Lethal zoonotic coronavirus infections of humans – comparative phylogenetics, epidemiology, transmission, and clinical features of coronavirus disease 2019, The Middle East respiratory syndrome and severe acute respiratory syndrome : Current Opinion in Pulmonary Medicine

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INFECTIOUS DISEASES: Edited by Michael S. Niederman and Alimuddin Zumla

Lethal zoonotic coronavirus infections of humans – comparative phylogenetics, epidemiology, transmission, and clinical features of coronavirus disease 2019, The Middle East respiratory syndrome and severe acute respiratory syndrome

Hui, David S.a,b; Zumla, Alimuddinc,d; Tang, Julian W.e

Author Information

aDepartment of Medicine & Therapeutics & Stanley Ho Center for Emerging Infectious Diseases

bThe Chinese University of Hong Kong, Shatin, New Territories, Hong Kong

cDepartment of Infection, Division of Infection and Immunity, Centre for Clinical Microbiology, University College London

dNational Institute for Health Research Biomedical Research Centre, University College London Hospitals, London

eRespiratory Sciences, University of Leicester, Leicester, UK

Correspondence to Professor David S. Hui, MD, FRCP, Department of Medicine & Therapeutics & Stanley Ho Center for Emerging Infectious Diseases, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong. Tel: +852 35053128; fax: +852 2648 9957; e-mail: [email protected]

Current Opinion in Pulmonary Medicine 27(3):p 146-154, May 2021. | DOI: 10.1097/MCP.0000000000000774
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Abstract

INTRODUCTION

Coronaviruses (CoV) were first identified as human pathogens in the 1960s. Over the past two decades, three lethal zoonotic coronaviruses have jumped the species barrier and cause lethal disease in humans: severe acute respiratory syndrome coronavirus (SARS-CoV-1) emerged in China in November 2002 and caused the SARS epidemic and disappeared by 2004; The Middle East respiratory syndrome (MERS) coronavirus (MERS-CoV) causing MERS, first identified in September 2012 in Jeddah, Saudi Arabia, 2012 and continues to cause sporadic and localized outbreaks; and SARS-CoV-2, the cause of the ongoing global coronavirus disease 2019 (COVID-19) pandemic. In this article, we review the phylogenetics, epidemiology, transmission, and comparative clinical features of SARS-CoV-2, SARS-CoV-1, and MERS-CoV. 

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Box 1:
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CLASSIFICATION AND PHYLOGENETICS

CoVs (order Nidovirales, family Coronaviridae, subfamily Coronavirinae) are a group of enveloped, positive-sense, highly diverse, single-stranded, RNA viruses that may cause respiratory and diseases of other systems of varying severity in many animal species, including humans. There are four genera of CoVs including αCoV, βCoV, γCoV and δCoV [1]. Prior to the SARS epidemic, the main coronaviruses causing respiratory tract infection in humans were HCoV-229E, HCoV-OC43, HCoV-NL63, and HCoV-HKU1. A novel group 2b βCoV (SARS-CoV-1) was discovered in March 2003 as the causative agent responsible for SARS outbreaks [2]. SARS-CoV-2 emerged at the end of 2019 in Wuhan, China [3▪▪] and led to a pandemic since March 2020. SARS-CoV-1 and SARS-CoV-2 and MERS-CoV are βCoV. SARS-CoV-1 and SARS-CoV-2 belong to lineage B whereas MERS-CoV belongs to lineage C (Fig. 1) [4].

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FIGURE 1:
A maximum likelihood tree of the full genomes of the 7 known human coronaviruses, including SARS-CoV-1, SARS-CoV-2 (including South African 501Y.V2, Brazilian B.1.1.28(K417N/E484K/N501Y) and UK VOC-202012/01 variants), MERS-CoV and seasonal coronaviruses 229E, OC43, NL63, HKU1. Sequences were aligned using MAFFT (https://www.ebi.ac.uk/Tools/msa/mafft/) and manually edited using BioEdit v7.2.5. Phylogenetic tree construction was performed using FastTree v2.1.11 and displayed using FigTree v1.4.4. Shimodaira-Hasegawa-like local values (as implemented in FastTree) are shown as branch supports. MERS-CoV, The Middle East respiratory syndrome; SARS-CoV, severe acute respiratory syndrome-coronaviruses.

