swab sampling recovered significantly more vRNA from Formica than ABS and SS, and sponge stick sampling recovered significantly more vRNA from ABS than Formica and SS, suggesting that material and sampling method choice can affect surveillance results. Time since initial contamination significantly affected infectious virus recovery from all materials, with vRNA recovery showing limited to no difference, suggesting that SARS-CoV-2 vRNA can remain detectable after viral infectivity has dissipated. This study showed that a complex relationship exists between sampling method, material, time from contamination to sampling, and recovery of SARS-CoV-2. In conclusion, data show that careful consideration be used when selecting surface types for sampling and interpreting SARS-CoV-2 vRNA recovery with respect to presence of infectious virus.

Passive Sampler Technology for Viral Detection in Wastewater-Based Surveillance: Current State and Nanomaterial Opportunities

Although wastewater-based surveillance (WBS) is an efficient community-wide surveillance tool, its implementation for pathogen surveillance remains limited by ineffective sample treatment procedures, as the complex composition of wastewater often interferes with biomarker recovery. Moreover, current sampling protocols based on grab samples are susceptible to fluctuant biomarker concentrations and may increase operative costs, often rendering such systems inaccessible to communities in low-to-middle-income countries (LMICs). As a response, passive samplers have emerged as a way to make wastewater sampling more efficient and obtain more reliable, consistent data. Therefore, this study aims to review recent developments in passive sampling technologies to provide researchers with the tools to develop novel passive sampling strategies. Although promising advances in the development of nanostructured passive samplers have been reported, optimization remains a significant area of opportunity for researchers in the area, as methods for flexible, robust adsorption and recovery of viral genetic materials would greatly improve the efficacy of WBS systems while making them more accessible for communities worldwide.

Assessment of environmental surface contamination with SARS-CoV-2 in concert halls and banquet rooms in Japan

BACKGROUND

Although crowds are considered to be a risk factor for SARS-CoV-2 transmission, little is known about the changes in environmental surface contamination with the virus when a large number of people attend an event. In this study, we evaluated the changes in environmental surface contamination with SARS-CoV-2.

METHODS

Environmental samples were collected from concert halls and banquet rooms before and after events in February to April 2022 when the 7-day moving average of new COVID-19 cases in Tokyo was reported to be 5000-18000 cases per day. In total, 632 samples were examined for SARS-CoV-2 by quantitative reverse transcription polymerase chain reaction (RT-qPCR) tests, and RT-qPCR-positive samples were subjected to a plaque assay.

RESULTS

The SARS-CoV-2 RNA detection rate before and after the events ranged from 0% to 2.6% versus 0%-5.0% in environmental surface samples, respectively. However, no viable viruses were isolated from all RT-qPCR-positive samples by the plaque assay. There was no significant increase in the environmental surface contamination with SARS-CoV-2 after these events.

CONCLUSIONS

These findings revealed that indirect contact transmission from environmental fomite does not seem to be of great magnitude in a community setting.

COVID-19 surveillance in wastewater: An epidemiological tool for the monitoring of SARS-CoV-2

The coronavirus disease 2019 (COVID-19) pandemic has prompted a lot of questions globally regarding the range of information about the virus's possible routes of transmission, diagnostics, and therapeutic tools. Worldwide studies have pointed out the importance of monitoring and early surveillance techniques based on the identification of viral RNA in wastewater. These studies indicated the presence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in human feces, which is shed via excreta including mucus, feces, saliva, and sputum. Subsequently, they get dumped into wastewater, and their presence in wastewater provides a possibility of using it as a tool to help prevent and eradicate the virus. Its monitoring is still done in many regions worldwide and serves as an early "warning signal"; however, a lot of limitations of wastewater surveillance have also been identified.

Art-science multidisciplinary collaborations to address the scientific challenges posed by COVID-19

