Transmission, and the Immune System Nourishment
8.2 When, What, and Where of COVID-19
8.2.1 The Family Coronaviridae
The subfamily Orthocoronavirinae is within the family Coronaviridae, along with the subfamily Coronavirinae. The genera of the subfamily Orthocoronavirinae are alphacoronavirus, beta- coronavirus, gammacoronavirus, and deltacoro- navirus. Betacoronavirus is a genus with subgenera Sarbecovirus and Merbecovirus to which SARS-CoV and MERS-CoV species belong (Millán-Oñate et al. 2020). The first caused the outbreak of severe acute respiratory syndrome (SARS) in 2002–2003, and the other one succeeded in opening the outbreak of the Middle East respiratory syndrome (MERS) in 2012–2013. The SARS and MERS outbreak cor- related with a death rate of 10% and 34%, respec- tively, indicating their high potential of pathogenicity for humans. They caused together about 1600 deaths. However, the recent outbreak of pneumonia of unknown etiology, which seems to be the result of a novel coronavirus, the so- called SARS-CoV-2, has to date caused over 3 million cases and claimed more than 200,000 deaths in only 4 months (Fig. 8.1).
8.2.2 What Have Coronaviruses Brought for Human Beings?
Since the mid-1960, seven coronaviruses have occurred in humans by consideration of this new one. Four coronaviruses, including 229E, NL63, OC43, and HKU1, are endemic in humans and correlate commonly with mild symptoms affect-
ing the respiratory system, gastrointestinal system, and the nervous system. Three most recent human coronaviruses, SARS-CoV, MERS- CoV, and SARS-CoV-2, appear to be originated by zoonotic transmission and can cause poten- tially fatal condition characterized by respiratory failure.
Human coronaviruses are positive-sense single- stranded RNA viruses that possess two main groups of proteins: structural and nonstruc- tural proteins. Structural proteins include the spike (S), nucleocapsid (N), matrix (M), and envelope (E). Nonstructural proteins (NSP) include proteases, such as nsp3 and nsp5, and RNA-dependent RNA polymerase (RdRP) such as nsp12. The spike protein is the key to binding the virus to its cell surface receptor. Sequence analyses reveal that the spike glycoprotein of the SARS-CoV-2 has a high sequence identity of greater than 70% to that of the 2002 SARS-CoV (Fig. 8.2).
8.2.3 SARS-CoV-2: Where Does It Come from, and How Does It Go?
8.2.3.1 In 2015, the application of reverse genet- ics of SARS-CoV led to the development of a recombinant virus that through binding the same surface receptor caused infection in human lung parenchymal cells but was resis- tant to SARS-CoV vaccine and monoclonal antibodies targeting SARS-CoV spike protein In 2015, a group of American, European, and Chinese researchers obtained a SARS-like coro- navirus WIV1 (SL-CoV-WIV1) from Chinese horseshoe bats, isolated the spike protein of SL-CoV-WIV1, the RsSHC014-CoV sequence, and developed a hybrid virus utilizing the RsSHC014-CoV sequence and the SARS-CoV (mouse-adapted) backbone (Menachery et al.
2015).
Despite very similarities, compared to human SARS-CoV, SL-CoV-WIV1 expresses 14 differ- ent residues involved in binding the ACE2 recep- tor (Menachery et al. 2015). Also, the lentivirus
Fig. 8.1 Three epidemics caused by virulent human coronaviruses:
SARS-CoV, MERS- CoV, and 2019-nCoV
expressing the spike protein of SL-CoV-WIV1 could not bind human ACE2, while human SARS-CoV can bind the ACE2 receptor.
Consequently, the authors used the SARS-CoV backbone to create a chimeric virus composed of the spike protein of SL-CoV-WIV1. They named this novel virus the chimeric CoV or SHC014-MA15. SHC014-MA15 required the ACE2 receptor for the cell entry; could use its orthologs in humans, civet, and bats; and repli- cated in the human epithelial airway cell line Calu-3 2B4 and primary human airway epithelial (HAE) cultures enough so that a severe infection occurred.
Ten-week-old mice faced weight loss and death upon infection with SHC014-MA15 (Menachery et al. 2015). Weight loss, but no death, occurred in mice infected with SARS- CoV Urbani (SARS-MA15). Lungs from both mice infected with SHC014-MA15 and mice infected with SARS-MA15 revealed the same viral titers. However, pathological findings were different; SHC014-MA15 mainly involved the parenchyma, while SARS-MA15 affected both airways and the parenchyma. For 12-month-old mice, both SARS-MA15 and SHC014-MA15 infection caused weight loss and death.
