CHAPTER 1: What We Know About the Life-threatening Novel Human Coronavirus

Coronaviruses are a large family of zoonotic single-stranded RNA viruses that occur in numerous wild and domesticated animal species and are known to occasionally cross species barriers. Human coronaviruses were first identified by Dr June Almeida in 1964 at her laboratory in St Thomas' Hospital in London, UK. The new discovery from strain B814 was described in the British Medical Journal in 1965.¹  The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the seventh member of enveloped RNA coronaviruses. The emergence of severe life-threatening human coronavirus-related diseases began intensely during the 21st century with the severe acute respiratory syndrome coronavirus (SARS-CoV) and the Middle East Respiratory Syndrome coronavirus (MERS-CoV). Human coronaviruses cause illness in humans ranging from the common cold to more severe diseases such as MERS and SARS. SARS-CoV and MERS-CoV likely originated in bats and then infected other mammalian hosts – the Himalayan palm civet for SARS-CoV, and the dromedary camel for MERS-CoV – before being transmitted to humans. The dynamics of the novel coronavirus (SARS-CoV-2) are currently unknown, but it is likely that the new virus also originated in the same manner, as its overall genome sequence is 96.2% identical to that of bat coronavirus (BatCoV RaTG13) and its overall genetic architecture is very similar to SARS-CoV.

On 11 January 2020 Yong-Zhen Zhang and his colleagues at Fudan University in Shanghai, China deposited into a public database the genome sequence of a virus isolated from a 41 year-old man who had worked at the Huanan seafood wholesale market.²  This seafood market, since closed, also sold live animals of many species, including bats and pangolins. In so doing, Zhang et al. alerted the world to the existence of a new coronavirus that was obviously related to SARS-CoV.²  Their findings were subsequently published in Nature (Wu, Zhao et al. 2020).³ 

Although Zhang's team had sequenced the virus from only a single patient, simultaneous work by other groups identified the same virus from other people with pneumonia. Together, these researchers firmly implicated this new coronavirus as the cause of the disease. One of the teams, led by Shi Zhengli at the Wuhan Institute of Virology, also determined that the closest known relative of the new virus was a bat coronavirus.²  In another study, full-length genome sequences were obtained from five patients at an early stage of the outbreak. These sequences are almost identical and share 79.6% sequence identity with SARS-CoV.⁴  Although not definitive, this suggested that the new virus was potentially closely linked to the zoonotic virus source and that bats were the primary reservoir for SARS-CoV-2.⁴ 

Beginning in the month of December, during a festive season of celebrations, the SARS-CoV-2 outbreak in Wuhan rapidly engulfed an unprepared world. A red-letterhead document bearing the official seal of the Wuhan Municipal Health Commission had circulated on social media in China and had issued an emergency notice: “Cases of a pneumonia of unknown cause have intermittently surfaced at Wuhan's Huanan Seafood Market”. On 31 December 2019, the first of many cases of “pneumonia of unknown etiology” were reported to the World Health Organization (WHO) country office in China.

The timeline of initial events in China over the first 10 weeks of the pandemic as documented by Yan et al.⁵  is illustrated in Figure 1.1. Chapter 3 of this volume provides a unique Chinese perspective on that period and its significance. The symptom onset date of the first patient identified could be traced to 1 December 2019.

In response, the Chinese Center for Disease Control and Prevention (China CDC) and local health groups organized an intensive outbreak investigation program, and the etiology of this illness was soon attributed by the Chinese CDC to a novel virus belonging to the coronavirus family. An epidemic of unexplained lower respiratory tract infections with distinctive bilateral “ground-glass” radiographic findings on chest X-ray and computed tomography was occurring in Wuhan, the largest metropolitan area in China's Hubei province (estimated population: 10 607 700). From 3 January 2020, information concerning newly identified coronavirus disease 2019 (COVID-19) cases was reported daily by China to the World Health Organization (WHO). The virology of SARS-CoV-2 was first studied from a bronchoalveolar lavage fluid sample revealing its genome size to be 29.9 kb, which includes genomic RNA, phosphorylated nucleocapsid (N) protein, spike (S) protein, hemagglutinin esterase, membrane (M) protein, and envelope (E) protein.⁶ 

The common symptoms of COVID-19 reported in infected individuals included fever, shortness of breath, tiredness, dry cough, and abnormalities in smell and/or taste. These symptoms were often accompanied by a number of clinical observations that were documented in the literature.^7,8  Clinical laboratory and imaging findings demonstrated that in more advanced cases the disease could result in pneumonia and even profound multisystem clinical pathologies.⁹  However, it was observed very early that a patient could test positive for the virus and yet be entirely without symptoms, and this is now thought to be the case in approximately 40% of persons who test positive.¹⁰ 

Full genomic sequencing of the new virus was shared with the WHO and the international community soon after the pathogen was identified on 7 January. On 10 January, an expert group involving Hong Kong, Macao and Taiwanese technical experts and a WHO team was invited to visit Wuhan. The full disease outbreak news update, which appeared on the WHO website on 12 January 2020, can be found at https://www.who.int/docs/default-source/coronaviruse/situation-reports/20200121-sitrep-1-2019-ncov.pdf?sfvrsn=20a99c10_4.

A set of nucleic acid primers and probes for polymerase chain reaction (PCR) detection of COVID-19 was released on 21 January 2020. As of 23 January 2020, China had reported cases in 25 provinces (autonomous regions and municipalities). 25% of confirmed cases reported by China were classified by the Chinese health authorities as seriously ill (from Hubei Province: 16% severely ill, 5% critically ill, and 4% having died). Cases infected in China had been exported to the United States, Thailand, Japan, and the Republic of Korea, with the expectation that more cases would be exported to other countries and that further transmission might occur.

Although the initial source of the 2019 novel coronavirus (2019-nCoV) remained unknown, it was clear that the growing outbreak was no longer due to ongoing exposures at the Huanan seafood market, as <15% of new cases reported having visited the Huanan market. There was more evidence that 2019-nCoV spreads from human to human and across generations of cases. Moreover, family clusters involving persons with no reported travel to Wuhan had been reported from Guangdong Province.