The ongoing coronavirus pandemic COVID-19 constitutes a scientific and social challenge. The application of mixed-methods research with multidisciplinary collaborations increases the success of experimental design and interpretation of results to approach scientific challenges. The objective is to develop and implement protean art algorithms with interactions between artists and scientists for scientific research in areas of molecular biology, immunology, ecology and biomedicine. In this perspective, artists were invited to contribute pieces related to the pandemic, and scientists were then challenged to contribute their view and proposed research inspired by artist contribution to face COVID-19 scientific challenges. Proposed research objectives inspired by artist contributions contribute to approach COVID-19 scientific and social challenges with results that may translate into new diagnosis and control interventions. The proposed research objectives approach vaccine protective mechanisms and the development of nutritional interventions with possible impact on boosting protective response to vaccination, the impact of fuel pollutants on host immunity and virus transmission, the possible role of ectoparasite vectors in the appearance of SARS-CoV-2 variants and virus transmission, collaboration between different sectors to contribute to virus surveillance and reduce risks of contagion, characterization of the incidence of zoonotic diseases during and after the COVID-19 pandemic in relation to modifications in the interactions between humans and reservoir animal species, evaluation of the risks associated with sexual or congenital transmission of SARS-CoV-2, development of new methods for the easy and rapid detection of very low SARS-CoV-2 virus amounts in infected but asymptomatic individuals, and understanding society perceptions about the socio-ecological relationships between decoupled environments and the risks and effects of pandemics. This approach may be used to promote social participation in science through combined scientific and artistic perspectives with impact on science and society.KEY MESSAGEMixed-methods research with multidisciplinary collaborations increases the success of experimental design and interpretation of results.Implementation of protean art algorithms through interactions between artists and scientists advances scientific research.Proposed research objectives inspired by artist contributions contribute to approach COVID-19 scientific and social challenges with results that may translate into new diagnosis and control interventions.

The Efficient and Practical virus Identification System with ENhanced Sensitivity for Solids (EPISENS-S): A rapid and cost-effective SARS-CoV-2 RNA detection method for routine wastewater surveillance

Wastewater-based epidemiology has attracted attention as a COVID-19 surveillance tool. Here, we developed a practical method for detecting SARS-CoV-2 RNA in wastewater (the EPISENS-S method), which employs direct RNA extraction from wastewater pellets formed via low-speed centrifugation. The subsequent multiplex one-step RT-preamplification reaction with forward and reverse primers for SARS-CoV-2 and a reverse primer only for pepper mild mottle virus (PMMoV) allowed for qPCR quantification of the targets with different abundances in wastewater from the RT-preamplification product. The detection sensitivity of the method was evaluated using wastewater samples seeded with heat-inactivated SARS-CoV-2 in concentrations of 2.11 × 103 to 2.11 × 106 copies/L. The results demonstrated that the sensitivity of the EPISENS-S method was two orders of magnitude higher than that of the conventional method (PEG precipitation, followed by regular RT-qPCR; PEG-QVR-qPCR). A total of 37 untreated wastewater samples collected from two wastewater treatment plants in Sapporo, Japan when 1.6 to 18 new daily reported cases per 100,000 people were reported in the city (March 4 to July 8, 2021), were examined using the EPISENS-S method to confirm its applicability to municipal wastewater. SARS-CoV-2 RNA was quantified in 92 % (34/37) of the samples via the EPISENS-S method, whereas none of the samples (0/37) was quantifiable via the PEG-QVR-qPCR method. The PMMoV concentrations measured by the EPISENS-S method ranged from 2.60 × 106 to 1.90 × 108 copies/L, and the SARS-CoV-2 RNA concentrations normalized by PMMoV ranged from 5.71 × 10-6 to 9.51 × 10-4 . The long-term trend of normalized SARS-CoV-2 RNA concentration in wastewater was consistent with that of confirmed COVID-19 cases in the city. These results demonstrate that the EPISENS-S method is highly sensitive and suitable for routine COVID-19 wastewater surveillance.

Biosensors for the detection of disease outbreaks through wastewater-based epidemiology

Wastewater-Based Epidemiology (WBE) is a novel community-wide monitoring tool that provides comprehensive real-time data of the public and environmental health status and can contribute to public health interventions, including those related to infectious disease outbreaks (e.g., the ongoing COVID-19 pandemic). Nonetheless, municipalities without centralized laboratories are likely still not able to process WBE samples. Biosensors are a potentially cost-effective solution to monitor the development of diseases through WBE to prevent local outbreaks. This review discusses the economic and technical feasibility of eighteen recently developed biosensors for the detection and monitoring of infectious disease agents in wastewater, prospecting the prevention of future pandemics.

