**3. Animal coronavirus diseases**

### **3.1 Pet coronavirus (dogs and cats)**

*Canine coronaviruses*: Canine enteric coronavirus (CCoV) typically infects dogs, especially those housed in large groups such as kennels, shelters, and breeding facilities. CCoV belongs to the family *Coronaviridae*, order *Nidovirales*, and was first isolated in 1971 during an outbreak of gastroenteritis in military dogs and then perceived as a pathogen of dogs [47]. Dogs attracted with CCoV developed self-limiting enteritis with mild diarrheal disease. Two types of canine coronaviruses are known: CCoV is a member of the Alpha-coronavirus genus [48], and canine respiratory coronavirus (CRCoV) belonging to the beta coronavirus genus [49]. CCoV is closely associated with infectious gastroenteritis virus (TGEV) of pigs, ferret coronavirus, and feline coronavirus (FCoV) [48], while CRCoV is more related to bovine coronavirus [50]. All enteric CCoVs (along with the related viruses of cats, pigs, and ferrets) are given the similar strain designation (Alpha-coronavirus-1) from a taxonomic perspective. However, there are two distinct serotypes of CCoV: type I and type II [51, 52].

*Cat coronaviruses*: Two alpha coronaviruses are known for cats: feline enteric coronavirus or feline enteric peritonitis (FECV) associated with mild or asymptomatic diarrhea and can mutate to cause more serious feline infectious peritonitis (FIP) or feline infectious peritonitis (FIPV). Subclinical carriers of FECV handle the shedding and transmission of the virus to different felines through the fecal-oral route. Experiences realized on young, ancient, or immunocompromised subjects have revealed two clinical forms of FIP, a wet form, and a dry form. The wet form

*Emerging Human Coronaviruses (SARS-CoV-2) in the Environment Associated with Outbreaks… DOI: http://dx.doi.org/10.5772/intechopen.103886*

developed ascites which can be clinically apparent (abdominal distention) and confirmed by ultrasound. The dry form is associated with granulomatous lesions of various locations, basically affecting the eye, the central nervous system, the liver, and kidneys. In Addition, uveitis with keratin deposits on the level of the cornea was reported. The FIP is lethal and there is no particular treatment or vaccine marketed in France for this disease. Cats can also be infected with other coronaviruses such as SARS-CoV-2, transmissible porcine gastroenteritis, canine coronavirus, or human coronavirus 229E [53].

### **3.2 Coronaviruses of production animals**

The bovine, porcine, and avian coronaviruses are mainly affecting production animals. These coronaviruses belong to alpha, beta, gamma, and/or delta-coronaviruses.

*Bovine Coronavirus*: Bovine coronaviruses (BCoVs) are pneumo-enteric viruses that infect the upper and lower respiratory tract of cattle and wild ruminants and it is rejected in feces and nasal secretions.. In cattle, BCoV causes 3 different clinical syndromes in cattle: calf diarrhea, winter dysentery with hemorrhagic diarrhea in adults and respiratory infections in cattle of different ages and the bovine respiratory disease complex or shipping fever of feedlot cattle. Distinction between these syndromes is not yet possible as antigenic or genetic specific markers have not been recognized. To our knowledge, no BCoV vaccines to prevent respiratory BCoV diseases in cattle [54].

*Swine Coronavirus:* Porcine coronaviruses are members of three genera: alpha-, beta- and delta- coronavirus. Since 1946, transmissible gastroenteritis virus or TGEV in alpha coronaviruses has been discovered. It developed severe, often fatal enteritis in piglets. Symptoms of vomiting and profuse diarrhea are registered for piglets less than a week old and the mortality rate was about 100%.

