Molecular Epidemiology of SARS-CoV-2 in Diverse Environmental Samples Globally

Global and genetic diversity of SARS-CoV-2 in wastewater

The analysis of SARS-CoV-2 in wastewater has enabled us to better understand the spread and evolution of the virus worldwide. To deepen our understanding of its epidemiological and genomic characteristics, we analyzed 10,147 SARS-CoV-2 sequences from 5 continents and 21 countries that were deposited in the GISAID database up until January 31, 2023. Our results revealed over 100 independent lineages of the virus circulating in water samples from March 2020 to January 2023, including variants of interest and concern. We observed four clearly defined periods of global distribution of these variants over time, with one variant being replaced by another. Interestingly, we found that SARS-CoV-2 water-borne sequences from different countries had a close phylogenetic relationship. Additionally, 40 SARS-CoV-2 water-borne sequences from Europe and the USA did not show any phylogenetic relationship with SARS-CoV-2 human sequences. We also identified a significant number of non-synonymous mutations, some of which were detected in previously reported cryptic lineages. Among the countries analyzed, France and the USA showed the highest degree of sequence diversity, while Austria reported the highest number of genomes (6,296). Our study provides valuable information about the epidemiological and genomic diversity of SARS-CoV-2 in wastewater, which can be employed to support public health initiatives and preparedness.

Assessment of Hygiene Practices, Awareness, and Water Consumption Regarding Covid-19 Among Children in a Refugee Camp

INTRODUCTION

At the outbreak of infectious diseases, the response of different communities to the disease varies, and children are most affected by the collective anxiety and grief that consequently arises. In this research, the behavior of children and their parents in terms of hygiene and precautions before and during the COVID-19 pandemic was investigated.

METHODOLOGY

The focus of the present research was on sanitation facilities, particularly access to end-use of water for hand washing. The research was conducted in Barika Camp, Kurdistan, Iraq and 311 parents and children were interviewed. A data collection team consisting of two females and one male was responsible for gathering data, primarily from women who served as the main respondents. Questionnaires consisted of three main parts: demography, COVID-19 pandemic effects, and sanitary shelter specifications.

RESULT

The results demonstrated that the behavior of refugees during the COVID-19 pandemic regarding the priority of child protection, type of disinfectants, and water consumption has significantly altered. These changes mainly depended on the women's age and education level.

DISCUSSION

Overall results showed that in 61.09% of the participants, the number of hand washes and in 58.58%, the washing time increased, leading to water shortage in the refugee camp.

Molecular and Structural Analysis of Specific Mutations from Saudi Isolates of SARS-CoV-2 RNA-Dependent RNA Polymerase and their Implications on Protein Structure and Drug-Protein Binding

The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has stressed the global health system to a significant level, which has not only resulted in high morbidity and mortality but also poses a threat for future pandemics. This situation warrants efforts to develop novel therapeutics to manage SARS-CoV-2 in specific and other emerging viruses in general. This study focuses on SARS-CoV2 RNA-dependent RNA polymerase (RdRp) mutations collected from Saudi Arabia and their impact on protein structure and function. The Saudi SARS-CoV-2 RdRp sequences were compared with the reference Wuhan, China RdRp using a variety of computational and biophysics-based approaches. The results revealed that three mutations-A97V, P323I and Y606C-may affect protein stability, and hence the relationship of protein structure to function. The apo wild RdRp is more dynamically stable with compact secondary structure elements compared to the mutants. Further, the wild type showed stable conformational dynamics and interaction network to remdesivir. The net binding energy of wild-type RdRp with remdesivir is -50.76 kcal/mol, which is more stable than the mutants. The findings of the current study might deliver useful information regarding therapeutic development against the mutant RdRp, which may further furnish our understanding of SARS-CoV-2 biology.