The WHO initially assessed the risk of this event to be “moderate” in situation reports published on 23, 24, and 25 January, and later revised them to “very high” in China, “high” at the regional level, and “high” at the global level¹¹  (Figure 1.2). The distribution of 2019-nCoV cases in China (and other countries, territories, or areas with reported known cases) is shown in Figure 1.2.

By the time of the total lockdown of the city of Wuhan on 23 January, it was reported¹²  that 5 million people had left the city for other destinations and an outbreak of pandemic scale had begun worldwide.

A harbinger of future revelations, Ma Xiaowei, the Director of China's National Health Commission, was reported on 27 January 2020 to have said¹²  “From observations, the virus is capable of transmission even during incubation period”.

And as a fifth case of the coronavirus was confirmed in the United States on that same date, the mayor of the city of Wuhan warned that the world that it should expect COVID-19 infections to keep climbing.¹²  The complete report, as published by MarketWatch, can be found at: https://www.marketwatch.com/story/mayor-of-wuhan-epicenter-of-coronavirus-outbreak-says-5-million-people-left-the-city-before-travel-restrictions-were-imposed-2020-01-26.

The world had been warned as to what to expect with the pandemic of COVID-19. Some countries heeded the warning and suffered relatively few fatalities at the hand of SARS-CoV-2, but others dismissed it and continue to suffer the consequences.

The chronology of the ensuing events in the outbreak is as follows:

On 30 January 2020, the WHO declared the novel coronavirus outbreak a Public Health Emergency of International Concern as it had spread to 18 countries, with four countries reporting human-to-human transmission (per the International Health Regulations, 2005 ¹³ ).

On 11 February 2020, the WHO Director General, Dr Tedros Adhanom Ghebreyesus, announced that the symptomatic disease caused by this new coronavirus was “COVID-19”, which is the acronym of “coronavirus disease 2019”.

By 13 February 2020, the disease had spread to 25 different countries and there had been a total of 60 412 confirmed cases with 1370 fatalities.⁵ 

Between 16 and 24 February 2020, the WHO–China Joint Mission on Coronavirus Disease 2019 (COVID-19) met in Wuhan, China.

On 28 February 2020, the WHO raised the threat of a SARS-CoV-2 epidemic to the “very high” level and the comprehensive report of the WHO–China Joint Mission on Coronavirus Disease 2019 (COVID-19) was issued.¹⁴  See the concluding technical recommendations from the report in Box 1.1.

On 11 March 2020, the WHO declared COVID-19 a global pandemic, as the number of COVID-19 cases outside China increased 13-fold, the number of countries involved tripled, with more than 118 000 cases in 114 countries resulting in more than 4000 deaths.¹⁵ 

By 31 March 2020, COVID-19 had infected 750 890 people globally with 36 405 deaths.¹⁶ 

By 14 April 2020, approximately 1 844 683 cases had been confirmed with 117 021 deaths reported from at least 213 countries, areas, or territories.¹⁷ 

As described in WHO reports, the first cases of the novel coronavirus disease were linked to direct exposure at the Huanan seafood wholesale market of Wuhan. For this reason, animal-to-human transmission was presumed to be the main mechanism of transfer. However, since subsequent cases were not associated with this location, it was determined that the virus could be directly transmitted from one human to another. The key epidemiological study in this regard was reported by Li and associates in the New England Journal of Medicine on 26 March 2020.¹⁸ 

Li et al.¹⁸  analyzed data on the first 425 confirmed cases in Wuhan to determine the epidemiological characteristics of the disease. They collected information on demographic characteristics, exposure history, and illness timelines of laboratory-confirmed cases that had been reported by 22 January 2020. The median age was 59 years and 56% of patients were male. The majority of cases (55%) had a disease onset before 1 January 2020, and were linked to the Huanan seafood wholesale market, as compared with 8.6% of subsequent cases. The mean incubation period was determined to be 5.2 days (95% CI 4.1–7.0 days), with the 95th percentile of the distribution at 12.5 days. In its early stages, the epidemic doubled in size every 7.4 days. With a mean serial interval of 7.5 days (95% CI 5.3–19 days), the basic reproductive number (R₀) was estimated to be 2.2 (95% CI 1.4–3.9). In general, an epidemic will increase as long as R₀ is >1, and control measures aim to reduce the reproductive number to <1. The longest time frame from infection to symptoms was 12.5 days (95% CI 9.2–18 days).¹⁸  In other words, these data showed that the infection rate for this novel virus doubled approximately every 7 days. For comparison, the R₀ of the SARS-CoV epidemic in 2002–2003 was ∼3 (that is, one person infects approximately three other people; if this occurred within approximately 10 days, the prevalence of the epidemic would double within 1 week).¹⁹  On the basis of this information, Li et al. concluded that evidence suggested that human-to-human transmission had occurred among close contacts since the middle of December 2019 and that considerable efforts to reduce transmission would be required to control outbreaks if similar dynamics applied elsewhere. Apart from China, human-to-human transmission has been reported in other countries such as Germany, Japan, Thailand, the United States and elsewhere.²⁰ 

As with other respiratory pathogens, including flu and rhinovirus, transmission was believed to occur through respiratory droplets (particles >5–10 µm in diameter) from coughing and sneezing. Aerosol transmission was also believed possible in cases of protracted exposure to elevated aerosol (≤5 µm) concentrations in closed spaces. Analysis of data related to the spread of SARS-CoV-2 in China indicated that close contact (6 feet, 1.8 m) between individuals is necessary for transmission, most of which occurs between family members, healthcare professionals, and other close contacts. Surprisingly, it was speculated that pre- and asymptomatic individuals account for up to 80% of viral transmission.²¹  All of the above suggested that the virus could easily spread among totally asymptomatic individuals in close contact with one another and remain undetected for days.