Later, in 1971, porcine epidemic diarrhea or DEP (Porcine enteritis disease virus or PEDV) was first described in England and caused watery diarrhea occasionally accompanied by vomiting [55]. Since 2013, a severe pathogenic variant of DEP has affected North America and then spread throughout the world, causing serious economic losses. This disease has been included in France to the list of first-category health hazards for emerging animal species. Several variants of the TGE virus are the source of several strains of porcine respiratory coronavirus (Porcine respiratory coronavirus or PRCV), responsible for discreet respiratory disorders [53]. Among these viruses, one of them infected almost most European pig herds in 1984. Two other coronaviruses were identified in 2016 also with digestive tropism [55]: the porcine enteritis coronavirus (swine enteritis coronavirus or SeCoV), a recombinant virus containing a TGEV genome in which the gene S is replaced by that of PEDV, and the porcine acute diarrhea virus (swine acute diarrhea syndrome or SADS) [56].

### **3.3 Avian coronaviruses**

*CoVs in the chicken*: Among avian coronaviruses classified as gamma and deltacoronaviruses, the first avian coronavirus (infectious bronchitis virus or IBV virus) was described in 1931 and caused many economic losses in poultry farms (laying eggs and broilers). The disease is characterized by various lesions and damages in the genital tract with a drop in the rate of laying, malformation of the eggs, and low mortality. Besides other systems may be affected such as the respiratory tract, kidneys, etc. [53].

*CoV of turkeys*: Aside from IBV in chickens, the main avian species in which CoV has been definitively associated with the disease are the turkey, pheasant, and guinea fowl. Turkey coronavirus (TCoV) has been known, since the 1940s, to cause of enteric disease in turkeys in the USA. This disease is reported is found worldwide [57, 58]. Turkeys of all ages can be infected with high mortality in young poults. Most frequently reported clinical signs include decreased feed and water intake, wet droppings, diarrhea, and loss of body weight. TCoV is likewise associated with poultry enteritis and mortality syndrome (PEMS) which means high mortality, growth retardation, and immune dysfunction. Inbreeding turkeys, aberrant egglaying performance is related to TCoV disease, similar to that seen in IBV infections of chickens [57, 58].

*CoVs of pheasants (PhCoV)*: In pheasants, respiratory and renal problems have been associated with infections with CoV. PhCoV is closely related closely related to IBV and TCoV [59].

*CoVs of guinea fowl (GfCoV)*: GfCoV causes acute enteritis, showing a high death rate, possibly pancreatic degeneration, and fulminating disease in guinea fowl [60]. Genetically, GfCoV shows similarity to both IBV and TCoV, however, differences were observed in the spike gene, and a common ancestor has been suggested for the three viruses [60].

### **3.4 SARS-CoV-2 animal infections**

Under natural conditions, SARS-CoV-2 infection has been observed in ownerinfected animals. This case is called Spillback when infections are gained by animals through contact with humans. Few confirmed cases of SARS-CoV-2 in pets were reported in diverse countries: France (2 cats), Spain (2 cats), Germany (1 cat), Russia (1 cat), China (2 dogs and a cat in Hong Kong), Belgium (4 cats), the United States (31 cats and 24 dogs), United Kingdom (one cat), Japan (4 dogs), Chile (one cat), Canada (one dog), Brazil (one cat), Denmark (a dog), Italy (a dog) [61]. A recent French study has shown for the first time a significant circulation of SARS-CoV-2 in a population of pets (34 cats and 13 dogs) whose owners were infected with COVID-19 [62].

Experimental conditions have revealed that pigs and poultry are resistant to every inoculation with SARS-CoV-2 [63] while rabbits (which are also pets or laboratory animals) [64], and other laboratory animals include the golden hamster (*Mesocricetus auratus*) and rhesus macaque (*Macaca mulatta*) have been susceptible to SARS-CoV-2 [65]. Contrarily, laboratory mice and rats were resistant to SARS-CoV-2 [66]. The SARS-CoV-2 could also threaten many species beyond the great apes. In January 2021, gorillas at the San Diego Zoo were tested positive for COVID-19. None of the animals died, luckily, but were suffered from high fevers, lethargy, and cough like humans [67].