HEPA filters of portable air cleaners as a tool for the surveillance of SARS-CoV-2

Studies about the identification of SARS-CoV-2 in indoor aerosols have been conducted in hospital patient rooms and to a lesser extent in nonhealthcare environments. In these studies, people were already infected with SARS-CoV-2. However, in the present study, we investigated the presence of SARS-CoV-2 in HEPA filters housed in portable air cleaners (PACs) located in places with apparently healthy people to prevent possible outbreaks. A method for detecting the presence of SARS-CoV-2 RNA in HEPA filters was developed and validated. The study was conducted for 13 weeks in three indoor environments: school, nursery, and a household of a social health center, all in Ciudad Real, Spain. The environmental monitoring of the presence of SARS-CoV-2 was conducted in HEPA filters and other surfaces of these indoor spaces for a selective screening in asymptomatic population groups. The objective was to limit outbreaks at an early stage. One HEPA filter tested positive in the social health center. After analysis by RT-PCR of SARS-CoV-2 in residents and healthcare workers, one worker tested positive. Therefore, this study provides direct evidence of virus-containing aerosols trapped in HEPA filters and the possibility of using these PACs for environmental monitoring of SARS-CoV-2 while they remove airborne aerosols and trap the virus.

Monitoring SARS-CoV-2 in air and on surfaces and estimating infection risk in buildings and buses on a university campus

BACKGROUND

Evidence is needed on the presence of SARS-CoV-2 in various types of environmental samples and on the estimated transmission risks in non-healthcare settings on campus.

OBJECTIVES

The objective of this research was to collect data on SARS-CoV-2 viral load and to examine potential infection risks of people exposed to the virus in publicly accessible non-healthcare environments on a university campus.

METHODS

Air and surface samples were collected using wetted wall cyclone bioaerosol samplers and swab kits, respectively, in a longitudinal environmental surveillance program from August 2020 until April 2021 on the University of Michigan Ann Arbor campus. Quantitative rRT-PCR with primers and probes targeting gene N1 were used for SARS-CoV-2 RNA quantification. The RNA concentrations were used to estimate the probability of infection by quantitative microbial risk assessment modeling and Monte-Carlo simulation.

RESULTS

In total, 256 air samples and 517 surface samples were collected during the study period, among which positive rates were 1.6% and 1.4%, respectively. Point-biserial correlation showed that the total case number on campus was significantly higher in weeks with positive environmental samples than in non-positive weeks (p = 0.001). The estimated probability of infection was about 1 per 100 exposures to SARS-CoV-2-laden aerosols through inhalation and as high as 1 per 100,000 exposures from contacting contaminated surfaces in simulated scenarios.

SIGNIFICANCE

Viral shedding was demonstrated by the detection of viral RNA in multiple air and surface samples on a university campus. The low overall positivity rate indicated that the risk of exposure to SARS-CoV-2 at monitored locations was low. Risk modeling results suggest that inhalation is the predominant route of exposure compared to surface contact, which emphasizes the importance of protecting individuals from airborne transmission of SARS-CoV-2 and potentially other respiratory infectious diseases.

IMPACT

Given the reoccurring epidemics caused by highly infectious respiratory viruses in recent years, our manuscript reinforces the importance of monitoring environmental transmission by the simultaneous sampling and integration of multiple environmental surveillance matrices for modeling and risk assessment.

Environment and Offspring Surveillance in Porcine Brucellosis

Porcine brucellosis, caused by Brucella suis (B. suis), is a notifiable disease causing significant economic losses in production systems. Most infected pigs may act as carriers and shed B. suis even if asymptomatic. This can contribute to environmental persistence, thus hindering control efforts. Here, the environment and the offspring were investigated during and after a B. suis outbreak at a sow breeding farm. The diagnosis of B. suis in sows (n = 1,140) was performed by culture and polymerase chain reaction (PCR) from vaginal swabs, indirect enzyme-linked immunosorbent assay (I-ELISA) from sera, and brucellin skin test (BST). B. suis diagnosis in post-weaning pigs (n = 899) was performed by I-ELISA in sera and BST. The environmental surveillance programme was implemented by placing gauze sponges (n = 175) pre-hydrated in a surfactant and inactivating liquid for Brucella DNA detection by PCR in different farm areas. Our results showed that the offspring of infected sows reacted to in vivo techniques for B. suis. Furthermore, the offspring born during the outbreak displayed higher seropositivity (I-ELISA) and reactivity (BST) than those pigs born after. Brucella DNA was detected in pregnant sow areas, boxes, boots, and post-weaning pig areas. In addition, Brucella DNA environmental detection was higher during the B. suis outbreak than the post B. suis outbreak. The environmental approach has proven to be a simple, practical, valuable, and safe method to detect and monitor B. suis. These results suggest a role of the environment and the offspring that should be considered in porcine brucellosis surveillance and control programmes.

