Moroccan Journal Of Public Health Vol. 1, N° 1 (2020), 52-63 ISSN: 2658-8099 Review

Comparative Epidemiology of in humans and animals

Mohamed Mahi FASSI-FEHRIa and Ouafaa FASSI FIHRIa*

Microbiology, Immunology and Contagious Diseases,Institut agronomique et vétérinaire AV Hassan II, Rabat. Corresponding Author Email: Ouafae FassiFihri: [email protected]

Article info SUMMARY Received June 2020 are a group of RNA that cause diseases in and Accepted September 2020 Online September 2020 . In humans and birds, they cause respiratory tract infections that can range from mild to lethal. Mild illnesses in humans include some cases of the

, which can also be caused by other viruses, predominantly Keywords , while more lethal varieties cause Severe Acute Respiratory epidemiology, coronavirus, pathogenicity, evolution, Syndrome (SARS), Respiratory Syndrome (MERS), or the current characteristics. Coronavirus disease 2019 (COVID-19). In cows and Coronaviruses cause like the transmissible gastroenteritis (TGEV), while in young calves, the Bovine Coronavirus (BCV) causes severe profuse enteritis. In this review we will go over the microbiology of

coronaviruses, their classifications and the different infections caused by it in animals and humans.

various fields joined the urgent fight against this deadly Introduction

Since December 2019, the world has been confronted disease. In the light of preliminary observations and with the torments of an emerging pandemic, designated raised questions, it is interesting to carry out a by the name of COVID-19, which stands for comparative study on the coronaviruses involved in Coronavirus Disease-19. It is caused by the Severe acute human and animal infections, which could contribute in respiratory syndrome coronavirus 2 (SARS-CoV-2) understanding the natural and spontaneous models. In (WHO, 2020). Health, social, economic and this review we will be covering the morphological, environmental consequences of the pandemic, in the structural and biological characteristics of the short and medium term, seem immeasurable. The global coronaviruses and their nomenclature and classification. battle against the virus continues up to this date. With no Then we will go over some pathologies caused by drugs or treatments in the market, researchers from

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coronaviruses in animals. Finally we will go over the noticeable infections caused by the coronaviruses over the years in humans. We will briefly summarize the 2003 Severe acute respiratory syndrome coronavirus (SARS- CoV) epidemic, followed by the 2012 Middle East Respiratory Syndrome (MERS) and then the recent outbreak of the Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in 2019.

1. Morphological, structural and biological Photo 1. Coronavirus in negative contrast electron characteristics of Coronaviruses microscopy (Image courtesy of Dr L. Kolesnikova, 1.1. Morphology Institute of Virology, Marburg, Germany) Coronaviruses are presented in negative contrast electron 1.1. The structural characteristics of viral particles 1.1.1. Viral proteins Virions are composed of structural and non-structural proteins. The S protein assembles into trimers on the virion surface and is responsible for attachment of particles to host cellular receptors and fusion of viral envelope with the host cell membrane, a process that involves mechanisms of translation, fusion and recombination of the surface, which results in an intracellular penetration of the virion (Hofmann and Pöhlmann, 2004). Protein S undergoes large microscopy as spherical or polymorphic particles, conformational rearrangements during the viral envelope presenting an envelope of 60 to 220 nm in diameter. fusion with the cell membrane (Fehr et al., 2015). Most Club-shaped surface projections (12 to 24 nm long), the Coronaviruses depend on host cellular proteases for their spicules (S) or spikes, protrude from the envelope, giving entry into cells. Protein S induces the synthesis of it the crown appearance, hence the latin name corona neutralizing antibodies. It is a major Coronavirus antigen (Stadler et al., 2003) (photo 1). An empty space separates with several domains; the S1 domain containing most of the viral core, constituted by the helical nucleocapsid, the epitopes recognized by neutralizing antibodies during from the envelope (Photo 1). an . The M protein integrated into the membrane is essential for encapsidation. Other major components include The nucleocapsid (N) proteins, the envelope (E) protein and hemagglutinin esterase (Schoeman and Fielding, 2019), and the non-structural