On November 29, 2021, recent reports have proven that SARS-CoV-2 has been transmitted from humans to wild white-tailed deer in the United States, but conversely, no cases of transmission from deer to humans have been reported. All were "apparently in good health," and "showed no clinical signs of the disease" [67].

In the United States, 4 tigers and 3 lions were probably infected by humans in a zoo in the Bronx. They presented mild respiratory symptoms. Since then, a tiger and a puma have been also reported infected [68]. Recent studies from the Friedrich-Loeffler Institute in Germany reported raccoon dogs (canids bred in China for their fur) previously susceptible to SARS-CoV-1 were also susceptible to SARS-CoV-2 and could contaminate other raccoon dogs by direct contact with no clinical signs. These animals can be intermediate hosts potentially involved in the emergence

*Emerging Human Coronaviruses (SARS-CoV-2) in the Environment Associated with Outbreaks… DOI: http://dx.doi.org/10.5772/intechopen.103886*

of COVID-19 [69]. On the other side, infected mink farms by SARS-CoV-2 were detected (2 on April 26, 33 to August 14, then 52 to September 14). Two million mink were then culled by the Dutch authorities. As of September 1, the first human cases contaminated by mink were reported [70] 66 of the 97 employees of these farms tested positive for SARS-CoV-2, with whole-genome sequencing revealing mink-like variants in 47 cases [71].

### **4. Detection of SARS-CoV-2 in wastewater**

Wastewater-Based epidemiology (WBE) has been successfully used to investigate polio circulation within the community. This novel biomonitoring tool has been successfully used to evaluate international poliovirus vaccine campaigns and to investigate the use of some illicit drugs. Additionally, this tool has been successfully used to detect the occurrence of hepatitis and norovirus outbreaks [72, 73].

The environmental circulation of viruses as human pathogens has been given more attention since the first occurrence an spread of Severe Acute Respiratory Syndrome Coronavirus 1 appeared (SARS-CoV-1) in 2003 and Middle East Respiratory Syndrome (MERS) in 2012. Even more focus on the development of surveillance systems of viruses in the environment has been reported since the first occurrence of COVID-19 in December 2019 in Wuhan, China [73, 74].

Since most patients infected with SARS-Cov-2 might be asymptomatic, rapid and accurate detection of potential virus carriers is a critical step to suppress the risk of disease transmission at an early stage of the disease [75]. SARS-CoV-2 has been shown to replicate actively in enterocytes of the human intestine, where there is the highest expression of ACE2 in the human body and the virus is excreted in the feces [76]. SARS-CoV-2 RNA has been detected worldwide in raw wastewater and sometimes in treated wastewater, which could imply potential environmental transmission via the water cycle [77–79]. SARS-CoV-2 RNA has been reported in wastewater treatment plants in various nations around the world such as Australia, Italy, Spain, the Netherlands, the United States, Japan, Germany, the Arab Emirates States, Istanbul, and Brazil [12]. The duration of the shedding through feces can be as long as 33 days, with a decreased shedding rate, ranging from 106 to 1012 gc/L, which is lower than some other infectious viruses, like MERS-CoV, and SARS-CoV-1 [80, 81].

Detection of SARS-CoV-2 RNA in wastewater was performed by PCR-based methods such as reverse transcription-polymerase chain reaction (RT-PCR) and digital PCR using the amplification of parts of the viral genome, such as the genes coding for the nucleocapsid [82] and the viral envelope [83]. To gain insights into the fate and transport of SARS- CoV-2 in WWTFs, the general workflow for SARS-CoV-2 testing in wastewater is conducted in the following order sample collection, sample concentration, RNA extraction and analysis, and data reporting [84, 85]. Molecular detection of viral RNA involves three major steps:

*Viral concentration/enrichment*: A viral enrichment step is recommended before RNA extraction because of the potential low concentration of viral titer in the wastewater. Viral particles are concentrated and recovered by polyethylene glycol (PEG) precipitation, or by filtration using 0.2 μm filters [7] ultrafilters [78], and ultracentrifugation [86]. Direct RNA extraction from electronegative membranes (0.45 μm) is another method that can be used [87]. For virus concentration, a variety of techniques have been explored, including polyethylene glycol (PEG)-NaCl precipitation, ultrafiltration, AlCl3, flocculation, and others [88]. Because of its better selectivity

and tolerance to PCR inhibitors in wastewater, PEG-NaCl precipitation is the most widely used technique [89].