Longitudinal analysis of built environment and aerosol contamination associated with isolated COVID-19 positive individuals

The indoor environment is the primary location for the transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), largely driven by respiratory particle accumulation in the air and increased connectivity between the individuals occupying indoor spaces. In this study, we aimed to track a cohort of subjects as they occupied a COVID-19 isolation dormitory to better understand the impact of subject and environmental viral load over time, symptoms, and room ventilation on the detectable viral load within a single room. We find that subject samples demonstrate a decrease in overall viral load over time, symptoms significantly impact environmental viral load, and we provide the first real-world evidence for decreased aerosol SARS-CoV-2 load with increasing ventilation, both from mechanical and window sources. These results may guide environmental viral surveillance strategies and be used to better control the spread of SARS-CoV-2 within built environments and better protect those caring for individuals with COVID-19.

A subunit vaccine candidate based on the Spike protein of SARS-CoV-2 prevents infectious virus shedding in cats

Of the numerous animal species affected by the SARS-CoV-2 virus, cats are one of the most susceptible, and cat-to-cat transmission has been described. Although cat-to-human infection has not, as yet, been demonstrated, preventive measures should be taken in order to avoid both viral infection in cats and transmission among them. In this respect, the application of an effective vaccine to at-risk populations would be a useful tool for controlling the disease in this species. Here, we test a new vaccine prototype based on the Spike protein of the virus in order to prevent infection and infectious virus shedding in cats. The vaccine employed in experimentation, and which is easily produced, triggered a strong neutralizing antibody response in vaccinated animals. In contrast to that which occurred with control animals, no infectious virus was detected in the oropharyngeal or rectal swabs of vaccinated cats submitted to a SARS-CoV-2 challenge. These results are of great interest as regards future considerations related to implementing vaccination programs in pets. The value of cats as vaccination trial models is also described herein.

The challenge of SARS-CoV-2 environmental monitoring in schools using floors and portable HEPA filtration units: Fresh or relic RNA?

Testing surfaces in school classrooms for the presence of SARS-CoV-2, the virus that causes COVID-19, can provide public-health information that complements clinical testing. We monitored the presence of SARS-CoV-2 RNA in five schools (96 classrooms) in Davis, California (USA) by collecting weekly surface-swab samples from classroom floors and/or portable high-efficiency particulate air (HEPA) units (n = 2,341 swabs). Twenty-two surfaces tested positive, with qPCR cycle threshold (Ct) values ranging from 36.07-38.01. Intermittent repeated positives in a single room were observed for both floor and HEPA filter samples for up to 52 days, even following regular cleaning and HEPA filter replacement after a positive result. We compared the two environmental sampling strategies by testing one floor and two HEPA filter samples in 57 classrooms at Schools D and E. HEPA filter sampling yielded 3.02% and 0.41% positivity rates per filter sample collected for Schools D and E, respectively, while floor sampling yielded 0.48% and 0% positivity rates. Our results indicate that HEPA filter swabs are more sensitive than floor swabs at detecting SARS-CoV-2 RNA in interior spaces. During the study, all schools were offered weekly free COVID-19 clinical testing through Healthy Davis Together (HDT). HDT also offered on-site clinical testing in Schools D and E, and upticks in testing participation were observed following a confirmed positive environmental sample. However, no confirmed COVID-19 cases were identified among students associated with classrooms yielding positive environmental samples. The positive samples detected in this study appeared to contain relic viral RNA from individuals infected before the monitoring program started and/or RNA transported into classrooms via fomites. High-Ct positive results from environmental swabs detected in the absence of known active infections supports this conclusion. Additional research is needed to differentiate between fresh and relic SARS-CoV-2 RNA in environmental samples and to determine what types of results should trigger interventions.

Prevention of tick-borne diseases: challenge to recent medicine

Abstract

Ticks represent important vectors and reservoirs of pathogens, causing a number of diseases in humans and animals, and significant damage to livestock every year. Modern research into protection against ticks and tick-borne diseases focuses mainly on the feeding stage, i.e. the period when ticks take their blood meal from their hosts during which pathogens are transmitted. Physiological functions in ticks, such as food intake, saliva production, reproduction, development, and others are under control of neuropeptides and peptide hormones which may be involved in pathogen transmission that cause Lyme borreliosis or tick-borne encephalitis. According to current knowledge, ticks are not reservoirs or vectors for the spread of COVID-19 disease. The search for new vaccination methods to protect against ticks and their transmissible pathogens is a challenge for current science in view of global changes, including the increasing migration of the human population.