CORONAVIRUS DISEASE 2019

Epidemiology

On December 31, 2019, unusual cases of pneumonia in Wuhan, China were reported to the World Health Organization (WHO) and the outbreak was associated with a seafood market where game meat was also sold. A novel CoV, later named as SARS-CoV-2, was identified as the cause of this outbreak on January 7, 2020. There was 79.6% similarity of SARS-CoV-2 in genetic sequence to SARS-CoV-1 and 96% similarity at the whole genome level to a bat CoV [5]. SARS-CoV-2 appears to be a mutated version of bat CoV-RaTG13, detected and isolated in bats from the species Rhinolophus affinis in Yunnan Province in China, between 2015 and 2017 [5,6]. Lu et al.[7] examined the genome from nine patients (eight of whom had visited the Huanan seafood market in Wuhan) and found that SARS-CoV-2 was more related to two SARS-like bat CoV from Zhoushan in eastern China: bat-SL-CoVZC45 (with 87.99% identity) and bat-SL-CoVZXC21 (with 87.23% identity), and more distant from SARS-CoV-1 (about 79%) and MERS-CoV (50%) The data suggest that bat SARS-like CoVs and human SARS-CoV-2 might share the same ancestor [8]. Pangolins were implicated as a potential intermediary source but there was only 91.02% similarity between pangolin-CoV and SARS-CoV-2 at the whole-genome level [9]. Minks were the first farm animals to experience COVID-19 outbreaks in Europe and appear to be a highly susceptible species to SARS-CoV-2 [10]. It is plausible that the widespread infection on the mink farms is related to human-to-animal transmission. Nonetheless, evidence of mink-to-human transmission is limited to one worker, according to the preliminary sequencing data [10]. Although dogs and cats can be infected, it does not necessarily mean that they are potential reservoirs of the original virus and most of these animals had mild to no symptoms [10,11].

Despite lockdown of Wuhan city on January 23, 2020, the outbreak quickly spread throughout China and many other countries by travelers from Wuhan. The outbreak was declared a Public Health Emergency of International Concern on January 30, 2020 and the WHO announced a name on February 11, 2020 for the new CoV disease as COVID-19. On March 11, 2020, the WHO announced the extent and evolution of the global outbreak of COVID-19 as reaching a pandemic [12].

As of February 9, 2021, more than 106 million cases of COVID-19 have been confirmed worldwide with over 2.3 million deaths [13]. Common presenting symptoms of COVID-19 include fever (44% on admission and then increased to 89% during hospitalization), cough mainly nonproductive (67.8%) whereas diarrhea is uncommon (3.8%). The median incubation period is 4 days (interquartile range, 2–7). The absence of fever in a high proportion of patients makes it difficult to detect these cases in the community in the early stage of infection [14▪▪].

According to the WHO, people aged ≥60 years, and those with underlying medical comorbidity (such as hypertension, cardiac and pulmonary problems, diabetes mellitus, obesity, or cancer) are at higher risk of developing serious illness from COVID-19 [15]. In the USA, the prevalence of reported severe outcomes increased with age; the percentages of hospitalization, intensive care admissions, and deaths were highest among persons aged ≥70 years, regardless of underlying conditions, and lowest among those aged ≤19 years [16]. Age is an independent risk factor for severe illness, whereas the risk in older adults is also partly related to the increased likelihood that older adults have other underlying medical conditions [17].

Transmission

Human to human transmission has been documented in the Wuhan seafood market outbreak [3▪▪]. There is evidence that patients in the presymptomatic stage and those with mild disease may transmit infection to others [18]. At least 50% of community transmission may be related to asymptomatic infection [19]. Laxminarayan et al. have shown that 5% of infected individuals account for spreading of 80% of cases [20]. Transplacental transmission of SARS-CoV-2 infection has been documented [21].

Viral kinetic studies have shown that the viral load peaks on days 2–3 of the patient's illness [22] and this explains the high potential of SARS-CoV-2 in causing community transmission among close contacts. Serology response starts on day 7 of illness whereas PCR positivity in deep throat saliva could last for at least 3 weeks in one-third of patients [23].

There have been increasing reports of COVID-19 outbreaks in long-term care facilities (LTCF) from countries in Europe and in the UK. High community prevalence of COVID-19 increases the risk of importation of the virus to institutions, possibly through asymptomatic visitors and staff with COVID-19. With the increased vulnerability of LTCF residents, COVID-19 outbreaks in these settings could have devastating effects. Increased morbidity and mortality have been reported in LTCF even with the implementation of specific control measures in these settings. The overall risk related to COVID-19 infection is assessed as being very high [24]. Short-range airborne transmission is possible in the presence of poor environmental ventilation [25].

The emergence of genetic mutants such as D614G, N501Y and the related South African (501Y.V2), Brazilian (B.1.1.28: K417N/E484K/N501Y) and UK (VOC-202012/01) variants has led to an increase in transmissibility in the community without increase in severity (Fig. 1) [26]. How wide these new variants have spread and how they may affect existing treatments and vaccines remain to be defined.

SEVERE ACUTE RESPIRATORY SYNDROME

Epidemiology

SARS-CoV-1 first emerged in Guangdong in the southern part of China in November 2002 before spreading to Singapore, Canada, Vietnam, and other countries by travelers through Hong Kong (HK) in February and March 2003 [27,28]. In November 2002, there was an unusual outbreak of ‘atypical pneumonia’ in Foshan, Guangdong Province in China, with a very high rate of nosocomial transmission to healthcare workers (HCWs) [29,30]. A retrospective study of 55 patients hospitalized with ‘atypical pneumonia’ in Guangzhou between January and February 2003 revealed positive SARS-CoV1 in their nasopharyngeal aspirates (NPA) whereas 48 (87%) patients had positive antibody to SARS-CoV-1 in their convalescent sera. Genetic analysis subsequently showed that the SARS-CoV-1 isolates from Guangzhou shared the same origin with those in other countries, with a phylogenetic pathway that matched the spread of SARS-CoV-1 to other parts of the world [31].