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proteins that are not required for viral replication: e.g. Orthocoronavirinae. Coronavirus contains 4 genra: ⍺, replicase, NSP1, 2, 3...up to14 (Angelini et al., 2013). β, Ɣ and δ coronavirus. The alpha-Coronavirus genus 1.1.1. Coronavirus Genome includes Porcine, feline and canine Coronaviruses. The coronavirus genome is a single-stranded positive- Viruses isolated from , The beta-coronavirus genus, sense RNA, ranging from 26 to 32 Kb in length. It is include viruses involved in seasonal human diseases, capped at the 5' end and has a 3′ poly (A) tail. It is an viruses responsible for epidemics and of infectious mRNA molecule whose function is to initiate human SARS, Bovine disease viruses and viruses mRNAs for protein synthesis necessary for infection isolated from bats. Lastly, the gamma and delta- (Snijder et al., 2003). coronavirus genera include viruses responsible for avian 1.2. Viral replication disease and viruses of migratory birds. Tables 1 2 and 3 list the main animal and human Coronavirus diseases, as The viral replication of the coronaviruses includes well as the list of virus reservoir host animals. several steps. It begins by the recognition and attachment to target cells by S glycoproteins. There are many types Table 1. Inventory of major coronavirus of cellular receptors, namely the aminopeptidase for diseases (Saif, 2004) Porcine transmissible gastro-enteritis virus (TGEV) Porcine diseases (alpha-coronavirus) (Bin Wang et al., 2018) and  Porcine transmissible gastroenteritis (1945) (H229E) (Jamie et al., 2003), feline or canine  Porcine respiratory disease (1970) aminopeptidase N and carcinoembryonic antigen  Porcine epidemic diarrhea (1970) (Tresnan et al., 1996). After attachment, a protease of Bovine diseases (beta-coronavirus) the host cell cleaves and activates the receptor-attached  Bovine pneumo-enteritis spike protein. After the entry to the host cell, the virus is  Calf enteritis uncoated and its genome enters the cell's cytoplasm. Avian diseases (gamma-coronavirus) Translation of the positive-strand genomic RNA gives  Avian infectious bronchitis (1937)  Coronaviral enteritis of turkeys rise to a large polyprotein that undergoes proteolytic processing to generate an RNA-dependent RNA Other affected species (alpha-coronavirus)  Feline infectious peritonitis polymerase. RNA polymerase then generates an  Canine enteric coronavirus antisense negative-strand template (Sethna et al., 1991).

1. Etymology and classification

According to the International Committee of Taxonomy of Viruses report (ICTV, 2018), Coronaviruses belong to Order : Nidovirales, Family : , Subfamily :

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Table 2. Inventory of the main human coronavirus diseases (Corman et al., 2018; Cui et al., 2019)  Coronavirus encephalitis 229E and NL-63 (alpha-coronavirus)  Coronavirus enteritis in children (alpha-coronavirus)  Seasonal upper respiratory tract infections (OC-43, B-14, HKU1, NL-63) (beta- coronavirus)  Epidemics and pandemics of severe acute respiratory syndrome (SARS) (beta- coronavirus) including : ✓ SARS-CoV 2002-2003 ✓ MERS-CoV 2012 ✓ SARS-CoV 2019

Table 3. Coronaviruses isolated from virus-reservoir host animals (Zhengli and Zhihong, 2008)

 Coronavirus of palm civet cats (Paguma larvata)  Coronavirus of raccoon dog (Nyctereutes procyonoides)  Coronavirus of (Manis javanica)  Coronaviruses isolated from bats (Pipistrellus, Rousettus, Rhinolophus, Miniopterus) ✓ SARSr-CoV (W1V1) ✓ SARSr-CoV (HK 43) ✓ SARSr-CoV (RP3) ✓ HKU4 and HKU5

