At the end of December, 2019, a new disease of unknown aetiology appeared in Wuhan,
China. It was quickly identified as a novel betacoronavirus, and related to SARS-CoV
and a number of other bat-borne SARS-like coronaviruses. The virus rapidly spread
to all provinces in China, as well as a number of countries overseas, and was declared
a Public Health Emergency of International Concern by the Director-General of the
World Health Organization on 30 January 2020. This paper describes the evolution of
the outbreak, and the known properties of the novel virus, SARS-CoV-2 and the clinical
disease it causes, COVID-19, and comments on some of the important gaps in our knowledge
of the virus and the disease it causes. The virus is the third zoonotic coronavirus,
after SARS-CoV and MERS-CoV, but appears to be the only one with pandemic potential.
An outbreak of cases of pneumonia of unknown aetiology in the city of Wuhan in Hubei
Province, China, was announced and notified to the World Health Organization (WHO)
by the Wuhan Municipal Health Commission on 31 December 2019
1
. The outbreak was linked epidemiologically to the Hua Nan seafood and wet animal
wholesale market in Wuhan, and the market was subsequently closed on 1 January 2020.
A week later, on 7 January, the isolation of a previously unknown betacoronavirus
was reported as the aetiological agent.
Wuhan is a city of 11 million inhabitants and is a major transport hub, and over the
ensuing weeks the virus spread to other provinces in China and later to an increasing
number of other countries. This spread prompted the WHO Director-General to establish
an Emergency Committee (EC) under the International Health Regulations (IHR). The
EC recommended that the outbreak constituted a public health emergency of international
concern at its meeting on 30 January
2
. In so doing, the Committee believed that it was still possible to interrupt virus
spread, provided that countries put in place strong measures to detect disease early,
isolate and treat cases, trace contacts, and promote social distancing measures commensurate
with the risk.
The city of Wuhan was placed in quarantine by the Chinese Government on 23 January,
stopping all rail, road and air transport out of the city. The quarantine was subsequently
extended to a further 17 cities in Hubei Province, affecting over 57 million people,
which was particularly challenging as it came two days before the Chinese New Year,
the most important festival in the country, and traditionally the peak traveling season.
Since then there have been increasing measures to control and manage the epidemic
within China, and the introductions of numerous travel restrictions by other countries
that either have had cases or are trying to prevent entry.
Early events in determining the identity and origin of the novel coronavirus
Whole virus genome sequences were obtained either directly from patient samples or
from cultured viruses from a number of patients hospitalised with pneumonia in Wuhan,
showing that the aetiological agent was a betacoronavirus belonging to a new clade
in subgenus Sarbecovirus in the Orthocoronavirinae subfamily
3
–
7
. Phylogenetic studies of the new virus showed it shared about 79% nucleotide homology
with SARS-CoV
4
–
7
, as well as to two SARS-like coronaviruses isolated from Chinese horseshoe bats (Rhinolophus
sinicus) in Zhoushan, with which it shared 89% nucleotide homology
3
,
5
–
8
, and to a third SARS-like coronavirus from an Intermediate horseshoe bat (R. affinis),
with which it shared 96% nucleotide homology
4
,
9
. Based on established practice, the new virus was named SARS-CoV-2 by the Coronavirus
Study Group of the International Committee for the Taxonomy of Viruses
10
, and the disease it causes as COVID-19 by WHO
11
.
How this virus moved from animal to human populations is yet to be determined. The
outbreak clearly began epidemiologically at the Wuhan market, and a number of environmental
samples from around the live animal section of the market were subsequently found
to be positive for SARS-CoV-2
12
, but based on current evidence, it may not have actually emerged in the market. The
earliest recognised case of infection with SARS-CoV-2 was an elderly and infirm man
who developed symptoms on 1 December 2019. None of his family members became infected,
and the source of his virus remains unknown
13
. Furthermore, 14 of the first 41 cases had no contact with the seafood market
13
. In another report, five of the first seven cases of COVID-19 had no link to the
seafood market
14
. Thus, it seems very likely that the virus was amplified in the market, but the market
might not have been the site of origin nor the only source of the outbreak. A recent
phylo-epidemiological study has suggested that the virus was circulating but unrecognised
in November, and was imported to the seafood market from elsewhere, where it subsequently
was amplified
15
.