Transmission of SARS-CoV-2 can occur via contact with contaminated surfaces. The virus can live for 2–3 days on plastic and stainless steel, up to 1 day on cardboard, and up to 4 hours on copper.²²  However, because data so far available have been generated under experimental conditions, these estimates must be interpreted with caution. Additionally, assessing risk from exposures to contaminated surfaces must also consider that the presence of viral RNA does not necessarily indicate that the virus is viable and potentially infectious. Higher contamination rates have been reported in intensive care units than general wards, as SARS-CoV-2 has been reported on floors, computers, trash cans, and sickbed handrails, as well as 4 m in the air above patient beds.²³ 

Based on these data from the first cases in Wuhan and investigations conducted by the China CDC and local CDCs, the incubation time is generally estimated to be 3–7 days (median 5.1 days, similar to SARS).²⁴  This early observation combined with the likelihood that approximately 40–45% of those infected with SARS-CoV-2 will remain asymptomatic suggested that the virus might have greater potential than previously estimated to spread silently and extensively through human populations.²⁵  He et al. estimated that 44% (95% CI 30–57%) of secondary cases were infected during the index cases' presymptomatic stage and argued that control measures should be adjusted to account for probable substantial presymptomatic transmission.²⁶  Indeed, the long duration of viral shedding and high proportion of asymptomatic patients make asymptomatic transmission a critical concern for effective public health management.

It must be emphasized that much of the information presented thus far was the result of the early reports. Thus, further studies are needed to understand mechanisms of transmission, incubation times, clinical symptoms and course, and duration of infectivity. Differing symptoms experienced by different people might be dictated by a combination of factors including: (1) which cells and tissues are infected; (2) the direct damage the virus causes to these cells; (3) interference with the normal function of host cells' angiotensin-converting enzyme (ACE)2 receptors, to which the virus binds; and (4) individual variations in the immune response to the virus.²  For example, severely ill patients show hyperactivation of their immune response, which damages the lungs and other organs. What is generally known to date regarding these topics is covered in subsequent sections.

At the time of this writing the data provided by the WHO Coronavirus Disease (COVID-19) Dashboard is “Globally, as of 12:44 pm CEST, 15 August 2020, there have been 20 995 433 confirmed cases of COVID-19, including 760 774 deaths, reported to WHO”. The most up-to-date information on the emerging pandemic can be found at the following sources:

The WHO Coronavirus (COVID-19) Dashboard Situation Board: https://covid19.who.int/, and the Johns Hopkins Center for Systems Science and Engineering site for Coronavirus Global Cases COVID-19 has reported the Coronavirus COVID-19 Global Cases since the beginning of the pandemic: https://coronavirus.jhu.edu/map.html

World governments are currently at work to establish countermeasures to stem the devastating effects of the virus. Health organizations coordinate information flow and issue directives and guidelines to best mitigate the impact of the threat. At the same time, scientists around the world are working tirelessly to discern information about transmission mechanisms, the clinical spectrum of disease, new diagnostics, prevention, and therapeutic strategies. Many uncertainties remain regarding the virus, virus–host interactions, and the evolution of the pandemic, with specific reference to the times when it will reach its peaks in various regions and globally. At this moment, therapeutic strategies to treat COVID-19 are only supportive, and prevention aimed at reducing transmission in the community remains our best tactic. Aggressive isolation measures in China have led to a progressive reduction of cases.

In northern Italy, where the coronavirus ravaged cities from late February through April, doctors credited the turnaround to the country's strict nationwide lockdown, widespread testing, robust contact tracing.

When Italy's “father of the swabs”, Andrea Crisanti, learned of the first Italian COVID-19 fatality in Vo, Italy, he saw it as an ideal place to perform an epidemiological experiment: a small population, universally tested, whose progress could be monitored closely. He tested everyone in the village and then retested them after 9 days. In the first round, 73 residents were positive for the virus and more than 40% of them had no symptoms, yet they had levels of the virus similar to those who were visibly ill. The Vo study confirmed asymptomatic transmission and showed that isolating people helps stop transmission, since everyone who tested positive was confined to their home, regardless of whether they had symptoms. By the second round of testing, a week and a half later, the number of positives had dropped to 29, and they too were isolated. A third round of tests 2 months later found no positive cases.²⁷ 

In Germany, mass testing was not performed at the highest rates – as was seen in South Korea with 10 000 tests per day – but Germany was meticulous about the process. Once an individual tested positive, officials traced each one of their contacts and proceeded to test and quarantine those individuals, again essentially breaking “infection chains”.²⁸ 

In the United States, before 24 August 2020, the CDC website stated that testing was recommended “for all close contacts of persons with SARS-CoV-2 infection”. On 24 August, that was changed to say that someone who was in close contact (within 6 feet) of a person with COVID-19 for at least 15 minutes, but who didn't have symptoms does not “necessarily need a test”.²⁹  As of this writing, that change has caused significant concern among public health and medical professionals, especially since most states have been unable to perform contact tracing due to the high numbers of individuals testing positive.³⁰ 

Details on the public management of COVID-19 in various countries are provided in Chapters 9–11 of Volume 2 of this book.

As mentioned previously, coronaviruses are positive-stranded RNA viruses with a crown-like (coronam is Latin for crown) appearance under an electron microscope due to the presence of spike glycoproteins on the outer envelope. SARS-CoV-2 is a Betacoronavirus enveloped positive-sense RNA virus (subgenus Sarbecovirus, Orthocoronavirinae subfamily).⁷  As be discussed in greater detail later, the subfamily Orthocoronavirinae of the Coronaviridae family (order Nidovirales) classifies into four genera of coronaviruses: Alphacoronavirus (alphaCoV), Betacoronavirus (betaCoV), Deltacoronavirus (deltaCoV), and Gammacoronavirus (gammaCoV). The Betacoronavirus genus further divides into five subgenera.³¹  The coronaviruses found in various groups of bat and bird species serve as natural reservoirs. Genomic characterization has shown that bats and rodents are probably the sources of alphaCoVs and betaCoVs. Avian species are the likely sources of deltaCoVs and gammaCoVs. How coronaviruses in each species originated is elusive, and associated with varied evolution models. The first evolutionary model on coronaviruses proposed bat species as the gene source for all coronaviruses.³²  However, confirmation studies over the following 2 years (after 2007) did not support this hypothesis.³³  Figure 1.3 illustrates the animal origins of coronaviruses.