Highlights

• Tick-borne diseases have an increasing incidence due to climate change and increased human migration

• To date, there is no evidence of transmission of coronavirus COVID-19 by tick as a vector

• To date, there are only a few modern, effective, and actively- used vaccines against ticks or tick-borne diseases

• Neuropeptides and their receptors expressed in ticks may be potentially used for vaccine design

Discrimination of non-infectious SARS-CoV-2 particles from fomites by viability RT-qPCR

The ongoing coronavirus 2019 (COVID-19) pandemic constitutes a concerning global threat to public health and economy. In the midst of this pandemic scenario, the role of environment-to-human COVID-19 spread is still a matter of debate because mixed results have been reported concerning SARS-CoV-2 stability on high-touch surfaces in real-life scenarios. Up to now, no alternative and accessible procedures for cell culture have been applied to evaluate SARS-CoV-2 infectivity on fomites. Several strategies based on viral capsid integrity have latterly been developed using viability markers to selectively remove false-positive qPCR signals resulting from free nucleic acids and damaged viruses. These have finally allowed an estimation of viral infectivity. The present study aims to provide a rapid molecular-based protocol for detection and quantification of viable SARS-CoV-2 from fomites based on the discrimination of non-infectious SARS-CoV-2 particles by platinum chloride (IV) (PtCl4) viability RT-qPCR. An initial assessment compared two different swabbing procedures to recover inactivated SARS-CoV-2 particles from fomites coupled with two RNA extraction methods. Procedures were validated with human (E229) and porcine (PEDV) coronavirus surrogates, and compared with inactivated SARS-CoV-2 suspensions on glass, steel and plastic surfaces. The viability RT-qPCR efficiently removed the PCR amplification signals from heat and gamma-irradiated inactivated SARS-CoV-2 suspensions that had been collected from specified surfaces. This study proposes a rapid viability RT-qPCR that discriminates non-infectious SARS-CoV-2 particles on surfaces thus helping researchers to better understand the risk of contracting COVID-19 through contact with fomites and to develop more efficient epidemiological measures.

Occurrence of SARS-CoV-2 in Indoor Environments With Increased Circulation and Gathering of People

At the time of sampling (2020/2021), the number of new cases of SARS-CoV-2-positive individuals in the Czech Republic significantly exceeded the numbers in neighboring countries and in the EU. In terms of the number of deaths, the country ranked near the top of the list. Legislative orders required wearing masks indoors, disinfecting surfaces in public places, and limiting the number of people per sales area in commercial spaces. Due to an situation, most schools and shops were closed. The entire country anticipated a total lockdown. To assess the risk to public health regarding SARS-CoV-2 transmission, air and surfaces were sampled in two public places: a post office and a shopping center. Samples were also collected at the COVID-19 unit at the local hospital. Neither air nor surface samples were positive for SARS-CoV-2 virus particles in the post office or shopping center. Positive results were found in the hospital ward, with floors being the most and highest contaminated surface. Based on our results, we believe that public places do not pose a risk in relation to SARS-CoV-2 transmission, especially when epidemiological measures to reduce transmission are followed, such as wearing masks, using disinfectant or limiting the number of customers per retail establishment.

A new method for sampling African swine fever virus genome and its inactivation in environmental samples

African swine fever (ASF) is currently the most dangerous disease for the global pig industry, causing huge economic losses, due to the lack of effective vaccine or treatment. Only the early detection of ASF virus (ASFV) and proper biosecurity measures are effective to reduce the viral expansion. One of the most widely recognized risks as regards the introduction ASFV into a country is infected animals and contaminated livestock vehicles. In order to improve ASF surveillance, we have assessed the capacity for the detection and inactivation of ASFV genome by using Dry-Sponges (3 M) pre-hydrated with a new surfactant liquid. We sampled different surfaces in ASFV-contaminated facilities, including animal skins, and the results were compared to those obtained using a traditional sampling method. The surfactant liquid successfully inactivated the virus, while ASFV DNA was well preserved for the detection. This is an effective method to systematically recover ASFV DNA from different surfaces and skin, which has a key applied relevance in surveillance of vehicles transporting live animals and greatly improves animal welfare. This method provides an important basis for the detection of ASFV genome that can be assessed without the biosafety requirements of a BSL-3 laboratory at least in ASF-affected countries, which may substantially speed up the early detection of the pathogen.