*RNA extraction*: RNA extraction has typically been performed using commercial kits from a variety of supplies. The most commonly used RNA extraction kits are the RNeasy Power Microbiome kit [78, 87, 90], the BioMérieux Nuclisens kit [78], Power Fecal Pro-Kit [78], and RNeasy Power water Kit [87].

*Amplification of viral RNA*: Amplification of viral RNA extracted from wastewater was performed with a set of five primers/probes. These primers and probes target different regions of the viral particle in **Table 3**.


### **Table 3.**

*Primers/probes used for amplification of SARS-CoV-2 RNA in wastewater [91].*

*Emerging Human Coronaviruses (SARS-CoV-2) in the Environment Associated with Outbreaks… DOI: http://dx.doi.org/10.5772/intechopen.103886*

Varying results have been reported using these primer/probe sets targeting different parts of the viral genome. For example, [79] found that primer N1 resulted in positive amplification of all study sites (6), but primers N3 and E resulted in positive amplification of 5 and 4 study sites, respectively. However, Rimoldi et al. [97] found a high frequency of positive amplification targeting the ORF1ab gene, compared to only three positive wastewater samples for the N and E genes. As a result, our findings are equivocal in terms of the optimum primer/probe combination for viral RNA amplification in wastewater. This could be attributed to the sensitivity of primers/probes, PCR inhibitors in wastewater samples from different regions/sites, and the potential stability of the virus and viral genome in these different areas [98]. Droplet digital PCR is another molecular technique used for the detection of coronaviruses in clinical and sewage samples. This was found to have an improved, more sensitive, and more accurate lower limit of detection than RT-PCR for environmental samples [99, 100].

Khan et al. [101] discovered that smaller sample volumes (50–100 ml), 30% (w/v) PEG-NaCl, a 12-hour incubation interval, and a 24-hour storage period resulted in improved RNA recoveries in terms of N1 and N2. RNA concentrations were always at least one order of magnitude greater in RT-qPCR than in RT-ddPCR. However, under all test conditions, both RT-qPCR and RT-ddPCR revealed that RNA is generally absent in the sludge samples, resulting in a false-negative result.

### **5. Risks of environmental transmission of SARS-CoV-2 in wastewater**

Fecal-oral transmission of SARS-CoV-2 is yet to be approved, but additional research is essential to clarify the potential risks of the novel coronavirus in sanitation systems. The SARS-CoV-2 virus has been detected in fecal samples and effluents. Contaminated drinking water, contaminated raw, undercooked aquatic aquaculture, sewage-irrigated food, and vector-mediated transmission are all possible sub-pathways of the fecal-oral mode of transmission. Seepage from sanitation systems (pit latrines and septic tanks), landfill leachates without geomembrane protection toward shallow groundwater systems can pollute drinking water sources. In other types of coronaviruses, one study found 99.9% percent fatality after 10 days in tap water at 23°C and over 100 days at 4°C. This data also suggests that coronaviruses have a longer survival duration in tap water than in wastewater [102].

The exposure of humans to viruses, including SARS-CoV-2 through bioaerosol and wastewater aerosols has been highlighted. For example, a laboratory study investigating the persistence of SARS-CoV-2 in aerosols showed that the virus keeps its viability and infectivity in aerosols for up to 16 h [103].