Initially, these viruses had not been considered harmful to humans, but investigations gained momentum after SARS spread in 2002 and 2003 in China.^34–36  Coronaviruses of each genus are found in many species including cows, cats, pigs, birds, horses, dogs, and ferrets, which result in enteric hepatitis and respiratory, neurologic, renal and other disease.

To date, seven human coronaviruses (HCoVs) capable of infecting humans have been identified. Gastrointestinal and pulmonary infections are caused in both humans and animals by coronaviruses.³⁷  In general, estimates suggest that 2% of the population are healthy carriers of a coronavirus and that these viruses are responsible for approximately 10–20% of common colds.^38–40  Common human alphaCoVs (HCoV-229E and HCoV-NL63) and betaCoVs of the A lineage (HCoV-OC43 and HCoV-HKU1) typically cause common colds and self-limiting upper respiratory infections in immunocompetent individuals; they can cause lower respiratory infections in immunocompromised subjects and the elderly. Human betaCoVs of the B and C lineage (SARS-CoV, SARS-CoV-2, and MERS-CoV) have resulted in epidemics with variable clinical severity featuring respiratory and extra-respiratory manifestations.

Mortality rates reported for SARS-CoV were ∼10% and for MERS-CoV ∼35%. The mortality rate for SARS-CoV-2 is considerably lower, but many survivors display enhanced morbidities.

The genome of SARS-CoV-2, isolated from a cluster of patients displaying atypical pneumonia after visiting Wuhan, had 89% nucleotide identity with bat SARS-like-CoVZXC21 and 82% with human SARS-CoV.⁴¹  For this reason, the new virus was called SARS-CoV-2 by the International Committee on Taxonomy of Viruses, and it was thought that several SARS-CoV-2 variants probably exist. Its single-stranded RNA genome contains 29 891 nucleotides, encoding for 9860 amino acids.

Although the origins of SARS-CoV-2 are not entirely understood, genomic analyses suggest that SARS-CoV-2 probably evolved from a strain found in bats. It is still not definitively known if there is an intermediate mammalian host between bats and humans, or if a mutation in the original strain directly enabled virulence towards humans.

SARS-CoV-2 is ∼60–140 nM in diameter and has a round or elliptic and often pleomorphic form. Like other coronaviruses, SARS-CoV-2 is sensitive to ultraviolet rays and heat. As high temperature decreases the replication of any species of virus, SARS-CoV-2 is estimated to be inactivated at ∼27 °C (80–81 °F), but may resist the cold even below 0 °C (32 °F). This class of viruses can be effectively inactivated by lipid solvents including ether (75%), ethanol (60%), chlorine-containing disinfectant, peroxyacetic acid, and chloroform (except for chlorhexidine).

Some 6 months into the pandemic, the coronavirus has continued to spread and has ravaged the world. Scientists have now generated more than 80 000 viral sequences. This new genetic information has allowed transmission chains to be traced – revealing, for example, cryptic community transmission in the United States – as well as showing that a variant that seems to be particularly infectious to cultured cells has now become dominant around the world.^42,43  What this altered infectivity means for transmission and disease is not yet clear.² 

Phylogenetic trees have been projected for different regions of the coronavirus genome, in which four coronavirus clusters are distinguished. Three have been classified as genera alpha-CoV, beta-CoV and gamma-CoV. The fourth type includes recently detected coronaviruses of birds and seems to characterize a novel genus named delta-CoV. In the beta-CoV, four separate lineages were distinguished, and they are designated as A through D, in accordance with previous subgroups 2A through D correspondingly. Figure 1.4 depicts the classification of coronaviruses.

The viruses in this genus are a distinct monophyletic group within the Coronavirinae subfamily. The general characteristics that are different from other coronaviruses are (1) a distinctive type of non-structural protein (nsp) 1, different in size and sequence from beta-CoV nsp1 and without a counterpart in the gamma-CoV and (2) the presence of a shared gene for an unnecessary multispanning alpha-CoV membrane protein (αmp). As mentioned previously, while for some alpha-CoVs, αmp is the only additional protein, others may include up to six additional genes.

Beta-CoVs fall under murine coronaviruses, which form a diverse monophyletic group in the Coronavirinae subfamily. Excepting for their comparatively close phylogenetic association, the only known general characteristics that would be different from other coronaviruses is their nsp1, distinctive in size and sequence from alpha-CoV nsp1 and without equivalent in the gamma-CoV genus.

Gamma-CoVs are avian coronaviruses which form a distinct monophyletic group in the Coronavirinae subfamily. Besides their moderately close phylogenetic relationship, there are no known mutual characteristics of virion morphology, genome organization and gene replication, composition or biology that would differ from other coronaviruses. This group lacks an nsp1 moiety.

Delta-CoVs fall under the type Bulbul coronavirus. Recombination is common in delta-CoV and occurs commonly in the viral genome region that encrypts the receptor binding protein. Recombination between different viral roots may contribute to the advent of novel viruses capable of interspecies transmission and adaptation to novel animal hosts.

The main targets of the alpha-CoVs and beta-CoVs are mammals, while gamma-CoVs and delta-CoVs are found in birds, along with mammals.⁴⁴  Members of this large family of viruses can cause respiratory, enteric, hepatic, and neurological diseases in many species, including camels, cattle, cats, and bats. The dangerous viruses that have spread among humans, the SARS-CoV and MERS-CoV, cause severe respiratory illness in humans, whereas the other four human coronaviruses (HCoV-NL63, HCoV-229E, HCoV-OC43, and HKU1) only cause mild upper respiratory infections in humans, often with a compromised host immune system.⁴⁵  Alpha-CoVs and beta-CoVs cause various diseases in domestic animals; they include porcine transmissible gastroenteritis virus,⁴⁶  porcine enteric diarrhea virus,⁴⁷  and swine acute diarrhea syndrome-CoV.⁴⁸  From recent studies, it has been established that the origin of coronaviruses in general can be attributed to animals. SARS-CoV, MERS-CoV, HCoV-NL63, and HCoV-229E are thought to have originated from bats; HCoV-OC43 and HKU1 supposedly from rodents.^45,49  These animals are associated with the spreading of the virus from their normal hosts to humans. Moreover, these animals also succumb to certain diseases that have originated in bats.⁵⁰ 