Transmission dynamics and susceptibility patterns of SARS-CoV-2 in domestic, farmed and wild animals: Sustainable One Health surveillance for conservation and public health to prevent future epidemics and pandemics

The exact origin of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and source of introduction into humans has not been established yet, though it might be originated from animals. Therefore, we conducted a study to understand the putative reservoirs, transmission dynamics, and susceptibility patterns of SARS-CoV-2 in animals. Rhinolophus bats are presumed to be natural progenitors of SARS-CoV-2-related viruses. Initially, pangolin was thought to be the source of spillover to humans, but they might be infected by human or other animal species. So, the virus spillover pathways to humans remain unknown. Human-to-animal transmission has been testified in pet, farmed, zoo and free-ranging wild animals. Infected animals can transmit the virus to other animals in natural settings like mink-to-mink and mink-to-cat transmission. Animal-to-human transmission is not a persistent pathway, while mink-to-human transmission continues to be illuminated. Multiple companions and captive wild animals were infected by an emerging alpha variant of concern (B.1.1.7 lineage) whereas Asiatic lions were infected by delta variant, (B.1.617.2). To date, multiple animal species - cat, ferrets, non-human primates, hamsters and bats - showed high susceptibility to SARS-CoV-2 in the experimental condition, while swine, poultry, cattle showed no susceptibility. The founding of SARS-CoV-2 in wild animal reservoirs can confront the control of the virus in humans and might carry a risk to the welfare and conservation of wildlife as well. We suggest vaccinating pets and captive animals to stop spillovers and spillback events. We recommend sustainable One Health surveillance at the animal-human-environmental interface to detect and prevent future epidemics and pandemics by Disease X.

Transmission Dynamics and Genomic Epidemiology of Emerging Variants of SARS-CoV-2 in Bangladesh

With the progression of the global SARS-CoV-2 pandemic, the new variants have become more infectious and continue spreading at a higher rate than pre-existing ones. Thus, we conducted a study to explore the epidemiology of emerging variants of SARS-CoV-2 that circulated in Bangladesh from December 2020 to September 2021, representing the 2nd and 3rd waves. We collected new cases and deaths per million daily data with the reproduction rate. We retrieved 928 SARS-CoV-2 sequences from GISAID and performed phylogenetic tree construction and mutation analysis. Case counts were lower initially at the end of 2020, during January-February and April-May 2021, whereas the death toll reached the highest value of 1.587 per million on the first week of August and then started to decline. All the variants (α, β, δ, η) were prevalent in the capital city, Dhaka, with dispersion to large cities, such as Sylhet and Chattogram. The B.1.1.25 lineage was prevalent during December 2020, but the B.1.617.2/δ variant was later followed by the B.1.351/β variant. The phylogeny revealed that the various strains found in Bangladesh could be from numerous countries. The intra-cluster and inter-cluster communication began in Bangladesh soon after the virus arrived. The prominent amino acid substitution was D614G from December 2020 to July 2021 (93.5 to 100%). From February-April, one of the VOC's important mutations, N501Y substitution, was also estimated at 51.8%, 76.1%, and 65.1% for the α, β and γ variants, respectively. The γ variant's unique mutation K417T was detected only at 1.8% in February. Another frequent mutation was P681R, a salient feature of the δ variant, detected in June (88.2%) and July (100%). Furthermore, only one γ variant was detected during the entire second and third wave, whereas no η variant was observed in this period. This rapid growth in the number of variants identified across Bangladesh shows virus adaptation and a lack of strict quarantine, prompting periodic genomic surveillance to foresee the spread of new variants, if any, and to take preventive measures as soon as possible.

Wastewater and marine bioindicators surveillance to anticipate COVID-19 prevalence and to explore SARS-CoV-2 diversity by next generation sequencing: One-year study

This study presents the results of SARS-CoV-2 surveillance in sewage water of 11 municipalities and marine bioindicators in Galicia (NW of Spain) from May 2020 to May 2021. An integrated pipeline was developed including sampling, pre-treatment and biomarker quantification, RNA detection, SARS-CoV-2 sequencing, mechanistic mathematical modeling and forecasting. The viral load in the inlet stream to the wastewater treatment plants (WWTP) was used to detect new outbreaks of COVID-19, and the data of viral load in the wastewater in combination with data provided by the health system was used to predict the evolution of the pandemic in the municipalities under study within a time horizon of 7 days. Moreover, the study shows that the viral load was eliminated from the treated sewage water in the WWTP, mainly in the biological reactors and the disinfection system. As a result, we detected a minor impact of the virus in the marine environment through the analysis of seawater, marine sediments and, wild and aquacultured mussels in the final discharge point of the WWTP.