2. Coronaviruses in animal pathology 1960, were found in benign seasonal, endemic, respiratory (colds, rhinitis, laryngitis) (Kahn and Coronaviruses are associated with a wide range of McIntosh, 2005) or enteric infections, in humans and in enteric, respiratory and systemic infections in several many domestic (cattle, pigs, dogs, cats, etc...) or wild species of domestic and wild animals with varying (rodents, ferrets, hamsters, etc...) animal species. The degrees of severity. The first studies concerning animal human Coronaviruses HCoV-229E, HCoV43, HCoV infections with Coronaviruses were those of the avian NL63 and HKU1 have been detected in various infectious bronchitis or porcine transmissible countries, indicating a worldwide distribution of these gastroenteritis, whose viruses were identified in 1937 viruses that are well adapted to humans and do not and 1945 respectively (Beaudette and Hudson, 1937; appear to be maintained by an animal reservoir (Hamre Cheever et al., 1949). However, viral strains identified in and Procknow, 1966; Kahn and McIntosh, 2005). Since

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2002, highly contagious zoonotic epidemics and TGEV. The new virus has an essentially respiratory pandemics have emerged in humans with high levels of tropism, multiplying in the epithelial cells of the severity (Guan et al., 2003; Cui et al., 2019), starting respiratory mucosa. Numerous TGEV strains were with the 2003 SARS-CoV epidemic, followed by the subsequently isolated in Europe, USA and Japan. They 2012 MERS-CoV outbreak and lastly the 2019 Covid all belong to the same serotype. In addition, they have pandemic (Table III). close antigenic relationships with feline and canine Coronaviruses, leading to the hypothesis of a common 2.1. Porcine transmissible gastroenteritis origin of all these strains which would be host mutants of (TGE) an ancestral strain. Transmissible gastroenteritis (TGE) is a highly 2.2. Bovine coronavirus (BCoV) contagious viral disease, manifested by profuse diarrhea, vomiting and high mortality in 2-3 weeks old piglets. It BCoV is responsible for a digestive and respiratory is caused by an alpha-Coronavirus (Enjuanes et al., disease in calves causing significant losses on the farm. 1995). It was first reported in the USA in 1945, and has The virus was first isolated in the USA in 1970 from then been observed in Japan, , and calves with diarrhea (Stair et al., 1972). It is actually several countries in Europe, America and Southeast associated with different clinical pictures, Asia. Two important points should be considered: host including neonatal calf diarrhea that is associated with specificity and tissue tropism of the virus. Both aspects various pathogens (E.coli, rotavirus, cryptosporidium, are involved in the emergence of infectious diseases, etc...) (Reynolds et al., 1986), winter dysentery which is porcine epidemic diarrhoea (PED) and porcine manifested by diarrhea in adult cattle and respiratory respiratory disease (PRD) (Saif, 2004). problems in calves (Saif et al., 1988; Lathrop et al., The TGEV replicates in the small intestinal epithelial 2000). It appears these diseases are bovine species- cells resulting in cell destruction and functional specific. Sheep can be infected but the impact remains alterations (Saif, 2004). At the end of 1970s, a new very low. Only one serotype is recognized, but there is porcine Coronavirus emerged causing the porcine some antigenic variability between the different strains. epidemic diarrhea virus (PEDV). It appeared in Europe The transmission can be direct or indirect. It occurs and then spread to Asia causing the severe diarrhea that through the introduction into the herd of individuals gradually became enzootic (Takahashi et al., 1983). carrying the virus, which they eliminate through nasal However, in 1986, a new disease manifested by severe secretions or faeces. appeared in farms in Europe (Denmark, From a clinical point of view, incubation in calves at Belgium, France, United Kingdom, Spain). This disease birth is 24 to 48 hours and clinical signs appear at 5 days is caused by a Coronavirus very close to the TGEV. It is of age when the secretory antibody (secretory IgA) level distinguished by an important tropism for the respiratory decreases in the calf's colostrum and gastrointestinal system. It is a spike (S) gene deletion mutant of TGEV, a tract. The disease is characterized by yellow liquid mutation which results in an alteration of the S protein diarrhea with traces of mucus and blood. Fatal responsible for recognition of intestinal cell receptors by dehydration ensues. In the feedlots, the respiratory form