Large-scale study on virological and serological prevalence of SARS-CoV-2 in cats and dogs in Spain

The disease produced by the severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) is currently one of the primary concerns worldwide. Knowing the zoonotic origin of the disease and that several animal species, including dogs and cats, are susceptible to viral infection, it is critical to assess the relevance of pets in this pandemic. Here, we performed a large-scale study on SARS-CoV-2 serological and viral prevalence in cats and dogs in Spain in order to elucidate their role and susceptibility. Samples from animals in contact with COVID-19 positive people and/or compatible symptoms (n = 492), as well as from random animals (n = 1024), were taken. Despite the large number of animals analyzed, only 12 animals (eight dogs and four cats), which represents 0.79% of the total analyzed animals (n = 1516), were positive for viral SARS-CoV-2 RNA detection by reverse transcription quantitative PCR (RT-qPCR) in which viral isolation was possible in four animals. We detected neutralizing antibodies in 34 animals, four of them were also positive for PCR. This study evidences that pets are susceptible to SARS-CoV-2 infection in natural conditions but at a low level, as evidenced by the low percentage of positive animals detected, being infected humans the main source of infection. However, the inclusion of animals in the surveillance of COVID-19 is still recommended.

Are the Portable Air Cleaners (PAC) really effective to terminate airborne SARS-CoV-2?

The transmission of SARS-CoV-2 virus through aerosols has become an outstanding issue, where plenty of spread aspects are being analyzed. Portable Air Cleaners (PAC) with high-efficiency particulate air (HEPA) filters have been discussed as an adjunctive means for indoor environments coronavirus decontamination. This study evaluates, first, the air and surfaces SARS-COV-2 RNA contamination due to positive patients in households, and second, the efficiency of a PAC with HEPA filter to eliminate virus. A total of 29 air and surface samples were collected inside 9 households, by using an air portable collector with gelatin filters and swabs. SARS-CoV-2 RNA detection was performed using real-time reverse transcription polymerase chain reaction (RT-PCR). Overall, all the air samples collected before using PAC and 75% of swab samples were positive for SARS-CoV-2. After the PAC usage, all samples except one were negative, displaying a 80% device effectiveness. Portable HEPA cleaners usage allowed the removal of SARS CoV-2 and, therefore, they could be recommended for places with inadequate ventilation, considering the limitations and functionality of the device.

Detection of SARS-CoV-2 RNA on contact surfaces within shared sanitation facilities

Contamination of contact surfaces with SARS-CoV-2 has been reported as a potential route for the transmission of COVID-19. This could be a major issue in developing countries where access to basic sanitation is poor, leading to the sharing of toilet facilities. In this study, we report SARS-CoV-2 contamination of key contact surfaces in shared toilets and the probabilistic risks of COVID-19 infections based on detection and quantification of the nucleic acid on the surfaces. We observed that 54-69% of the contact surfaces were contaminated, with SARS-CoV-2 loads ranging from 28.1 to 132.7 gene copies per cm². Toilet seats had the highest contamination, which could be attributed to shedding of the virus in feces and urine. We observed a significant reduction in viral loads on the contaminated surfaces after cleaning, showing the potential of effective cleaning on the reduction of contamination. The pattern of contamination indicates that the most contaminated surfaces are those that are either commonly touched by users of the shared toilets or easily contaminated with feces and urine. These surfaces were the toilet seats, cistern handles and tap handles. The likelihood (probability) of infection with COVID-19 on these surfaces was highest on the toilet seat (1.76 × 10^-4(1.58 × 10^-6)) for one time use of the toilet. These findings highlight the potential risks for COVID-19 infections in the event that intact infectious viral particles are deposited on these contact surfaces. Therefore, this study shows that shared toilet facilities in densely populated areas could lead to an increase in risks of COVID-19 infections. This calls for the implementation of risk reduction measures, such as regular washing of hands with soap, strict adherence to wearing face masks, and effective and regular cleaning of shared facilities.