In March 2003, a novel CoV was confirmed as the causative agent for SARS, and recently referred to as SARS-CoV-1. A retrospective serologic survey suggested that cross-species transmission of SARS-CoV-1 or its variants from animal species to humans might have occurred frequently in the wet market where a high sero-prevalence of 16.7% was detected among asymptomatic animal handlers [32]. It was once thought that masked palm civets might have been responsible for transmission of SARS-CoV-1 to humans following detection of a close variant of SARS-CoV1 in 2003 from palm civets in Dongmen market, Shenzhen [33]. During the small-scale SARS-CoV1 infection outbreaks in late 2003 and early 2004 in China, three of the four patients had direct or indirect contact with palm civets [34,35]. However, viral genomic sequence analysis revealed that the SARS-CoV-like virus had not been present among masked civets in markets for that long. CoVs highly similar to SARS-CoV-1 were isolated in horseshoe bats in 2005 [36,37]. These bat SARS-like CoVs shared 88–92% sequence homology with human or civet isolates and the data suggest that bats could be a natural reservoir of a close ancestor of SARS-CoV-1 [38].

A 64-year old nephrologist who came from southern China to HK on February 21, 2003 was the index case causing subsequent outbreaks of SARS-CoV-1 infection in HK, Singapore and Toronto [27,28,39,40]. Sixteen hotel guests/visitors were infected by the renal physician whereas staying or visiting friends on the same floor of the hotel M, where the physician had briefly stayed. Through international air travel, these visitors spread the infection to 29 countries/regions with a total of 8098 cases and a mortality rate of 774 (9.6%) by the end of the epidemic in July 2003 [41].

Transmission

SARS-CoV1 appears to have spread by close person-to-person contact via droplet transmission or contact with fomite [42]. Super-spreading event was a hallmark of SARS-CoV-1 infection, as reflected by the nosocomial outbreak at a major teaching hospital in HK where 138 subjects (many being HCWs and previously healthy) were infected within a fortnight following exposure to one patient (a visitor of Hotel M), who was hospitalized with community-acquired pneumonia to a general medical ward [27,43]. This super-spreading event was likely caused by several factors including the use of a jet nebulizer for delivering bronchodilator to the index case, overcrowding, and poor ventilation in the hospital ward [27,43]. In addition, the temporal-spatial spread of SARS-CoV-1 among inpatients in the index medical ward of the hospital in HK was consistent with airborne transmission [44].

In addition, SARS-CoV-1 might have spread by opportunistic airborne transmission in a major community outbreak involving over 300 residents in a private residential complex, Amoy Gardens, in HK [45,46]. Drying up of ‘U-shaped’ bathroom floor drains and backflow of contaminated sewage (from a SARS-CoV1 patient with renal failure and diarrhea) related to negative pressure generated by the toilet exhaust fans might have created infectious aerosols that moved upward through the warm airshaft of the building. Based on analysis of the distribution of all confirmed cases, airborne spread was the most likely explanation in the Amoy Gardens outbreak and the SARS-CoV-1 could have spread over 200 m to nearby residential complexes [47]. Air samples obtained from a hospital room in Toronto occupied by a SARS patient and swab samples taken from frequently touched surfaces in rooms and in a nurses’ station in Toronto were positive by PCR testing [48]. These data suggest the possibility of airborne transmission and stress the importance of taking appropriate respiratory protection apart from implementing strict surface hygiene practices.

Asymptomatic SARS-CoV-1 infection appears uncommon as a meta-analysis has shown overall sero-prevalence rates of 0.1% for the general population and 0.23% for HCWs although the true incidence of asymptomatic infection remains unknown [49]. A case control study involving 124 medical wards in 26 hospitals in HK and Guangzhou has identified six independent factors of super-spreading nosocomial outbreaks of SARS-CoV-1 infection: performance of resuscitation, minimum distance between beds < 1m, staff working whereas experience symptoms, SARS-CoV-1 patients requiring oxygen therapy or noninvasive ventilation (NIV) whereas availability of washing or changing facilities for staff was protective (Table 1) [45]. A systematic review has shown that four aerosol-generating procedures would increase the risk of nosocomial SARS-CoV-1 transmission to HCWs including tracheal intubation, NIV, tracheotomy, and manual ventilation before intubation (Table 2) [46]. Thus it is important for HCWs to implement airborne precaution measures before carrying out aerosol-generating procedures.

Table 1 - Independent factors associated with increased risk ofa super-spreading events of SARS-CoV infection in the healthcare setting [data from [50]]:
Performance of resuscitation (OR 3.81, 95%CI 1.04–13.87, P = 0.04)
Staff working although experiencing symptoms (OR 10.55, 95% CI 2.28–48.87, P = 0.003)
SARS patients requiring oxygen therapy at least 6L/min (OR 4.30, 95% CI 1.00–18.43, P = 0.05)
SARS patients requiring noninvasive positive pressure ventilation (OR 11.82, 95% CI 1.97–70.80, P = 0.007)
Minimum distance between beds <1m (OR 6.94, 95% CI 1.68–28.75, P = 0.008)
Washing or changing facilities for staff (OR 0.12, 95% CI 0.02–0.97, P = 0.05)
SARS-CoV, severe acute respiratory syndrome-coronaviruses.
aA super-spreading event was defined as one patient that could infect at least 3 others.