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is manifested by nasal and lacrimal secretions with signs epidemic period; the virus is maintained by low-noise of bronchopneumonia. This is observed in shipping fever transmission in receptive species; 2) the narrow where the BCoV is involved. specificity of receptive species; and 3) the high variability of pathogenicity in organ and tissue tropism, which explains the frequency of emerging diseases. 2.3. Avian infectious bronchitis (IB)

Avian infectious bronchitis is a highly contagious 3. Human Coronaviruses infections: disease, specific to reared chicken and pheasant, which 3.1. The 2003 SARS epidemic occurs in countries with intensive poultry farming, causing high mortality in chicks and high morbidity in Initially described as "Acute Atypical Pneumonia", the adult chickens (Cook and Mockett, 1995). IB manifests disease was officially designated as Severe Acute as respiratory disorders resulting from damage to the Respiratory Syndrome (SARS). This syndrome appeared ciliated epithelium of the respiratory tract, which results as a highly contagious, human-specific, respiratory in coughing, sneezing, conjunctivitis and purulent infection caused by a . First reported sinusitis (Saif, 2004). Transmission is by inhalation of in November 2002 in the Guangdong province, China, respiratory secretions. It is also transmitted through the disease quickly spread throughout 32 countries the ingestion of contaminated feed or faeces, or through following year, causing a major outbreak with more than contact with infected equipment and surfaces. 8,400 people infected and more than 800 dead, according Survival and persistence of the virus in farms is due to a to WHO data (WHO, 2003). lack of control of disinfection and biosecurity. The virus After an incubation period of 4 to 5 days, the disease is maintained in the avian population by low-noise manifests by fever in 94% of cases, dry cough, dyspnea, transmission and the epidemic restarts when the headache, hypoxemia, myalgia, sometimes with percentage of the population that is immune decreases. digestive disorders. Death occurs as a result of There is no known wild reservoir of the virus. respiratory mechanism failures. The mortality rate is in Respiratory tropism is sometimes aggravated by the the order of 2 to 13% for people more than 60 years of appearance of stable mutants with tropism to the kidneys age (WHO, 2003). The asymptomatic form with virus or the reproductive system, particularly the oviduct, excretion seems relatively frequent. The virus is leading to high mortality. Because of these capacities for transmitted by inhaling droplets of saliva or by aerosols mutation and recombination, the IB Virus (IBV) offers emitted when infected individuals sneeze or cough. the opportunity for the emergence of stable variants Transmission by hand or through infected material can capable of spreading widely throughout the world. These occur in all clinical forms. antigenic variants, derived from an ancestral strain, Virus , genome sequencing and phylogenetic interfere with vaccines and compromise their efficacy. analysis have revealed the novel character of the virus, In summary, the epidemiology of animal coronavirus which raises the origin of contamination and the problem infections that we have just mentioned is characterized of the existence of a wild reservoir. Very rapidly, by: 1) the absence of virus reservoir hosts in the inter- experimental infections have shown that the SARS virus