Detection and Molecular Characterization of Canine Alphacoronavirus in Free-Roaming Dogs, Bangladesh

Canine coronavirus (CCoV) is widespread among the dog population and causes gastrointestinal disorders, and even fatal cases. As the zoonotic transmission of viruses from animals to humans has become a worldwide concern nowadays, it is necessary to screen free-roaming dogs for their common pathogens due to their frequent interaction with humans. We conducted a cross-sectional study to detect and characterize the known and novel Corona, Filo, Flavi, and Paramyxoviruses in free-roaming dogs in Bangladesh. Between 2009-10 and 2016-17, we collected swab samples from 69 dogs from four districts of Bangladesh, tested using RT-PCR and sequenced. None of the samples were positive for Filo, Flavi, and Paramyxoviruses. Only three samples (4.3%; 95% CI: 0.9-12.2) tested positive for Canine Coronavirus (CCoV). The CCoV strains identified were branched with strains of genotype CCoV-II with distinct distances. They are closely related to CCoVs from the UK, China, and other CoVs isolated from different species, which suggests genetic recombination and interspecies transmission of CCoVs. These findings indicate that CCoV is circulating in dogs of Bangladesh. Hence, we recommend future studies on epidemiology and genetic characterization with full-genome sequencing of emerging coronaviruses in companion animals in Bangladesh.

Escalating SARS-CoV-2 circulation in environment and tracking waste management in South Asia

The novel coronavirus disease of 2019 (COVID-19) pandemic has caused an exceptional drift of production, utilization, and disposal of personal protective equipment (PPE) and different microplastic objects for safety against the virus. Hence, we reviewed related literature on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA detected from household, biomedical waste, and sewage to identify possible health risks and status of existing laws, regulations, and policies regarding waste disposal in South Asian (SA) countries. The SARS-CoV-2 RNA was detected in sewage and wastewater samples of Nepal, India, Pakistan, and Bangladesh. Besides, this review reiterates the enormous amounts of PPE and other single-use plastic wastes generated from healthcare facilities and households in the SA region with inappropriate disposal, landfilling, and/or incineration techniques wind-up polluting the environment. Consequently, the Delta variant (B.1.617.2) of SARS-CoV-2 has been detected in sewer treatment plant in India. Moreover, the overuse of non-biodegradable plastics during the pandemic is deteriorating plastic pollution condition and causes a substantial health risk to the terrestrial and aquatic ecosystems. We recommend making necessary adjustments, adopting measures and strategies, and enforcement of the existing biomedical waste management and sanitation-related policy in SA countries. We propose to adopt the knowledge gaps to improve COVID-19-associated waste management and legislation to prevent further environmental pollution. Besides, the citizens should follow proper disposal procedures of COVID-19 waste to control the environmental pollution.

Evolutionary Dynamics and Epidemiology of Endemic and Emerging Coronaviruses in Humans, Domestic Animals, and Wildlife

Diverse coronavirus (CoV) strains can infect both humans and animals and produce various diseases. CoVs have caused three epidemics and pandemics in the last two decades, and caused a severe impact on public health and the global economy. Therefore, it is of utmost importance to understand the emergence and evolution of endemic and emerging CoV diversity in humans and animals. For diverse bird species, the Infectious Bronchitis Virus is a significant one, whereas feline enteric and canine coronavirus, recombined to produce feline infectious peritonitis virus, infects wild cats. Bovine and canine CoVs have ancestral relationships, while porcine CoVs, especially SADS-CoV, can cross species barriers. Bats are considered as the natural host of diverse strains of alpha and beta coronaviruses. Though MERS-CoV is significant for both camels and humans, humans are nonetheless affected more severely. MERS-CoV cases have been reported mainly in the Arabic peninsula since 2012. To date, seven CoV strains have infected humans, all descended from animals. The severe acute respiratory syndrome coronaviruses (SARS-CoV and SARS-CoV-2) are presumed to be originated in Rhinolopoid bats that severely infect humans with spillover to multiple domestic and wild animals. Emerging alpha and delta variants of SARS-CoV-2 were detected in pets and wild animals. Still, the intermediate hosts and all susceptible animal species remain unknown. SARS-CoV-2 might not be the last CoV to cross the species barrier. Hence, we recommend developing a universal CoV vaccine for humans so that any future outbreak can be prevented effectively. Furthermore, a One Health approach coronavirus surveillance should be implemented at human-animal interfaces to detect novel coronaviruses before emerging to humans and to prevent future epidemics and pandemics.