However, death occurred with SHC014-MA15 to a lesser extent than with SARS-MA15 (Menachery et al. 2015). ACE2-deficient mice developed no sign of infection upon exposure to SARS-MA15, indicating the critical role of the ACE2 receptor in the disease progression (Menachery et al. 2015).
None of the four human monoclonal antibod- ies targeting SARS-CoV spike protein showed significant potential as SHC014-MA15 therapeu- tics (Menachery et al. 2015). Not only double- inactivated whole SARS-CoV vaccine (DIV) did not offer protection against SHC014-MA15 but also was pathogenic to the aged animals (Menachery et al. 2015). Aged mice vaccinated with DIV developed eosinophilia traffics in the lungs. Also, their serum could not neutralize SHC014-MA15. A live attenuated SHC014-MA15 vaccine could bring both young and aged mice cross-protection against SARS- CoV (Menachery et al. 2015). However, it required a secondary antigen boost at 28 days postinoculation (dpi), and its minimum protec- tive dose caused death in the aged mice.
8.2.3.2 In 2020, genome analyses underscore the characteristic features of the SARS-CoV-2 – they add the view that SARS-CoV-2 has been produced by natural selection
Recently, an American-European research group (Andersen et al. 2020) proposed that SARS-CoV-2 is the result of a natural selection that might occur either in animals before trans- mission to humans or in humans after transmis- sion from animals. The proposition was based on specific characteristics of the virus.
8.2.3.3 Phylogenetic analyses estimated the ori- gin of SARS-CoV-2 from the same isolate to be about 2 years ago
Fig. 8.2 The sequence identity of the 2019-nCoV spike with the spike protein of other human coronaviruses
A study of 276 coronavirus genomes found five SARS-CoV-2 genome sequences with very high bootstrap support (Ji et al. 2020). Well- supported clades A and B (100%) contained coronavirus strains isolated from bats in China, Kenya, and Bulgaria. The clade C included 267 coronavirus genomes and was on a phylogenetic tree with 67% bootstrap support. By consider- ation of 0.000094 substitutions per site and the SARS-CoV-2 length of 29,865 bp, the evolution- ary rate was measured as 0.0038 substitutions per site per year. The time of the most recent com- mon ancestor (TMRCA) approximates the origin of current SARS-CoV-2 sequences from the same kind about 2 years ago.
8.2.3.4. Homologous recombination: a possible mechanism that may increase the cross- species transmission of SARS-CoV-2 spike glycoprotein
There are a variety of viral infections sup- posed to result from homologous recombination, including the human immunodeficiency virus (Ji et al. 2020). The high similarity in the viral genome between the SARS-CoV-2 and bat SARS-like CoVs posed the potential of recombi- nation events between coronaviruses from bats and another species before being transmitted to humans. Analysis of codon usage patterns indi- cated a biased occurrence of synonymous codon among the SARS-CoV-2, bat SARS-like CoV
ZC45, and Chinese snakes. As shown in Fig. 8.3, the squared Euclidean distance is useful for the measurement of dissimilarity between the SARS- CoV- 2 and its potential wildlife reservoirs, where the lesser the distance, the higher the strength of convergent forces.
8.2.3.5 Different viral genotypes shed light on the evolution of the SARS-CoV-2 – it has not been perfected yet and might become con- verted into a more pathogenic species Analysis of 27 genomes of SARS-CoV-2 iso- lates from different patients has associated the virus to at least six major genotypes (Zhang et al.
2020b). Using the higher number of genome samples (N = 97), there were 95 variable genome sites, containing only up to 3 mutations at coordi- nates 8750, 28,112, and 29,063 in most cases (Zhang et al. 2020c). Genome three coordinate- based data could define two major types to which SARS-CoV-2 strains belong (Fig. 8.4), and SARS-CoV-2 strains are mostly of type II strains.
Of note, the coordinates of interest retain the same codons for type I SARS-CoV-2 strains and the BatCoV RaTG13. Such a relation is weak for type II SARS-CoV-2 strains. As evidenced by functional analysis, mutations were either non- synonymous (28112) or synonymous at (8750 and 29,063), and those synonymous mutations in type II SARS-CoV-2 strains appear to have higher translational efficiencies relative to those
Fig. 8.3 The squared Euclidean distance between 2019-nCoV-WIV04 and putative reservoirs
in type I SARS-CoV-2 strains. Higher transla- tional efficiencies might increase the production rate of type II SARS-CoV-2 particles, and conse- quently, we might expect that type II SARS- CoV- 2 strains tend to become in a corresponding degree more contagious than type I SARS-CoV-2 strains.
8.3 Neither the Window of Viral