Sampling methods and assays applied in SARS-CoV-2 exposure assessment

The SARS-CoV-2 exposure assessment is critical to implement control measures and guarantee safety of patients and workers from different occupational environments. The aim of this review article was to identify methodologies applied for SARS-CoV-2 sampling and analyses in environmental samples in different occupational and indoor environments. This study reports the search of available data published between May 29th 2020 and November 1st 2020. The search strategy used allowed the identification of 48 papers that comply with selected inclusion and exclusion criteria. The most described indoor environment consisted of health care facilities. From all the analyzed studies, 34 sampled surfaces, 27 sampled air (impactors and impingers being the most used), and 9 sampled water. All studies were based on molecular detection by qPCR of viral RNA extracted from collected samples. SARS-CoV-2 was detected in 44 out of the 48 studies. The results suggest that the sampling approach should include both active and passive sampling methods in order to overcome each method limitations. Concerning the assays used, although most studies were based on qPCR detection, the fact that the digital PCR technique allows SARS-CoV-2 detection at lower concentrations, indicates that this should be the chosen method for future detection studies.

Natural SARS-CoV-2 Infection in Kept Ferrets, Spain

We found severe acute respiratory syndrome coronavirus 2 RNA in 6 (8.4%) of 71 ferrets in central Spain and isolated and sequenced virus from 1 oral and 1 rectal swab specimen. Natural infection occurs in kept ferrets when virus circulation among humans is high. However, small ferret collections probably cannot maintain virus circulation.

The viability of SARS-CoV-2 on solid surfaces

The COVID-19 pandemic had a major impact on life in 2020 and 2021. One method of transmission occurs when the causative virus, SARS-CoV-2, contaminates solids. Understanding and controlling the interaction with solids is thus potentially important for limiting the spread of the disease. We review work that describes the prevalence of the virus on common objects, the longevity of the virus on solids, and surface coatings that are designed to inactivate the virus. Engineered coatings have already succeeded in producing a large reduction in viral infectivity from surfaces. We also review work describing inactivation on facemasks and clothing and discuss probable mechanisms of inactivation of the virus at surfaces.

SARS-CoV-2 and other main pathogenic microorganisms in the environment: Situation in Galicia and Spain

In the context of the current COVID-19 pandemic, and mostly taking a broad perspective, it is clearly relevant to study environmental factors that could affect eventual future outbreaks due to coronaviruses and/or other pathogenic microorganisms. In view of that, the authors of this manuscript review the situation of SARS-CoV-2 and other main pathogenic microorganisms in the environment, focusing on Galicia and Spain. Overall, in addition to showing local data, it is put in evidence that, summed to all efforts being carried out to treat/control this and any other eventual future epidemic diseases, both at local and global levels, a deep attention should be paid to ecological/environmental aspects that have effects on the planet, its ecosystems and their relations/associations with the probability of spreading of eventual future pandemics.

Arthropod Ectoparasites Have Potential to Bind SARS-CoV-2 via ACE

Coronavirus-like organisms have been previously identified in Arthropod ectoparasites (such as ticks and unfed cat flea). Yet, the question regarding the possible role of these arthropods as SARS-CoV-2 passive/biological transmission vectors is still poorly explored. In this study, we performed in silico structural and binding energy calculations to assess the risks associated with possible ectoparasite transmission. We found sufficient similarity between ectoparasite ACE and human ACE2 protein sequences to build good quality 3D-models of the SARS-CoV-2 Spike:ACE complex to assess the impacts of ectoparasite mutations on complex stability. For several species (e.g., water flea, deer tick, body louse), our analyses showed no significant destabilisation of the SARS-CoV-2 Spike:ACE complex, suggesting these species would bind the viral Spike protein. Our structural analyses also provide structural rationale for interactions between the viral Spike and the ectoparasite ACE proteins. Although we do not have experimental evidence of infection in these ectoparasites, the predicted stability of the complex suggests this is possible, raising concerns of a possible role in passive transmission of the virus to their human hosts.