Table 2 - Respiratory procedures reported to present an increased risk of transmission of SARS-CoV-1 to healthcare workers [n; pooled OR (95% CI)] [51]
Tracheal intubation [n = 4 cohort; 6.6 (2.3, 18.9), and n = 4 case-control; 6.6 (4.1, 10.6)],
Noninvasive ventilation [n = 2 cohort; OR 3.1(1.4, 6.8)],
Tracheotomy [n = 1 case-control; 4.2 (1.5, 11.5)] and
Manual ventilation before intubation [n = 1 cohort; OR 2.8 (1.3, 6.4)].
SARS-CoV, severe acute respiratory syndrome-coronaviruses.

MIDDLE EAST RESPIRATORY SYNDROME CORONAVIRUS

Epidemiology

MERS-CoV was first identified in September 2012 when a novel βCoV was isolated from a male patient who had died of severe pneumonia and multiorgan failure in Saudi Arabia in June 2012 [52]. MERS-CoV infection has spread to 27 countries since its discovery in 2012. Globally, from September 2012 to September 2019 2016, WHO has been informed of 2468 laboratory-confirmed cases of infection with MERS-CoV, with at least 851 deaths [53].

Although the natural reservoir of MERS-CoV is still unclear, dromedary camels are an important natural host for the diversification and maintenance of MERS-CoV and appear to be the major source of zoonotic human infection [54]. The virus has been isolated from dromedary camels in the Arabian Peninsula and across North, East, West, and Central Africa, but is not found in dromedary camels in other countries such as Kazakhstan [55] or in Bactrian camels in Mongolia [56]. However, only a minority of reported MERS human cases have reported direct camel exposure [57].

Transmission

Although MERS-CoV was first described in September 2012 [52], a retrospective study of a cluster of hospital cases dated back to April 2012 in Jordan by RTPCR and serology confirmed MERS-CoV as the etiology of the outbreak that involved at least 10 HCWs [58]. The epidemiology of MERS-CoV is characterized by sporadic zoonotic transmission events, sometimes followed by nosocomial outbreaks within healthcare settings due to failure in infection control and prevention measures. Saudi Arabia has the largest MERS-CoV case load, followed by South Korea as the country with the highest case load outside the Arabic Peninsula [53].

The risk factors for primary MERS-CoV infection were examined in a case-control study of thirty primary MERS-CoV cases reported from March to November 2014 in Saudi Arabia, with two to four controls matched by age, sex and neighborhood for each case patient [59]. The investigators demonstrated by multivariate analyses that direct dromedary exposure in the two weeks before illness onset was strongly associated with MERS-CoV illness (adjusted OR 7.45, 95% CI 1.57–35.28), along with having diabetes mellitus (adjusted OR 6.99, 95% CI 1.89–25.86) or heart disease (adjusted OR 6.87, 95% CI 1.81–25.99) and current tobacco smoking (adjusted OR 6.84, 95% CI 1.68–27.94) [59]. The risk for secondary transmission from patients to household contacts was estimated at about 4% [60]. Risk factors for household transmission included sleeping in an index patient's room and touching respiratory secretions from an index patient whereas casual contact and simple proximity were not associated with transmission [61] (Table 3).

Table 3 - Risk factors for Primary and Household transmission
Independent factors associated with primary MERS-CoV illness (Saudi Arabia) [59]:
 a) Direct dromedary exposure in the 2 weeks before illness onset (adjusted OR 7.45, 95% CI 1.57–35.28)
 b) Diabetes mellitus (adjusted OR 6.99, 95% CI 1.89–25.86)
 c) Heart disease (adjusted OR 6.87, 95% CI 1.81–25.99) or currently smoking tobacco (adjusted OR 6.84, 95% CI 1.68–27.94)
 d) Direct physical contact with dromedaries in the previous 6 months (adjusted OR 14.59, 95% CI 2.38–89.55)
Risk factors for household transmission [61]:
 a) Sleeping in an index patient's room [RR 4.1 (1.5–11.2)]
 b) Removing patient's waste (urine, stool and sputum) [RR 3.2 (1.2–8.4)]
 c) Touching respiratory secretions from an index patient [RR 4.0 (1.6–9.8)]
MERS-CoV, The Middle East respiratory syndrome.

In a cross-sectional sero-surveillance study of 10,009 healthy individuals in Saudi Arabia, 0.15% had evidence of positive MERS-CoV serology, suggesting that the number of mild or asymptomatic infections far exceeds those that are recognized [62]. Sero-positivity was more common in males than in females, in central than in coastal provinces, and in camel shepherds (2.3%) and slaughterhouse workers (3.6%) than in others [62].