Serological techniques applied in epidemiological studies have demonstrated that human respiratory coronaviruses occur mostly during the winter and spring seasons. The first human coronavirus was detected in 1965, when Tyrrell and Bynoe discovered a virus designated B814.⁵¹  It was found in adult human embryonic tracheal organ cultures from people affected with a common cold. The infectious agent was studied by inoculating the cultures in the medium intranasally in human subjects; cold symptoms were noticed in these subjects, but the virus could not be grown in tissue culture. Simultaneously, Hamre and Procknow cultured the virus (229E) in tissue culture,⁵²  and B814 and 229E were found to be ether-sensitive and to possess a lipid-coated membrane to facilitate entry into host cells. However, B814 was not similar to either OC43 or 229E.⁵³  OC43 is the virus that is primarily involved with the common cold. Later, Almeida and Tyrrell viewed the organ cultures infected with B814 using electron microscopy and found particles resembling the bronchitis virus.⁵⁴  The morphologies of 229E and other isolated viruses by McIntosh et al. were similar.^52,55  In the late 1960s, Tyrrell, along with other virologists working with human and animal viruses confirmed that these viruses had similar morphology.^55,56  This group of viruses were then named coronaviruses (corona meaning crown-like appearance), which was later officially accepted as a new virus genus.⁵⁷ 

The coronaviruses are associated with many respiratory illnesses that are considered to have pathogenicity.^52,53,58,59  The major illness that was associated was pneumonia, which was predominantly found in infants and young adults.^60,61  These viruses caused asthma in children and chronic bronchitis in older people and adults.^62–64  Because many researchers explored the pathogenicity and epidemiology of human coronaviruses, the importance of animal coronaviruses also grew rapidly. In the family of coronaviruses with various strain differences, McIntosh et al. noticed that a few strains were distantly related to 229E or OC43.⁶⁵  Human and animal coronaviruses were divided into three groups based on their genomic structures. Group I includes the 229E viruses and group II includes the OC43 virus as well as the avian infectious bronchitis and related viruses.⁵⁷ 

SARS is a disease that has transmitted among populations, causing a significant number of deaths and other health problems. From 2002 to 2003, a total of 8098 of SARS cases were identified in 29 countries with 774 fatalities.⁶⁶  The first patient was from Guangdong in southern China. This patient had infected three family members at the initial stages of the disease.⁶⁷  This initial infection resulted in the surge of infections in various areas from November 2002 to January 2003. International transmission began when an infected doctor who had treated people with the condition travelled to Hong Kong and stayed at a hotel.⁶⁸  He eventually began to exhibit SARS symptoms, which progressed to respiratory failure and death.⁶⁹  During his stay, the virus had infected other individuals who were concurrently staying at the hotel. When these people flew back to their respective countries, the rise of the epidemic began in North America, Europe, and Asia.^70,71  Another patient from the same hotel spread the illness to many healthcare workers and medical students, who eventually spread it to people they were in contact with, thereby starting the transmission chain.⁷²  In addition, another patient reportedly having diarrhea had the infection and further increased community spread. The probable route of infection was through defective sewage pipes permitting infectious aerosol fecal materials to travel between buildings in expanding air currents. Despite the efforts to control the spread, by 23 June 2003, Hong Kong reported 1755 cases with 299 deaths in a population of 6.9 million.⁶⁶  SARS was defined by Dr Carlo Urbani from Hanoi in Vietnam, a pioneer in the field of infectious disease who worked for the WHO, and was the president of Medecins sans Frontières (Italy).⁷³  Later it was determined that SARS is disseminated through droplet transmission.^35,74,75 

A novel coronavirus was initially found in a patient with SARS in Saudi Arabia in June 2012. This virus was then termed the Middle East Respiratory Syndrome coronavirus (MERS-CoV).⁷⁶  From there, several outbreaks occurred in the Arabian Peninsula and up to April 2016, Saudi Arabia reported 1386 cases, of whom 587 individuals died.⁷⁷  With an elevated death rate, a dearth of specific antiviral medication, and lack of readily available vaccines, there was tremendous panic among the people of the region at that time. It was later indicated by a large study that MERS-CoV had originated from bats.⁷⁸  Interestingly, a bat-derived coronavirus was also reported in South Africa with a very similar in structure to MERS-CoV.⁷⁹  In Saudi Arabia, where bat feces was tested for MERS-CoV nucleic acids, it was reported that virus samples from the Egyptian tomb bat Taphozous perforatus shared 100% similarity to MERS-CoV.⁸⁰  However, the viral nucleic acid was not present in other bats from Egypt and Lebanon.⁸¹  An additional investigation of bats as potential carriers of MERS-CoV was reported in an experiment on the Jamaican fruit bat (Artibeus jamaicensis). When these bats were infected with the virus, they did not exhibit any clinical symptoms, but viral shedding was observed in their respiratory and intestinal tracts.⁸²  This report suggested that MERS-CoV can exist and survive in bats without causing any specific symptoms. This pointed to the hypothesis that these bats probably carried the ancestor of this virus, and that they could carry the virus for further transmission into subsequent hosts.

As mentioned earlier, recent studies have stated that SARS-CoV-2 probably originated in bats and then adapted to become the virus as we know it.^7,83  The infection of humans by this virus can be ascribed to zoonotic transmission.^7,83,84  A coronavirus from the Malayan pangolin shared 99% homology with SARS-CoV-2. In addition, the receptor-binding domain (RBD) of the pangolin coronavirus had only a single amino acid change when aligned with SARS-CoV-2. Moreover, it was also observed that the pangolins that had the disease exhibited symptoms similar to those of patients infected with COVID-19, and the antibodies in the pangolin also showed specific binding to the spike (S) protein of SARS-CoV-2.^83,85,86  Although a coronavirus specific to bats had a 96% similarity with SARS-CoV-2, the RBDs were distinctive, which resulted in a low binding capability to the ACE2 receptor in humans.⁸⁷  Interestingly, it was also discovered that six residues of the RBD of SARS-CoV-2 were analogous to SARS and MERS.^83,86  From these data it can be inferred that SARS-CoV-2 is an amalgamation of pangolin-CoV and the bat-CoV-RaTG13-like virus.^86,88,89  Hence, pangolins can be considered an intermediary between the bats and humans. However, other possible intermediate hosts such as snakes, minks, and turtles are currently being studied to enhance the understanding of the virus.^86,90,91  Interestingly, scientists observed a five (out of six) amino acid residue difference within the RBD of the S protein between SARS-CoV and SARS-CoV-2, which discredited speculation that the virus was constructed in a laboratory by genetic manipulation.⁹⁰ 

The rapid spread of this virus has made it a public health concern worldwide. As described earlier, COVID-19 was declared a pandemic on 11 March 2020, once the number of cases outside China had increased 13 times and 114 countries were affected with more than 118 000 cases and more than 4000 deaths.