Assessing the risks of SARS-CoV-2 in wildlife

The novel coronavirus SARS-CoV-2 likely emerged from a wildlife source with transmission to humans followed by rapid geographic spread throughout the globe and severe impacts on both human health and the global economy. Since the onset of the pandemic, there have been many instances of human-to-animal transmission involving companion, farmed and zoo animals, and limited evidence for spread into free-living wildlife. The establishment of reservoirs of infection in wild animals would create significant challenges to infection control in humans and could pose a threat to the welfare and conservation status of wildlife. We discuss the potential for exposure, onward transmission and persistence of SARS-CoV-2 in an initial selection of wild mammals (bats, canids, felids, mustelids, great apes, rodents and cervids). Dynamic risk assessment and targeted surveillance are important tools for the early detection of infection in wildlife, and here we describe a framework for collating and synthesising emerging information to inform targeted surveillance for SARS-CoV-2 in wildlife. Surveillance efforts should be integrated with information from public and veterinary health initiatives to provide insights into the potential role of wild mammals in the epidemiology of SARS-CoV-2.

Monitoring of SARS-CoV-2 infection in mustelids

American mink and ferret are highly susceptible to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), but no information is available for other mustelid species. SARS-CoV-2 spreads very efficiently within mink farms once introduced, by direct and indirect contact, high within-farm animal density increases the chance for transmission. Between-farm spread is likely to occur once SARS-CoV-2 is introduced, short distance between SARS-CoV-2 positive farms is a risk factor. As of 29 January 2021, SARS-CoV-2 virus has been reported in 400 mink farms in eight countries in the European Union. In most cases, the likely introduction of SARS-CoV-2 infection into farms was infected humans. Human health can be at risk by mink-related variant viruses, which can establish circulation in the community, but so far these have not shown to be more transmissible or causing more severe impact compared with other circulating SARS-CoV-2. Concerning animal health risk posed by SARS-CoV-2 infection the animal species that may be included in monitoring plans are American mink, ferrets, cats, raccoon dogs, white-tailed deer and Rhinolophidae bats. All mink farms should be considered at risk of infection; therefore, the monitoring objective should be early detection. This includes passive monitoring (in place in the whole territory of all countries where animals susceptible to SARS-CoV-2 are bred) but also active monitoring by regular testing. First, frequent testing of farm personnel and all people in contact with the animals is recommended. Furthermore randomly selected animals (dead or sick animals should be included) should be tested using reverse transcriptase-polymerase chain reaction (RT-PCR), ideally at weekly intervals (i.e. design prevalence approximately 5% in each epidemiological unit, to be assessed case by case). Suspected animals (dead or with clinical signs and a minimum five animals) should be tested for confirmation of SARS-CoV-2 infection. Positive samples from each farm should be sequenced to monitor virus evolution and results publicly shared.

Longitudinal Monitoring of SARS-CoV-2 RNA on High-Touch Surfaces in a Community Setting

Environmental surveillance of surface contamination is an unexplored tool for understanding transmission of SARS-CoV-2 in community settings. We conducted longitudinal swab sampling of high-touch non-porous surfaces in a Massachusetts town during a COVID-19 outbreak from April to June 2020. Twenty-nine of 348 (8.3%) surface samples were positive for SARS-CoV-2 RNA, including crosswalk buttons, trash can handles, and door handles of essential business entrances (grocery store, liquor store, bank, and gas station). The estimated risk of infection from touching a contaminated surface was low (less than 5 in 10,000) by quantitative microbial risk assessment, suggesting fomites play a minimal role in SARS-CoV-2 community transmission. The weekly percentage of positive samples (out of n = 33 unique surfaces per week) best predicted variation in city-level COVID-19 cases with a 7-day lead time. Environmental surveillance of SARS-CoV-2 RNA on high-touch surfaces may be a useful tool to provide early warning of COVID-19 case trends.

Longitudinal monitoring of SARS-CoV-2 RNA on high-touch surfaces in a community setting

Environmental surveillance of surface contamination is an unexplored tool for understanding transmission of SARS-CoV-2 in community settings. We conducted longitudinal swab sampling of high-touch non-porous surfaces in a Massachusetts town during a COVID-19 outbreak from April to June 2020. Twenty-nine of 348 (8.3 %) surface samples were positive for SARS-CoV-2, including crosswalk buttons, trash can handles, and door handles of essential business entrances (grocery store, liquor store, bank, and gas station). The estimated risk of infection from touching a contaminated surface was low (less than 5 in 10,000), suggesting fomites play a minimal role in SARS-CoV-2 community transmission. The weekly percentage of positive samples (out of n=33 unique surfaces per week) best predicted variation in city-level COVID-19 cases using a 7-day lead time. Environmental surveillance of SARS-CoV-2 RNA on high-touch surfaces could be a useful tool to provide early warning of COVID-19 case trends.