Nosocomial transmission is a hallmark of MERS-CoV infection. Super-spreading events of MERS-CoV infection were reported in Jordan [58], Al Hasa [63], Jeddah [64], Abu Dhabi [65] whereas the major outbreak in South Korea in 2015 was due to several super-spreading events in the hospital settings [66]. Failure in infection control and prevention measures in healthcare facilities (HCFs) resulted in large numbers of secondary cases of MERS-CoV infection involving HCWs, existing patients, and visitors in Saudi Arabia [63,64] and several other countries over the past few years [58,65,66]. Common predisposing factors include exposure to contaminated and overcrowded HCFs, poor compliance with appropriate personal protection equipment when assessing patients with febrile respiratory illness, application of potentially aerosol-generating procedures (resuscitation, continuous positive airway pressure, nebulized medications), and lack of proper isolation room facilities [58,63–67]. The customs of patients seeking care at different HCFs (‘doctor shopping’) and having friends and family members to stay with patients as caregivers at already overcrowded HCFs were unique factors in South Korea [68].

Cases specifically reported as ‘asymptomatic’ or ‘mild disease’ in Saudi Arabia occurred only among secondary cases [63,64] whereas most (90%) of index or sporadic cases had severe disease [63].

SUMMARY/CONCLUSION

Bats appear to be the common natural source of SARS-CoV-1 whereas more research is needed to examine their role in SARS-CoV-2 and MERS-CoV. The sale and consumption of the intermediary source of SARS-CoV-1 (civet cats) have been banned in China since 2003 and the transmission chain was cut.

In the Middle East, the intermediary reservoir (camels) is still widely available and there is sporadic spill-over infection from camels to humans through close contact whereas nosocomial transmission has become less frequent due to improvement in hospital infection control and prevention measures in recent years.

SARS-CoV-2 shows distinct transmission dynamics - being uniquely infectious in the presymptomatic and asymptomatic stages with high viral load peaking in the first week of illness and so the pattern of spread is different from SARS-CoV-1 and MERS-CoV because of these differing patterns of host-virus interactions. Peaking of viral loads of SARS-CoV-2 on days 2–4 of symptom onset leads to high transmission potential in the community [22]. Asymptomatic and presymptomatic transmission occurs commonly in COVID-19 [18,19].

Nosocomial outbreaks are hallmarks of SARS-CoV-1 [27–30] and MERS-CoV infections [58,63–66] whereas these are less common in COVID-19. Civet cats [32,33] and dromedary camels [59] are the intermediary animal sources for SARS-CoV-1 and MERS-CoV infection respectively whereas that of SARS-CoV-2 remains unclear (Table 4).

Table 4 - Comparative epidemiological, demographic and clinical features of SARS-CoV-2, MERS-CoV and SARS-CoV-1
SARS-CoV-2 [13,14▪▪] MERS-CoV [63,64] SARS-CoV-1 [27–29,31]
Natural reservoir Unclear (possibly bats) Unclear (possibly bats) Chinese horse shoe bats
Intermediate host Unclear Dromedary camels Civet cats
Date of first case report (place) December 2019 (Wuhan, China) April 2012 (Jordan)June 2012 (First KSA case) November 2002 (Foshan, China)
Incubation period Median 4 days (IQR 2–7)Range 2–14 days Mean: 5.2 days(95% CI:1.9–14.7). Range: 2–13 days Mean: 4.6 days (95% CI:3.8–5.8)Range: 2–14 days
Reproduction number 2.5 <1 2.4
Age group
 Adults Adults (98%) Adults (98%) Adults (93%)
 Children Children (2%) Children (2%) Children (5–7%)
Mortality
 Case fatality rate (CFR)-overall 2.2% 34.5% 9.6%
 CFR in patients with co-morbidities 73.3% 60% 46%
 Time from onset to death Mean 15.4 days Median 11.5 days Mean 23.7 days
Presenting symptoms
 Fever 43.8% on admission;88.7% on hospitalization 98% 99–100%
 Chills/rigors 11.4% 87% 15–73%
 Cough 67.8% 83% 62–100%
 -dry 34.1% 56% 29–75%
 -productive 33.7% 44% 4–29%
 Haemoptysis 0.9% 17% 0–1%
 Headache 13.6% 11% 20–56%
 Myalgia 14.9% 32% 45–61%
 Malaise 38.1% 38% 31–45%
 Shortness of breath 18.7% 72% 40–42%
 Nausea 5% 21% 20–35%
 Vomiting 5% 21% 20–35%
 Diarrhea 3.8% 26% 20–25%
 Sore throat 13.9% 14% 13–25%
 Rhinorrhoea 4.8% 6% 2–24%
 Anosmia 40–80% Unknown Unknown
MERS-CoV, The Middle East respiratory syndrome; SARS-CoV, severe acute respiratory syndrome-coronaviruses

The emergence of genetic variants, such as D614G, N501Y variants 1 and 2 [26], has led to an increase in transmissibility without increase in individual's severity and raised concern about the possibility of re-infection and impaired vaccine response. Although COVID-19 vaccination programs have commenced in many countries, continual surveillance for viral mutations is essential to monitor changing epidemiology due to viral variants and other factors.