Governmental organizations around the world had tried to slow the spread of the disease by delivering “social-distancing” guidelines and directives. Concurrently, scientists worked tirelessly to develop novel diagnostics, prevention methodologies, and therapies. Unfortunately, clarity on virus–host interaction and the disease outbreak is still lacking. Currently, therapeutic strategies are being developed and preventive measures have been implemented to reduce community transmission. In China, severe isolation strategies accomplished the reduction in progressive situations. Less severe isolation strategies have met with success in early outbreaks where infected individuals were identified through testing and contact tracing was employed. The number of COVID-19 cases continues to rise internationally. Data for 15 countries as of 31 May 2020 are depicted in Figure 1.5.

Five simple personal health measures (masking, social distancing, avoiding crowded places, convening outside in preference to indoors, and hand washing) and five straightforward public health measures (testing, contact tracing, quarantining of suspected and confirmed COVID-19 cases, travel restrictions, and lockdown of some or all places where the public gathers) would probably suffice to contain the virus in most instances (Staff Warren, personal observation).

Table 1.1 presents a comparison of the respiratory viruses SARS-CoV, MERS-CoV, and SARS-CoV-2 in terms of their infectivity and morbidity. These characteristics tend to explain the relative pathogenicity and probable persistence of SARS, MERS, and COVID-19, even in the absence of the discovery in real time, especially given the apparent possible asymptomatic transmission of COVID-19 and the large number of deaths already observed globally.

SARS-CoV-2 was first isolated from three COVID-19 patients using bronchoalveolar lavage fluid from Wuhan Jinyintan Hospital on 30 December 2019.⁷  After molecular analysis and phylogenetic tree study, SARS-CoV-2 was determined to be a beta-CoV.⁴  The reports noted that SARS-CoV-2 had 79.5% and 50% sequence similarity with SARS-CoV and MERS-CoV.⁹²  However, 94.6% of the sequences were alike in the seven replicase domains in the open reading frame (ORF)1ab of SARS-CoV-2 and SARS-CoV;⁴  SARS-CoV-2 also shared likeness with other beta-CoVs,⁷  suggesting that SARS-CoV-2 belonged to the lineage B (Sarbecovirus) of beta-CoVs.⁹³  The genome size of SARS-CoV-2 was calculated to be approximately 29.9 kb, which was inclusive of the genomic RNA and phosphorylated nucleocapsid (N) protein surrounded by a nucleocapsid.⁹³  The nucleocapsid is present within the phospholipid bilayers and covered with two different kinds of spike proteins: the spike glycoprotein trimmer (S) that is conserved in most of the coronaviruses, and the hemagglutinin-esterase, uncommon in coronaviruses. The membrane (M) protein and the envelope (E) protein are in between the S proteins in the viral envelope.⁹³  The 5′ and 3′ sequences of SARS-CoV-2 is like those of beta-CoVs, with a 5′-replicase ORF1ab-S-envelope (E)-membrane (M)-N-3′. Similar to SARS-CoV, SARS-CoV-2 has an ORF8 gene which is 366 nucleotides in length between the M and N ORF genes.⁹³  The basic structure of SARS-CoV-2 is illustrated in Figure 1.6.

SARS-CoV and SARS-CoV-2 both utilize the same receptor, ACE2, for entry into the host cells.^4,94  ACE2 is a type I membrane protein found in the kidney, lung, heart, and intestines.⁹⁵  ACE2 consists of an N-terminal peptidase domain and a C-terminal collectrin-like domain.⁹⁵  ACE2 is principally involved in the conversion of angiotensin (Ang) I to Ang-(1–7).⁹⁵  The S protein of the virus undergoes a change in its confirmation to promote the interaction between the cell membrane of the host and the viral membrane.⁹⁶  This process occurs after the receptor binds to the virus. This causes the cleavage of the S protein into its subunits S1 and S2. This results in the shedding of the S1 subunit that promotes a change in the S2 domain.⁹⁶  Then, the RBD of the S1 subunit experiences changes that can either display or conceal the factors associated with receptor binding.⁹⁷  Moreover, it has also been established that the that SARS-CoV-2 S binds to human ACE2 with an increased affinity compared to its SARS-CoV counterpart.⁹⁸  Furthermore, it has been unearthed that the ACE2-BOAT1 has the capability to bind two S proteins concurrently⁴  (Figure 1.7).

Tang et al. reported that there are two genotypes of SARS-CoV-2 designated L and S, depending on an amino acid site 84 (S84L) of ORF8 gene.⁹⁹  Genomic sequences of closely related coronaviruses such as bat-CoV RaTG13 and pangolin-CoV suggested that the ancestral genotype was S-type.⁹⁹  However, the L-type emerged with the SARS-CoV-2 outbreak and is the major type spreading worldwide (https://nextstrain.org/ncov/global). Zhang et al. analyzed clinical and immunological data from 326 patients with confirmed COVID-19 and compared genetic variation among them, including the S84L mutation, but could not find any association.¹⁰⁰  Korber et al. reported a mutation at an amino acid site 614 (D614G) of the S protein, which is currently dominant in Europe.¹⁰¹  Since the S protein is essential in infecting cells and is a primary target for neutralizing antibodies, the mutations in the S protein could be related to the virulence; however, this hypothesis must be evaluated experimentally using reverse genetics. Although more than 5000 mutations have accumulated in the infected population CoV-GLUE (http://cov-glue.cvr.gla.ac.uk), there is no evidence to supporting the contention that SARS-CoV-2 genomes are separating into distinct genotypes.¹⁰² 