Therefore, human and animal exposure to SARS-CoV-2 via wastewater aerosols could be significant in shared sanitation systems, especially in crowded informal settlements in developing countries [104]. Various studies have registered the prevalence of SARS-CoV-2 in urban and rural sewer systems. This wastewater might contaminate fresh water; it can pass through untreated effluent discharged to surface waters or leak and affect the supply of traditionally treated graywater. These recycled urban waters also represent possible modes of transmission [104].

In some regions with a high prevalence of COVID-19 disease, SARS-CoV-2 was prevalent in surface water, including both saltwater and freshwater. Coronaviruses from anthropogenic activities were confirmed in different water bodies [102, 105]. Marine

and fresh aquatic foods such as fish and crustaceans may be contaminated by raw wastewater. Marine foods from coastal areas receiving untreated wastewater, aquatic food acquired from surface aquatic systems receiving raw or partially treated wastewater, and raw wastewater-irrigated salad crops are all possible sources of food transmission.

Raw wastewater-aquacultural systems and raw wastewater irrigation of crops consumed raw, such as salads, are two more techniques that promote food contamination. However, more research is needed to determine the prevalence and durability of SARS-CoV-2 in marine and surface aquatic systems, as well as food derived from these sources. Such research should also look into the effects of various food pre-treatments and culinary processes on SARV-CoV-2 persistence. Studies based on genomic and phylogenetic analyses are needed to evaluate whether SARS-CoV-2 may leap from aquatic environments to humans. This is important given the interactions between humans and wildlife, including the widespread consumption of aquatic and terrestrial animals [106].

## **6. Disinfection and eradication procedures of SARS-CoV-2 in wastewater**

Information from the general suppression of viruses and surrogates of coronaviruses could be used, with caution, to give additional information on the possible suppression of these viruses. For example, [107] observed that activated sludge treatment (ASP) processes in subtropical conditions removed over 3 logs 10 of enteric viruses. ASP is a commonly used wastewater treatment process around the world [108–110]. This treatment process includes primary settling, biological degradation, and secondary clarification [107, 111]. Ye et al. [112] demonstrated that during ASP processes, the highest removal of coronaviruses can occur at the primary settling stage.

For example, a sewage pond system [113] reported an average reduction of 1 log10 of viruses for 14.5 to 20.9 days of retention. Besides adsorption on particles, a longer HRT (hydraulic retention time) may be required for coronavirus inactivation in wastewater. Because coronaviruses adsorb to solid surfaces, a large concentration can be expected in the sludge. Anaerobic digestion of sludge, which is a typical sludge treatment method, reduces pathogenic bacteria. The most commonly used membrane technologies in wastewater treatment are microfiltration (0.1–0.2 μm) and ultrafiltration (0.005 ≈ 10 μm). There are reports of microfiltration membranes with larger pore sizes (0.2 to 0.4) being used [114]. The best membrane technology for coronavirus removal is ultrafiltration with an average viral particle diameter of 120 nm (0.12 μm) and an envelope diameter of 80 nm (0.08 μm) [115]. Adsorption of coronaviruses on wastewater solids can enhance their removal. Tertiary wastewater treatment processes such as chlorination and UV treatment can also result in further removal of remaining coronaviruses in wastewater [98]. Chlorine has been reported to inactivate viruses through the cleavage of the virus capsid protein backbone, inhibiting the injection of the viral genome into host cells [116, 117].

The inactivation of coronaviruses by UV irradiation has also been reported in several studies [118–120]. Enveloped viruses, like coronaviruses, are more sensitive to UV than non-enveloped viruses. The mechanism by which UV inactivates coronaviruses is the generation of pyrimidine dimers which damage nucleic acid [94]. Methods of disinfection used in the drinking water treatment inactivate efficiently SARS-CoV-2 in water [121]. However, there is a need to investigate and ameliorate the performance of disinfection technologies to be adopted for the inactivation of SARS-CoV-2 in municipal and hospital wastewater to reduce the related risk of possible infections [121].

*Emerging Human Coronaviruses (SARS-CoV-2) in the Environment Associated with Outbreaks… DOI: http://dx.doi.org/10.5772/intechopen.103886*