Acknowledgements

Prof David S Hui is supported by the Commissioned Research on COVID-19 (COVID190110), Health & Medical Research Fund, Food & Health Bureau, HK. Professor Sir Zumla is co-principal investigator of the European and Developing Countries Clinical Trials Partnership the EU Horizon 2020 Framework Program, projects a) Pan-African Network on Emerging and Re-Emerging Infections (PANDORA-ID-NET https://www.pandora-id.net/), b) EDCTP NOEs CANTAM-2 and EACCR. Sir Prof Zumla is in receipt of a UK-National Institutes of Health Research senior investigator award and is a 2020 Mahathir Science Award Laureate.

None.

Financial support and sponsorship

None.

Conflicts of interest

There are no conflicts of interest.

REFERENCES AND RECOMMENDED READING

Papers of particular interest, published within the annual period of review, have been highlighted as:

▪ of special interest

▪▪ of outstanding interest

REFERENCES

1. Zumla A, Chan JF, Azhar EI, et al. Coronaviruses - drug discovery and therapeutic options. Nat Rev Drug Discov 2016; 15:327–347.
2. Peiris JSM, Lai ST, Poon LL, et al. SARS study group. Coronavirus as a possible cause of severe acute respiratory syndrome. Lancet 2003; 361:1319–1325.
3▪▪. Li Q, Guan X, Wu P, et al. Early transmission dynamics in Wuhan, China, of novel coronavirus-infected pneumonia. N Engl J Med 2020; 382:1199–1207.
4. Aboubakr HA, Sharafeldin TA, Goyal SM. Stability of SARS-CoV-2 and other coronaviruses in the environment and on common touch surfaces and the influence of climatic conditions: A review. Transbound Emerg Dis 2020; doi: 10.1111/tbed.13707. Online ahead of print.
5. Zhou P, Yang XL, Wang XG, et al. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature 2020; 579:270–273.
6. Andersen KG, Rambaut A, LipkinWI, et al. The proximal origin of SARS-CoV-2. Nat Med 2020; 26:450–452.
7. Lu R, Zhao X, Li J, et al. Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding. Lancet 2020; 395:565–574.
8. Guo YR, Cao QD, Hong ZS, et al. The origin, transmission and clinical therapies on coronavirus disease 2019 (COVID-19) outbreak- an update on the status. Mil Med Res 2020; 7:11https://doi.org/10.1186/s40779-020-00240-0
9. Zhang T, Wu Q, Zhang Z. Probable Pangolin origin of SARS-CoV-2 associated with the COVID-19 outbreak. Curr Biol 2020; 30:1578doi: 10.1016/j.cub.2020.03.063.
10. Boklund A, Hammer AS, Quaade ML, et al. SARS-CoV-2 in danish mink farms: course of the epidemic and a descriptive analysis of the outbreaks in 2020. Animals (Basel) 2021; 11:164doi: 10.3390/ani11010164.
11. Do Vale B, Lopes AP, Fontes M, et al. Bats, pangolins, minks and other animals - villains or victims of SARS-CoV-2? Vet Res Commun 2021; 45:1–19. doi: 10.1007/s11259-021-09787-2.
12. WHO. Listings of WHO's response to COVID-19. June 29, 2020, Statement. Accessed January 19, 2021. Available at: Listings of WHO's response to COVID-19. https://www.who.int/news/item/29-06-2020-covidtimeline
13. WHO Coronavirus Disease (COVID-19) Dashboard. Accessed February 9, 2021. Available at: WHO Coronavirus Disease (COVID-19) Dashboard | WHO Coronavirus Disease (COVID-19) Dashboard. https://covid19.who.int/
14▪▪. Guan WJ, Ni ZY, Hu Y, et al. Clinical characteristics of Coronavirus Disease 2019 in China. N Engl J Med 2020; 382:1708–1720.
15. WHO. COVID-19 Q&A. Accessed on January 19, 2021. Available at https://www.who.int/emergencies/diseases/novel-coronavirus-2019/question-and-answers-hub/q-a-detail/coronavirus-disease-covid-19.
16. Stokes EK, Zambrano LD, Anderson KN, et al. Coronavirus Disease 2019 case surveillance - United States, January 22–May 30, 2020. Morb Mortal WklyRep 2020; 69:759–765.
17. US CDC updates, expands list of people at risk of severe COVID-19 illness. Accessed January 19, 2021. Available at. https://www.cdc.gov/media/releases/2020/p0625-update-expands-covid-19.html.
18. Bai Y, Yao L, Wei T, et al. Presumed asymptomatic carrier transmission of COVID-19. JAMA 2020; 323:1406–1407.
19. Johansson MA, Quandelacy TM, Kada S, et al. SARS-CoV-2 transmission from people without COVID-19 symptoms. JAMA Open Netw Open 2021; 4:e2035057.
20. Laxminarayan R, Wahl B, Dudala SR, et al. Epidemiology and transmission dynamics of COVID-19 in two Indian states. Science 2020; 370:691–697.