In addressing the pathogenetic mechanisms of SARS-CoV-2, its viral structure and genome must be considered. Coronaviruses are the largest known RNA viruses, approximately 30 kb in length, with a 5′-cap and 3′-poly-A tail. Starting from the viral RNA, the synthesis of polyprotein 1a/1ab (pp1a/pp1ab) occurs within the host cell. The transcription works through the replication–transcription complex organized in double-membrane vesicles via the synthesis of subgenomic mRNA sequences. Of note, transcription termination occurs at transcription regulatory sequences, located between the ORFs that work as templates to produce subgenomic mRNAs. In the typical coronavirus genome, at least six ORFs can be present. Among these, a frameshift between ORF1a and ORF1b guides the production of both pp1a and pp1ab polypeptides that are processed by virally encoded chymotrypsin-like protease (3CLpro) or main protease (Mpro), as well as one or two papain-like proteases for producing 16 nsps. Apart from ORF1a and ORF1b, other ORFs encode for structural proteins, including spike, membrane, envelope, and nucleocapsid proteins, and accessory protein chains.¹⁰³  Different coronaviruses present special structural and accessory proteins translated by dedicated single-stranded guided RNAs.

Pathophysiology and virulence mechanisms of coronaviruses, and therefore also of SARS-CoV-2, have links to the function of the nsps and structural proteins. For instance, research underlined that nsp is able to block the host innate immune response.¹⁰⁴  Among functions of structural proteins, the envelope plays a crucial role in virus pathogenicity, as it promotes viral assembly and release. However, many of these features (e.g. those of nsp 2, and 11) have not yet been described. Among the structural elements of human coronaviruses are the spike glycoproteins composed of two subunits (S1 and S2). Homotrimers of S proteins comprise the spikes on the viral surface, guiding the link to host receptors.¹⁰⁵ 

Of note, in SARS-CoV-2, the S2 subunit – containing a fusion peptide, a transmembrane domain, and cytoplasmic domain – is highly conserved. Thus, it could be a target for antiviral (anti-S2) compounds. Indeed, the spike RBD presents only a 40% amino acid identity with other SARS-CoVs. Other structural elements on which research must necessarily focus are the ORF3b that has no homology with that of SARS-CoVs and a secreted protein (encoded by ORF8) that is structurally different from those of SARS-CoV.

As mentioned earlier, both SARS-CoV and SARS-CoV-2 use the same cell receptor, ACE2,⁴  and the same protease, TMPRSS2,¹⁰⁶  to enter cells. However, SARS-CoV-2 can also infect cell lines that don't express TMPRSS2, which could stymie drug development.²  Researchers used Vero cells – which do not express TMPRSS2 – in an early study that suggested that the drug chloroquine might work as a treatment for COVID-19.¹⁰⁷  Chloroquine did not prove effective in clinical trials, and scientists discovered that it does not inhibit the virus in lung cells that express TMPRSS2.¹⁰⁸  Despite the overall structural similarity between the spike proteins of the two SARS coronaviruses, scientists found that the SARS-CoV-2 spike binds the ACE2 receptor at least 10 times more tightly than SARS-CoV-1 does.⁹⁸  This might explain some of the differences between how the two viruses infect people and cause disease.

The SARS-CoV-2 spike also has a feature that SARS-CoV-1 lacks: a sequence of amino acids that allows it to be recognized and cleaved by an enzyme called furin.¹⁰⁹  How this sequence contributes to the virulence of SARS-CoV-2 is not yet known. But similar sequences are also found in the receptor-binding protein of some influenza viruses and contribute to their virulence.

In international gene banks such as GenBank, researchers have published numerous SARS-CoV-2 gene sequences. This gene mapping is of fundamental importance allowing researchers to trace the phylogenetic tree of the virus and, above all, the recognition of strains that differ according to the mutations. According to recent research, a spike mutation, which probably occurred in late November 2019, triggered the jump to humans. Angeletti et al. compared the SARS-CoV-2 gene sequence with that of SARS-CoV. They analyzed the transmembrane helical segments in the ORF1ab encoded 2 (nsp2) and nsp3 and found that position 723 presents a serine instead of a glycine residue, while the position 1010 is occupied by proline instead of isoleucine.¹¹⁰  The matter of viral mutations is key for explaining potential disease relapses. Further research will be needed to determine the structural characteristics of SARS-CoV-2 that underlie its pathogenetic mechanisms.

Initial reports of the disease, named COVID-19 on 11 February, described a severe respiratory illness similar to that caused by SARS-CoV. Chest scans showed patchy shadows – known as “ground-glass opacities” – in the lungs of many patients, according to early studies from hospitals in Wuhan.¹¹¹  Moreover, older people, men, and those with other diseases were more likely to be admitted to intensive care, whereas children seemed to have milder disease.¹¹² 

The pathogenic mechanism that produces pneumonia seems to be particularly complex. But it quickly became apparent that SARS-CoV-2 is not just a respiratory virus. It also affects blood vessels, causing thrombosis¹¹³  and strokes.¹¹⁴  In rare cases, children can develop what is called a multisystem inflammatory syndrome, reminiscent of Kawasaki disease.¹¹⁵  Clinical and preclinical research will have to explain many aspects that underlie the clinical presentations of the disease.