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can infect a wide range of hosts, both domestic and wild the and humans remains to be proven (Ithete et al., animals (dogs, cats, wolves, foxes, mink, etc.). These 2013). Camel breeders, slaughterhouse staff and fresh animals can potentially carry the virus (carrier), under camel milk consumers are most exposed to natural conditions. In addition, Coronaviruses genetically contamination. The MERS epidemic is still ongoing but similar to SARS have been isolated from the clinically limited to the Arabian Peninsula with several hundred normal civet cats (Paguma larvata) and raccoon dogs cases recorded each year. (Neycterentes procyonoides). During the 2002-2003 pandemic, many Coronaviruses, closely resembling 3.3. The Covid-19 pandemic SARS, were discovered in bats (Guan et al., 2003). The current pandemic, caused by the emergence of a new These species would potentially be natural reservoir Coronavirus, began in December 2019, in , Hubei hosts for SARS-CoV 2003, which they transmit to the Province, China (WMHC, 2019). Covid-19 is civet host intermediate between bats and humans. responsible for a pandemic of rare violence, which 3.2. The 2012 MERS-CoV outbreak affected 196 countries around the world, causing the The Coronavirus associated with MERS (Middle East contamination of more than 31 million people and the Respiratory Syndrome) was identified in the Arabian death of approximately one million (WHO data, end of Peninsula in 2012 (Zaki et al., 2012). The disease September 2020). Coronaviruses, both SARS-Cov-2 and manifested by fever and respiratory problems (dry SARS-CoV-2003, have certain similarities in cough, dyspnea, pneumonia) with sometimes epidemiological and pathological characteristics gastrointestinal symptoms (diarrhea, vomiting, (WHO, 2020). abdominal pain). The asymptomatic form was common From a pathological point of view, the disease is among infected people. During the 2012-2014 epidemic, manifested by moderate fever, dry cough, dyspnea, a total of 1219 cases were registered with 449 deaths myalgia and altered general condition. Anosmia, (CCC, 2016). Arabian Peninsula is the geographical dysgeusia and diarrhea are sometimes noted. However, origin and the cradle of the epidemic that later spread to the vast majority of infected persons show no symptoms 27 countries, South-East Asia, Australia, Eastern Europe. (14%), or only mild symptoms (71%). The incubation The mortality rate is estimated at 35%, it mainly affects period is between 2 and 6 days. The patient excretes the people over 60 years old, particularly male patients with virus through saliva droplets and nasal secretions about 3 frailties (obesity, diabetes, cardiovascular or days before symptom onset. This secretion continues bronchopulmonary pathology, etc.). Both contagiousness throughout the duration of disease and the beginning of and pathogenicity appear much lower than in SARS- convalescence. The transmission risk is uniform and CoV-2003. depends on contaminating viral load and receptivity of Currently, it is accepted that the bats serve as natural exposed individuals (Chan et al., 2020). The severity of reservoirs for MERS-CoV-2012. The mode of illness, in other words, the prognosis, depends on the risk transmission to humans remains to be demonstrated. The factors which are: advanced age, overweight, role of the dromedary as an intermediate host between pathological conditions including diabetes, hypertension,

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asthma, cardiovascular disorders, etc... Healthy, washing, etc… . In a second step to achieve asymptomatic, virus-excreting carriers are an occult "eradication", the massive use of laboratory tests (RT- source of human-to-human contamination. PCR, serological tests) is designed to identify outbreaks Comparative genetic studies of viruses isolated during and pockets of infection, clusters, in areas of human the pandemic (SARS-CoV-2) and strains from bats concentration such as factories, stations, markets, places (SARSr-CoV) (Table IV) especially bats of the genus of conviviality, etc..., in order to ensure control, that is, Rhinolophus (Zhu et al., 2020), show 96% genomic identification of new contamination sources. similarity, hence the hypothesis of the role of bats as a natural reservoir of the human SARS-CoV-2 as well as In the inter-epidemic period, which can last several years the SARS-CoV-2003 of the first pandemic. (10 years between SARS-CoV-2003 and MERS-CoV- Furthermore, a virus similar to the bat SARSr-CoV have 12, 7 years between MERS-CoV-12 and Covid-19) been discovered in the pangolin (Manis javanica) (Lam (Hilgenfeld and Peiris, 2013), the virus can survive and et al., 2020), an insectivorous and cavernicolous multiply in a natural reservoir host, which is the bat. This of tropical regions, an animal sought after in host has no apparent symptoms or lesions, but is a China for its flesh and scales, suggesting that this animal potential occult source of virus transmission to humans. have played a key role as an intermediate reservoir The human Coronaviruses SARS-CoV-2003, MERS- between bats and humans. All these hypotheses require CoV-12 and SARS-CoV-2 are beta Coronaviruses; they confirmation. are derived from recombinations between several animal viruses and appear to have originated from bats. Indeed, 3.4. Pandemics, reservoir host of virus and SARS-related coronavirus of the beta genus have also breaking the species barrier been identified in at least 11 species of bats in Asia, The development of SARS and MERS can be viewed Africa and Europe including species of the genus from two angles: the active epidemic aspect and the Pipistrellus, Rousettus, Rhinolophus, Miniopterus among inter-epidemic aspect. The active epidemic is the result others (Fan and Zhou, 2019). of human-to-human transmission of virus and is manifested by clinical expression and more or less severe Table IV. Coronavirus isolated from bats (Fan and evolution. The SARS and MERS epidemics evolve Zhou, 2019) through peaks of transmission with an R0 reproduction ● SARSr-CoV (W1V1) rate of between 2 and 5 (Bell; 2004; Chowell et al., 2004). The reproduction rate R0 is the number of new ● SARSr-CoV (UK43) cases that an individual can produce when introduced ● SARSr-CoV (RP3) into a susceptible naïve population. The fight against ● HKU4 these epidemics, in the absence of a vaccine, consists of ● HKU5 reducing human-to-human transmission through the implementation of strict sanitary measures, now well The human cell receptors for all bat strains have not been known, such as: wearing masks, social distancing, hand