21. Vivanti AJ, Vauloup-Fellous C, Prevot S, et al. Transplacental transmission of SARS-CoV-2 infection. Nature Commun 2020; 11:3572doi: 10.1038/s41467-020-17436-6.
22. Zou L, Ruan F, Huang M, et al. SARS-CoV-2 viral load in upper respiratory specimens of infected patients. N Engl J Med 2020; 382:1177–1179.
23. To KK, Tsang OT, Leung WS, et al. Temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by SARS-CoV-2: an observational cohort study. Lancet Infect Dis 2020; 20:565–574.
24. European Centre for Disease Prevention and Control. Rapid Risk Assessment: Increase in fatal cases of COVID-19 among long-term care facility residents in the EU/EEA and the UK. Last updated November 19, 2020. Accessed December 15, 2020. Available at. https://www.ecdc.europa.eu/en/publications-data/rapid-risk-assessment-increase-fatal-cases-covid-19-among-long-term-care-facility.
25. Tang JW, Bahnfleth WP, Bluyssen PM, et al. Dismantling myths on the airborne transmission of severe acute respiratory syndrome coronavirus (SARS-CoV-2). J Hosp Infect 2021; S0195-6701(21)00007-4. doi: 10.1016/j.jhin.2020.12.022. Online ahead of print.
26. WHO. SARS-CoV-2 Variants. Disease Outbreak News. December 31, 2020. Accessed January 19, 2021. Available at: WHO | SARS-CoV-2 Variants. https://www.who.int/csr/don/31-december-2020-sars-cov2-variants/en/
27. Lee N, Hui DS, Wu A, et al. A major outbreak of severe acute respiratory syndrome in Hong Kong. N Engl J Med 2003; 348:1986–1994.
28. Tsang KW, Ho PL, Ooi GC, et al. A cluster of cases of severe acute respiratory syndrome in Hong Kong. N Engl J Med 2003; 348:1977–1985.
29. Zhao Z, Zhang F, Xu M, et al. Description and clinical treatment of an early outbreak of severe acute respiratory syndrome (SARS) in Guangzhou, PR China. J Med Microbiol 2003; 52:715–720.
30. Xu RH, He JF, Evans MR, et al. Epidemiologic clues to SARS origin in China. Emerg Infect Dis 2004; 10:1030–1037.
31. Zhong NS, Zheng BJ, Li YM, et al. Epidemiology and cause of severe acute respiratory syndrome in Guangdong, People's Republic of China, in February 2003. Lancet 2003; 362:1353–1358.
32. Du L, Qiu JC, Wang M, et al. Analysis on the characteristics of blood serum Ab-IgG detective result of severe acute respiratory syndrome patients in Guangzhou, China. Zhonghua Liu Xing Bing Xue Za Zhi 2004; 25:925–928.
33. Guan Y, Zheng BJ, He YQ, et al. Isolation and characterization of viruses related to the SARS coronavirus from animals in southern China. Science 2003; 302:276–278.
34. Wang M, Yan M, Xu H, et al. SARS-CoV infection in a restaurant from palm civet. Emerg Infect Dis 2005; 11:1860–1865.
35. Song HD, Tu CC, Zhang, et al. Cross-host evolution of severe acute respiratory syndrome coronavirus in palm civet and human. Proc Natl Acad Sci USA 2005; 102:2430–2435.
36. Lau SK, Woo PC, Li KS, et al. Severe acute respiratory syndrome coronavirus-like virus in Chinese horseshoe bats. Proc Natl Acad Sci 2005; 102:14040–14045.
37. Li W, Shi Z, Yu M, et al. Bats are natural reserviors of SARS-like coronaviruses. Science 2005; 310:676–679.
38. Shi Z, Hu Z. A review of studies on animal reservoirs of the SARS coronavirus. Virus Res 2008; 133:74–87.
39. Hsu LY, Lee CC, Green JA, et al. Severe acute respiratory syndrome in Singapore: clinical features of index patient and initial contacts. Emerg Infect Dis 2003; 9:713–717.
40. Booth CM, Matukas LM, Tomlinson GA, et al. Clinical features and short-term outcomes of 144 patients with SARS in the greater Toronto area. JAMA 2003; 289:2801–2809.
41. WHO. Summary of probable SARS cases with onset of illness from November 1 to July 31, 2003. Accessed 2 July 2016. Available at: https://www.who.int/publications/m/item/summary-of-probable-sars-cases-with-onset-of-illness-from-1-november-2002-to-31-july-2003.
42. Peiris JS, Yuen KY, Osterhaus AD, et al. The severe acute respiratory syndrome. N Engl J Med 2003; 349:2431–2441.
43. Wong RS, Hui DS. Index patient and SARS outbreak in Hong Kong. Emerg Infect Dis 2004; 10:339–341.
44. Yu IT, Wong TW, Chiu YL, et al. Temporal-spatial analysis of Severe acute respiratory syndrome among hospital inpatients. Clin Infect Dis 2005; 40:1237–1243.
45. Yu IT, Li Y, Wong TW, et al. Evidence of airborne transmission of the severe acute respiratory syndrome virus. N Engl J Med 2004; 350:1731–1739.