Angiotensin-converting enzyme II (ACE2) was known to be the cell receptor for SARS-CoV,
and also for some SARS-like bat coronaviruses
16
. Sequence studies found that the receptor-binding domain of the SARS-CoV-2 virus
was sufficiently similar to that of SARS-CoV to indicate it could efficiently use
the human ACE2 receptor for entry to human cells
6
,
7
. Infectivity experiments were undertaken with HeLa cells expressing or not expressing
ACE2 from humans, bats, civets, pigs and mice, and the results confirmed that SARS-CoV-2
virus was able to use entry receptors on all ACE2-expressing cells other than mice
5
. Molecular modelling has indicated that the binding affinity of SARS-CoV-2 to ACE-2
may be even higher than that of SARS-CoV and it may therefore be more efficient at
infecting human cells
17
. Evidence from the sequence analyses clearly indicates that the reservoir host of
the virus was a bat, probably a Chinese or Intermediate horseshoe bat, and it is probable
that, like SARS-CoV, an intermediate host was the source of the outbreak. To ensure
that future cross-species transmission events of this new virus don’t occur again
in the future, it is important to identify the reservoir and intermediate wildlife
hosts. The closest known wildlife sequence to SARS-CoV-2 remains the sequence from
the virus isolated from an Intermediate horseshoe bat, but there were significant
differences in the receptor-binding domain between the two viruses. Malayan pangolins
(Manis javanica) have been suggested as potential intermediate hosts, and SARS-like
viruses have been identified in pangolins seized in anti-smuggling operations in southern
China, but they only shared about 85–92%% homology with SARS-CoV-2
18
. No other possible intermediate wildlife host has been proposed at this time.
Next generation sequencing (NGS) was carried out on lung lavage samples from up to
17 patients between 24–30 December 2019 that would have demonstrated the presence
of a SARS-related coronavirus
3
–
7
, but this information was not widely available until a sequence was reported on 12
January 2020. Interestingly, this was the first time that NGS had alerted the world
to a new zoonotic virus before the virus had been isolated, and it suggests that a
new procedure for reporting outbreaks based on NGS rather than pathogen isolation
and identification needs to be considered
19
. The resulting information flow was a great improvement over the experience with
SARS-CoV in 2003, but it is important to continue improving this as the lack of the
earliest possible information about the sequences slowed down the development of diagnostics
and preparedness capacity. This lack of early information may have extended to case
notifications, as no cases were reported between 1 and 17 January 2020, but modelling
suggested there may have been over 450 cases unreported in that time
20
, and indeed a number of such cases were subsequently confirmed retrospectively
14
.
Table 1.
Cumulative cases of COVID-19 on a weekly basis from 21 January to 29 February 2020,
for Hubei Province, for the rest of China, and for other countries.
Cumulative number of cases
20 Jan
27 Jan
3 Feb
10 Feb
17 Feb
24 Feb
2 Mar
9 Mar
Cumulative number in Hubei
258
n/a
11 177
29 631
58 182
64 287
67 103
67 743
Cumulative number in China (excluding Hubei)
20
n/a
6061
10 604
12 453
12 975
13 071
13 161
Total cumulative number in China
278
2741
17 238
40 235
70 635
77 262
80 174
80 904
Cumulative number in other countries
4
37
153
319
794
2069
8774
28 673
Total cumulative number of cases
282
2798
17 391
40 554
71 429
79 331
88 948
109 577
Number of countries reporting cases
4
12
24
25
26
30
64
104
Transmission
Human-to-human transmission of SARS-CoV-2 has been widely shown in health care, community
and family settings. The dominant mode of transmission is from the respiratory tract
via droplets or indirectly via fomites, and to a lesser extent via aerosols. In addition,
as SARS-CoV and MERS-CoV can infect the human gastrointestinal tract
21
,
22
, it has been suggested that faecal-oral spread may occur for SARS-CoV-2
23
. The reproduction number (Ro) is generally thought to be between 2.0 and 2.8
20
,
24
–
27
, although higher reproduction numbers have been suggested in some reports. The mean
incubation time appears to be between 4.75 and 7 days
20
,
23
,
24
,
26
,
28
, ranging from 3 days to an upper limit of around 11–14 days. There is increasing
knowledge about the virus load. In one study of symptomatic patients, higher viral
loads were detected soon after symptom onset, with the viral loads higher in the nose
than in the throat. In a single asymptomatic patient, the viral load was similar to
the symptomatic patients
29
. In a second and more detailed study, the virus load was investigated over consecutive
days in two patients from the time of their hospitalisation, with serial samples throat
swabs, sputum, urine and stools. The viral loads peaked around 5–6 days after symptom
onset, with 104 to 107 copies/mL. The authors also studied the viral loads in throat
swabs, sputum and stool samples in other patients, and found viral loads were as high
as 1011 copies/mL in throat samples, but with a median of 7.99 × 104, and 7.52 × 105
in sputum. In addition, virus was detected by RT-PCR in stools from 9 of 17 confirmed
cases, but at titres lower than in respiratory samples
30
. Several studies have indicated that transmission may occur during the incubation
period
31
,
32
and from asymptomatic or very mild infections
29
,
33
,
34
.