The data so far available seem to indicate that the viral infection can produce an excessive immune reaction in the host. In some cases, a reaction takes place called a “cytokine storm”, resulting in extensive tissue damage with dysfunctional coagulation and damage to multiple organs. A new diagnostic term called MicroCLOTS (microvascular COVID-19 lung vessels obstructive thrombo-inflammatory syndrome) has been initiated to identify the underlying lung viral injury associated with the inflammatory reaction and with microvascular pulmonary thrombosis.¹¹⁶  While several cytokines such as tumor necrosis factor-α, interleukin (IL)-1β, IL-8, IL-12, interferon-gamma inducible protein (IP10), macrophage inflammatory protein 1A (MIP1A), and monocyte chemoattractant protein 1 (MCP1) are implicated in the pathogenic cascade of the disease, the protagonist of this storm is IL-6. IL-6 is produced primarily by activated leukocytes and acts on many cells and tissues. While it can promote the differentiation of B lymphocytes and growth of some categories of cells, it inhibits the growth of others. It also stimulates the production of acute-phase proteins and plays an important role in thermoregulation, bone maintenance, and the functionality of the central nervous system. Although the main role played by IL-6 is pro-inflammatory, it can also have anti-inflammatory effects. In turn, IL-6 increases during inflammatory diseases, infections, autoimmune disorders, cardiovascular diseases, and some types of cancer. It is implicated in the pathogenesis of the cytokine release syndrome that is an acute systemic inflammatory syndrome characterized by fever and multiple organ dysfunction. In addition to the IL-6 pathway, SARS-CoV-2 binds to the Toll-like receptor to induce the release of pro-IL-1β, which is cleaved into the active mature IL-1β, mediating lung inflammation, and later fibrosis.¹¹⁷ 

Tian et al.¹¹⁸  and others reported histopathological data obtained from the lungs of two patients who underwent lung lobectomies for adenocarcinoma and were found to have had SARS-CoV-2 infection at the time of surgery. Apart from the tumors, the lungs of both “accidental” cases showed edema and large proteinaceous exudative globules. The authors also reported vascular congestion combined with inflammatory clusters of fibrinoid material and multinucleated giant cells and hyperplasia of pneumocytes.

More recently, Zhang et al.¹¹⁹  performed a post-mortem transthoracic needle lung biopsy in a patient who died of COVID-19. Immunostaining showed diffuse alveolar injury and an important alveolar expression of viral antigens. The pathogenic mechanism that produces pneumonia seems to be particularly complex. However, it became apparent very early on that SARS-CoV-2 is not just a respiratory virus. It also affects blood vessels, causing thrombosis¹¹³  and strokes.¹¹⁴  In autopsies on COVID-19 cases, the authors¹²⁰  offered a detailed picture of the histological patterns in lung and extrapulmonary tissues. This picture was characterized by capillary congestion, necrosis of pneumocytes, hyaline membranes, interstitial edema, pneumocyte hyperplasia, and reactive atypia. Platelet–fibrin thrombi in small arterial vessels were the expression of intravascular coagulopathy. Moreover, in the lung they found infiltrates expressed as macrophages in alveoli and lymphocytes in the interstitium. Like SARS and MERS, severe COVID-19 lung damage was manifested in terms of diffuse alveolar disease with severe capillary congestion. Again, many findings were suggestive of vascular dysfunction in lung and other tissues. Other autopsies also have found the virus in organs other than the lungs, including the kidneys, liver, heart, and brain, as well as in the blood.¹²¹  It is now known that symptoms of COVID-19 can include gastrointestinal, neurological, renal, cardiovascular, and other complications.⁹ 

Many existing and approved drugs have been considered for use in the treatment of COVID-19.¹²²  The steroid drug dexamethasone, which calms the overactive immune response, has been shown to reduce mortality from severe COVID-19.¹²³  In May 2020, the United States Food and Drug Administration (FDA) issued an emergency use authorization (EUA) that authorized remdesivir (Veklury) for the treatment of hospitalized adult and pediatric patients with severe COVID-19. The EUA was limited to those patients with severe disease, which was defined as patients with low blood oxygen levels or needing oxygen therapy or more intensive breathing support such as a mechanical ventilator. On 28 August 2020, based ongoing review of the totality of scientific information available, the FDA expanded its authorization to include suspected or laboratory-confirmed COVID-19 in all hospitalized adult and pediatric patients. The Administration's review concluded that benefits inherent in the use of remdesivir in these patients outweigh the known and potential risks.¹²⁴  Other antiviral drugs, convalescent serum, and synthetic monoclonal antibodies are being studied in clinical trials as discussed in subsequent chapters. See Chapters 6 and 15 in Volume 1 and Chapter 8 in Volume 2.

• The spread of this novel coronavirus began in China and the numbers of persons now infected have drastically increased globally, such that the virus is uncontrollable except by the most extreme public health measures.

• The transmission of SARS-CoV-2 is yet to be fully determined, but it appears to transmit quite readily among both symptomatic and asymptomatic persons, especially via respiratory droplets and aerosols.

• Although SARS-CoV-2 is similar to SARS-CoV, the likelihood of dying from SARS-CoV-2 is less, but the likelihood of becoming infected is greater than for SARS-CoV. Part of the explanation for this may be that that SARS-CoV-2 can be frequently transmitted from an asymptomatic person, whereas SARS-CoV is typically transmitted only from a symptomatic person.

• Further research will be needed to fully determine the structural and biological characteristics of SARS-CoV-2 that underlie its ability to cause severe disease in some persons with derangement of their immune system and multi-organ failure, but cause no apparent disease in others who nevertheless test positive for the virus.

• For current pharmacological therapy, the steroid dexamethasone has been shown to reduce mortality in those with severe COVID-19, and the antiviral drug remdesivir has been shown to abbreviate the course of the disease and may also reduce mortality. Other antiviral drugs, convalescent serum, and synthetic monoclonal antibodies are being studied in clinical trials.

• There are at least a million zoonotic viruses that could potentially jump species to infect humans, via mammals or birds, and more careful attention will need to be given to safeguards in “wet markets” like the one in Wuhan, as well as avoiding the capture and ingestion of wild animals.

• The global spread of this virus and the economic and social disruption it has caused should serve as a warning to all countries that international collaboration and 10 simple personal and public health measures need to be priorities for all countries so that no future outbreak can again trigger a pandemic.

CDC

Centers for Disease Control and Prevention

CoVs

Coronaviruses, positive-sense, single-stranded RNA enveloped viruses belonging to the subfamily coronavirinae

MERS-CoV

Middle East respiratory syndrome coronavirus

SARS-CoV

Severe acute respiratory syndrome coronavirus

SARS-CoV-2

Severe acute respiratory syndrome coronavirus 2

+ssRNA

Single-stranded RNA (viruses)

The authors and editors thank Melanie K. Shadoan and Chris L. Ringwalt for their excellent editing of this chapter.