46. Chu CM, Cheng VC, Hung IF, et al. Viral load distribution in SARS outbreak. Emerg Infect Dis 2005; 11:1882–1886.
47. Yu IT, Qiu H, Tse LA, Wong TW. Severe acute respiratory syndrome beyond amoy gardens: completing the incomplete legacy. Clin Infect Dis 2014; 58:683–686.
48. Booth TF, Kournikakis B, Bastien N, et al. Detection of airborne Severe acute respiratory syndrome (SARS) coronavirus and environmental contamination in SARS outbreak units. J Infect Dis 2005; 191:1472–1427.
49. Leung GM, Lim WW, Ho LM, et al. Seroprevalence of IgG antibodies to SARS-coronavirus in asymptomatic or subclinical population groups. Epidemiol Infect 2006; 134:211–221.
50. Yu IT, Xie ZH, Tsoi KK, et al. Why did outbreaks of severe acute respiratory syndrome occur in some hospital wards but not in others? Clin Infect Dis 2007; 44:1017–1025.
51. Tran K, Cimon K, Severn M, et al. Aerosol generating procedures and risk of transmission of acute respiratory infections to healthcare workers: a systematic review. PLoS One 2012; 7:e35797.
52. Zaki AM, van Boheemen S, Bestebroer TM, et al. Isolation of a novel coronavirus from a man with pneumonia in Saudi Arabia. N Engl J Med 2012; 367:1814–1820.
53. World Health Organization. MERS situation update September 2019. Accessed January 20, 2021. Available at: MERS-CoV_September_2019 (who.int). https://applications.emro.who.int/docs/EMROPub-MERS-SEP-2019-EN.pdf?ua=1&ua=1
54. Haagmans BL, Al Dhahiry SH, Reusken CB, et al. Middle East respiratory syndrome coronavirus in dromedary camels: an outbreak investigation. Lancet Infect Dis 2014; 14:140–145.
55. Miguel E, Perera RA, Baubekova A, et al. Absence of middle east respiratory syndrome coronavirus in Camelids, Kazakhstan, 2015. Emerg Infect Dis 2016; 22:555–557.
56. Chan SM, Damdinjav B, Perera RA, et al. Absence of MERS-Coronavirus in Bactrian Camels, Southern Mongolia, November 2014. Emerg Infect Dis 2015; 21:1269–1271.
57. Saad M, Omrani AS, Baig K, et al. Clinical aspects and outcomes of 70 patients with Middle East respiratory syndrome coronavirus infection: a single-center experience in Saudi Arabia. Int J Infect Dis 2014; 29:301–306.
58. Hijawi B, Abdallat M, Sayaydeh A, et al. Novel coronavirus infections in Jordan, April 2012: epidemiological findings from a retrospective investigation. East Mediterr Health J 2013; 19: (Suppl 1): S12–18.
59. Alraddadi BM, Watson JT, Almarashi A, et al. Risk factors for primary Middle East respiratory syndrome coronavirus illness in humans, Saudi Arabia, 2014. Emerg Infect Dis 2016; 22:49–55.
60. Drosten C, Meyer B, Müller MA, et al. Transmission of MERS-coronavirus in household contacts. N Engl J Med 2014; 371:828–835.
61. Arwady MA, Alraddadi B, Basler C, et al. Middle East respiratory syndrome coronavirus transmission in extended family, Saudi Arabia, 2014. Emerg Infect Dis 2016; 22:1395–1402.
62. Müller MA, Meyer B, Corman VM, et al. Presence of Middle East respiratory syndrome coronavirus antibodies in Saudi Arabia: a nationwide, cross-sectional, serological study. Lancet Infect Dis 2015; 15:559–564.
63. Assiri A, McGeer A, Perl TM, et al. Hospital outbreak of Middle East respiratory syndrome coronavirus. N Engl J Med 2013; 369:407–416.
64. Oboho IK, Tomczyk SM, Al-Asmari AM, et al. 2014 MERS-CoV outbreak in Jeddah – a link to healthcare facilities. N Engl J Med 2015; 372:846–854.
65. Hunter JC, Nguyen D, Aden B, et al. Transmission of Middle East Respiratory Syndrome Coronavirus Infections in Healthcare Settings, Abu Dhabi. Emerg Infect Dis 2016; 22:647–656.
66. Korea Centers for Disease Control and Prevention. Middle East Respiratory Syndrome Coronavirus Outbreak in the Republic of Korea, 2015. Osong Public Health Res Perspect 2015; 6:269–278.
67. Oh MD, Choe PG, Oh HS, et al. Middle East Respiratory Syndrome Coronavirus Superspreading Event Involving 81 Persons, Korea 2015. J Korean Med Sci 2015; 30:1701–1705.
68. Hui DS, Peiris M. Middle East respiratory syndrome. Am J Respir Crit Care Med 2015; 192:278–279.
Keywords:

coronaviruses; coronavirus disease 2019; The Middle East respiratory syndrome; The Middle East respiratory syndrome coronavirus; severe acute respiratory syndrome; severe acute respiratory syndrome-coronaviruses-1; severe acute respiratory syndrome-coronaviruses-2

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