There are a number of important questions still to be answered about the transmission
dynamics. These include information about the infectivity during the incubation period;
the length of time and virus load during incubation and during the symptomatic period
of virus shedding; the incidence and infectiousness of asymptomatic cases, the risk
of vertical transmission from mother to fetus
35
, and other modes of transmission, such as from faeces, saliva and urine. There is
some evidence that virus can be isolated from saliva
36
and while the initial family cluster found no evidence of virus in stools or urine
8
, it has since been detected in faeces by PCR in other patients
30
,
37
,
38
and cultured in one patient, but there has been no evidence of virus in urine. The
number of mild or asymptomatic cases has not been determined and relatively few cases
have been recorded, but it is probable that current figures only see the tip of the
iceberg, and many cases remain undiagnosed
19
. They pose the greatest threat for increased virus spread
27
. Information is also needed on the stability of the virus in the environment to better
determine transmission risks, and especially the survival of the virus in aerosols
and on hard surfaces under different conditions of temperature and humidity.
Clinical features
It has become clear that asymptomatic infections and minimally symptomatic infections
occur with this virus. Exactly how frequently is not yet known as that requires serological
studies that have yet to be undertaken. The initial reports of the illness were heavily
biased to more severe and hospitalised cases in China, and as the number of confirmed
cases has increased within China and elsewhere, a clearer picture has emerged. The
commonest clinical features are fever plus a respiratory illness, and studies have
reported fever in 80–99% of cases, dry cough in 48–76% of cases, fatigue or myalgia
in 44–70% of cases, and dyspnoea in 30–55% of cases. Other relatively frequent manifestations
include anorexia and productive cough, and less frequently, headache, diarrhoea, nausea,
dizziness and vomiting
13
,
39
,
40
. Severe illness and death are more likely to occur in older individuals, and possibly
in those with pre-existing clinical illness such as diabetes, cardiovascular disease
and malignancies.
The case fatality rates have varied depending on the population affected. Initial
estimates that were based on severely ill patients were high, but more recent estimates
are around 2.3% on average, but significantly higher in the elderly and particularly
those aged 80 years and over
41
. As many milder or asymptomatic infections are likely to have been missed, the mortality
rate is expected to be lower than published figures as more information becomes available.
Disease in paediatric patients appears to be rare, and when it occurs, very mild,
but the role of children in transmission remains unknown.
More extensive and detailed studies are needed to understand the full spectrum of
illness caused by this virus, the pathogenesis of disease, especially the lung disease,
and the longer-term morbidity in survivors. The possibility of persistent and recurring
infections, especially in immunocompromised patients, is unknown; we still have very
limited data on the importance of pre-existing morbidities; more information is urgently
needed on the disease in pregnancy and the potential for infection of the fetus; and
we don’t understand the effect of past exposure to other coronaviruses on modifying
disease severity.
Diagnostic tests
Clinical diagnosis has largely been based on clinical and exposure history, and laboratory
and chest imaging findings. The laboratory findings will vary with the severity of
disease, but a low lymphocyte count is common and persisting low counts is associated
with poorer outcomes
13
,
39
,
40
. Testing for other respiratory pathogens should be undertaken to exclude viral and
bacterial co-infections.
Detection of the virus has been based on PCR, with various assays directed particularly
at the envelope (E), RdRp, spike protein (S) and nucleocapsid (N) genes. In-house
assays are in use in a number of Public Health Laboratory Network (PHLN) member laboratories,
with continual ongoing evaluation. In addition, there are several commercially available
assays with claimed capacity for detection of SARS-CoV-2 that are also being evaluated.
Virus can be found in the upper respiratory tract in nearly all patients beginning
at or just before the onset of clinical illness
29
. The preferred samples are combined nasopharyngeal and oropharyngeal swabs and if
they have a productive cough, also sputum. In patients with lower respiratory tract
infections, virus may be detectable in sputum or bronchoalveolar lavage samples even
if undetectable in the upper respiratory tract. Virus can be cultured relatively easily
in a number of cell lines, including Vero cells, but requires a PC3 containment laboratory.
Virus identification can be confirmed by sequencing if necessary, and a large number
of partial and whole genome sequences are available via GISAID and GenBank. PCR tests
have become increasingly available since about 25 January, but due to the rapid spread
in China and the huge number of cases access to timely and accurate testing has been
problematic, especially in the early stages, making it difficult to ascertain the
true extent of virus infections and illness
42
.