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identified and remain unknown, while for the human transmission involves the mechanism of breaking the strains SARS-CoV-2003 and SARS-CoV-2, as well as species barrier. It is, in fact, commonly accepted that for MERS CoV-12 strains, the cell receptor sites are: there is a kind of barrier which hinders the transmission Angiotensin Converting Enzyme (ACE2) and of a specific pathogen naturally from a receptive animal DiPeptidyl-Peptidase-4 (DPP4) (Hofmann et al., 2005). species to another species, the latter is considered resistant or refractory. Breaking the species barrier Bats, in which transmission of Coronaviruses occurs at means the crossing of all the biological mechanisms that low noise levels, offer all the potential to ensure oppose the transmissibility of a pathogen to a new transmission to humans either directly or indirectly species that proves capable of ensuring the complete and through intermediate host animals (civet, dromedary, autonomous development of a new disease, including pangolin, or others) that play the role of "transmission transmission in the population of the species that facilitator". These potentialities relate to the ecology and becomes receptive (Ji et al., 2020; Li et al., 2020). The biology of chiropterans: flying mammals, with different mechanisms of rupture relate to the pathogenic agent, the diets (frugivorous, insectivorous, etc...), different roost coronavirus, on the one hand, and to the animal species types, wintering, migratory, etc..., on the one part, and concerned on the other hand (human populations, human behavior on the other part, ensuring close contact different species of chiropterans, civets, dromedaries, and promiscuity resulting from human population etc...). density and reservoir hosts. Frequency and intensity of For Coronaviruses, this involves genetic processes contact favour the installation of virus-laden aerosols in including point mutations by insertion or deletion, and confined spaces such as barns, attics, various intergenomic recombinations. These processes are constructions, etc… . This situation is reminiscent of frequent in RNA viruses with large population size and other viruses such as the Ebola virus for example. The short replication time (a few hours per cell infection bats, natural reservoir hosts of the virus, ensure its cycle), as for example in influenza virus, Bunyavirus or transmission to chimpanzees, macaques or other polio virus etc... Such genetic modifications confer on primates, which contaminate humans during handling. coronaviruses a high capacity for adapting to changes in This is also the case of the 2009 H1N1 influenza host or environment. pandemic which followed a severe influenza epizootic in The mutant virus, or variant, as a result of changes in pig farms in Mexico (Mena et al., 2016). It is the spikes (S) composition and conformation, becomes genomic recombination between different strains (wild capable of binding to specific receptor sites on epithelial birds, reservoirs, pig farms in particular) that gives cells of human respiratory and digestive mucosa recombinants the ability of adapting to humans and (Gallagher and Buchmeier, 2001). Fixation is followed triggering a pandemic. This involves the mechanisms of by penetration, replication and release of variant breaking the species barrier. Indeed, the transmission of particles. The mutation occurs in the multiplying viral SARS virus from bats to humans or intermediate host population in chiropterans and mutant selection is animals (WHO, 2020), just as human-to-human performed in newly infected humans or in intermediate

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