Detailed PHLN recommendations for testing and for laboratory biosafety requirements
within Australia are available in the Virology Appendix of the Coronavirus Disease
2019 (COVID-19): CDNA National Guidelines for Public Health Units
43
. However, tests are still being developed and evaluated, and we cannot yet confidently
identify the best targets for PCR. Continual re-evaluation is required to identify
any genetic drift that may affect test sensitivity. We also need to be able to transfer
the tests onto platforms that can be delivered outside major laboratories, in resource
poor settings, near to the patient, and quickly. The lack of serological assays hampers
our ability to understand the true epidemiology of this virus and its impact, and
to identify PCR-negative infections.
Therapeutics and vaccines
There are no proven or registered therapeutics or vaccines for COVID-19 infection
at this time. Treatment is largely supportive
44
, though a number of therapeutics are under investigation with some undergoing clinical
trials in China and elsewhere. Of particular interest currently are the HIV protease
inhibitor combination lopinavir/ritonavir and a new broad-spectrum antiviral agent
called remdesivir, which has shown promising activity against MERS-CoV in animal models.
Combinations of these with interferon-β and/or ribavirin are being considered, while
other groups are looking at other antivirals, convalescent plasma, and monoclonal
antibodies.
Work on vaccines is also well underway, although it is unlikely that a vaccine will
be available for at least 18 months. The Coalition for Epidemic Preparedness and Innovations
(CEPI) is currently funding four vaccine initiatives in collaboration with the WHO.
One of these is at The University of Queensland where Prof Paul Young, and Drs Keith
Chappell and Dan Watterson are using their novel and exciting ‘molecular clamp’ technology
to develop a vaccine. This work is being carried out in collaboration with CSIRO’s
vaccine manufacturing plant in Clayton, and also partly funded by CSL Ltd. This Australian
collaboration is hoping to have the vaccine ready for use before the end of 2021.
Current status
The international public health response to COVID-19 has largely been based on measures
that have proved successful for many other outbreaks over past decades – rapid identification,
management and isolation of cases; identification and follow up of contacts; quarantine
measures; social distancing; infection prevention and control in health care settings;
community containment; and transparent risk communication; as well as a 14-day quarantine
period on travellers from China or who have had links to ongoing transmission sites
or known cases, such as the cruise liner in Japan. Australia’s response has been similar,
and to date has been moderately successful in limiting the number of chains of transmission
in NSW, Queensland and Victoria, whereas most cases elsewhere have been in returning
travellers or their close contacts. Table 1 shows cumulative cases in Hubei, elsewhere
in China, and in other countries on a weekly basis between 21 January and 9 March,
and shows the rapid rise in cases in China, particularly in Hubei Province, followed
by a slowing down over the past 2 weeks, and a continuing rise in cases outside China
with more and more countries reporting cases. As of 9 March, 105 countries had reported
cases, but only three countries accounted for nearly 75% of the cases; South Korea
with 7382 cases, Italy with 7375 cases, and Iran with 6566, and cases have been reported
from all continents except Antarctica
45
. It has been suggested that up to half of COVID-19 cases exported from mainland China
have remained undetected worldwide, and that 40% of travellers, largely asymptomatic,
mild or pre-symptomatic travellers, were not detected at airports, potentially resulting
in multiple chains of as yet undetected human-to-human transmission outside mainland
China
46
,
47
. Although WHO finally called the COVID-19 a pandemic on 11 March, in many respects
it had already begun. This was presaged by the observation that more new cases were
reported from the rest of the world than from China for the first time on 28 February,
and in addition, secondary and tertiary chains of transmission have been reported
in increasing numbers of countries. The Australian Government has already recognised
this, and has instituted its emergency response plan and is now operating on the basis
that the pandemic is here.
Final comments
SARS-CoV-2 is the seventh coronavirus known to infect humans, and the third zoonotic
virus after SARS-CoV and MERS-CoV. Bats are the reservoir hosts of a number of additional
novel coronaviruses, particularly Chinese horseshoe bats, and a number of these novel
coronaviruses can efficiently use multiple orthologs of the SARS receptor, human ACE2,
and replicate efficiently in primary human airway cells and achieve in vitro titres
equivalent to epidemic strains of SARS-CoV
48
,
49
. This indicates that other potential cross-species events could occur in the future.
There is therefore a strong reason to ban unregulated wild animal sales in Chinese
wet markets, particularly exotic species, both from a public health perspective and
for ecological reasons. Such a ban would be difficult to instigate for cultural reasons,
but China’s top legislative committee on 24 February 2020, passed a proposal to ban
all trade and consumption of wild animals. If this is legislated as a permanent ban,
it might help reduce the risk of another novel virus emerging from wildlife in China
in the future.
Conflicts of interest
The authors declare no conflicts of interest.