Newsdesk
The origin of SARS-CoV-2
The fact that severe acute respiratory syndrome coronavirus 2 derived from bat coronaviruses
highlights inherent issues of the way we interact with the environment. Talha Burki reports.
Researchers examining coronaviruses
and bats are used to working with
Flickr - Doug Beckers
large numbers. A 2017 study of
12 333 bats from Latin America,
Africa, and Asia found that
almost 9% carried at least one of
91 distinct coronaviruses. The authors
estimated that there are at least
3200 coronaviruses that infect bats.
Moreover, there are over 1400 species
of bat. Figuring out which ones are
susceptible to which coronaviruses
is no small task. Bats are incredibly
varied and successful creatures. In
evolutionary terms, fruit-eating bats
diverged from insect-eating bats
some 50 million years ago.
The picture becomes even more
complicated when we start to
consider which bat viruses are likely
to pose a threat to human beings.
“Going after bats will only give you
partial information—the viruses you
are looking at may or may not get
the additional mutations they need
to be transmissible among humans”,
explains Stanley Perlman, professor
of microbiology and immunology
at the University of Iowa, IA, USA.
“There has almost always been an
intermediary involved, and without
knowing what that is and what
changes the virus would have to
undergo, it is very hard to make any
kind of predictions.”
The story of severe acute respiratory
syndrome corona­virus 2 (SARS-CoV-2)
is a case in point. A paper published
in July, 2020, traced the origins of
SARS-CoV-2. The researchers concluded
that it came from a virus with relatively
generalist properties circulating in
horseshoe bats. “Everything points
to a bat sarbecovirus reservoir;
we are very confident about this”,
said David Robertson, head of
bioinformatics at the Medical Research
Council–University of Glasgow Centre
1018 www.thelancet.com/infection Vol 20 August 2020
for Virus Research, Scotland, UK, and co-
author of the paper. The evolutionary
analysis suggested that the lineage
from which SARS-CoV-2 emerged
has been present in bats for several
decades.
“The generalist property of the virus
means an intermediate host is not
required for any evolutionary change”,
said Robertson. “As the virus has
been around for decades it may have
emerged in another host and this
could be the missing intermediate
species but we are inferring that this
would only facilitate transmission.”
The fact that SARS-CoV-2 was
first detected in Wuhan, China, far
from where the horseshoe bat is
found, hints at the presence of an
intermediary.
Some have posited that the
pangolin could be this missing link.
Pangolins have reportedly fallen sick
as a result of coronavirus infection,
which would mean they are not a
natural reservoir. But that leaves
the possibility that the pangolin is
facilitating transmission to humans.
SARS-CoV-2 can jump to other
animals such ferrets and cats. “The
virus would not need to evolve in the
pangolin, it would just need to be
brought into contact with humans”,
explains Robertson. And it is still too
soon to rule out direct bat–human
transmission.
Still, there is one theory that can
be dismissed. From the earliest days
of the pandemic, there has been
speculation that the new virus had
escaped, or even been deliberately
released, from the Wuhan Institute
of Virology. At a White House
press conference on May 1, 2020,
US President Donald Trump declined
to assert that SARS-CoV-2 had
occurred naturally. When asked
what gave him a “high degree
of confidence that this [virus]
originated from the Wuhan Institute
of Virology”, Trump replied “I can’t
tell you that. I’m not allowed to tell
you that.”
“If the virus had been human-
made, that would show in its
genome”, counters Robertson.
“Besides, if you were going to create
a coronavirus that can be transmitted
by humans, you would almost
certainly start with the first SARS
virus. SARS-CoV-2 is like nothing we
have seen before. It really is highly
unlikely that someone created it; it
is not put together from pieces we
know about.” SARS-CoV-2 is closely
related to other beta coronaviruses
such as RaTG13, a bat virus that the
Wuhan Institute of Virology has been
working on. But it only shares 96% of
its genome sequence with RaTG13,
which makes them roughly as similar
as human beings and chimpanzees,
and points to a common ancestor
rather than one springing from the
other.
The plethora of bat coronaviruses,
coupled with the uncertainty about
the role of an intermediary animal,
makes it tricky to know how to go
about preventing a future spillover.
Live animal markets are an obvious
risk for the emergence and spread
of zoonotic diseases, but they are
part of the culture of south east Asia.
“Certainly having a society which
did not have such an interface with
animals would be helpful, but I am
not at all convinced that we should be
telling chunks of the world that they
should not be buying live animals”,
said Perlman.
The argument against insisting
that indigenous peoples discontinue
consuming bush meat is also
strong. “There are tens of millions
of tribal people around the world
 Newsdesk

who do not farm; they get their
animal protein through hunting”,
points out James Wood, head of the
Department of Veterinary Medicine at
the University of Cambridge, UK. “We
have to make sure they can continue
living the way they always have.
Stopping them from eating bush
meat would be downright dangerous
and unlikely to succeed”. Eliminating
markets for live, wild exotic animals is
a different matter entirely. That would
at least minimise intense contact
between different species. Perlman
believes the Chinese government will
eventually prove amenable to such a
measure.
There is evidence that preserving
natural habitats reduces the risk of
diseases spilling over from wildlife.
In early August, a paper published in
Nature found that ecosystems that
were heavily used by human beings
contained a greater abundance and
wider variety of wildlife that carried
pathogens and parasites capable
of infecting people. “We need to
look at the parts of the world where
spillover is common and think
about the effect that environmental
degradation may be having”, notes
Wood. “It seems that wildlife species
that are under environmental stress,
often due to land-use change, are
more likely to excrete large doses of
virus; that raises the risk of both an
epidemic in the host population and
of spillover.”
“The major thing is to change our
behaviour”, adds David Morens,
senior advisor to the director at the
US National Institute of Allergy and
Infectious Diseases. “That means
stopping deforestation, perturbing
the environment, bat cave tourism,
and intensive farming.” Prompt
detection of new viruses is also
crucial. But the places where new
zoonotic diseases tend to emerge
do not typically have strong public
health surveillance systems. “We have
to invest in infrastructure that would
allow outbreaks to be detected
far earlier than they currently are”,
Wood says.
None of these measures can be
meaningfully enacted without
cross-country collaboration.
Morens advocates strengthening
international bodies such as WHO
and the International Red Cross, as
well as incorporating applied research
into the international agenda. “There
is this entire universe of micro-
organisms and viruses out there and
we probably know 1–2% of it; we need
to find out where these pathogens are
and catalogue them and study them”,
he explained. “We need scientists
from all over the world to work out
what the priorities are and how we
can fund them.” The sooner all this
can happen, the better. If there is one
lesson from COVID-19, it is that a
pandemic virus is just a few mutations
away.
Talha Burki

Infectious disease surveillance update

Chikungunya in Cambodia
As of Aug 6, 2020, the Ministry of
Health has reported 2047 suspected
cases of chikungunya across
15 provinces in Cambodia. More
than 80% of the cases have been
reported from Banteay Meanchey,
Kampong Cham, Siem Reap, and
Takeo provinces. The Ministry of
Ontario (n=3), Quebec (n=1) and
Prince Edward Island (n=1). The
reported cases had symptom onset
between mid-June and late July. All
cases who became ill reported either
having consumed red onions at home,
or food items ordered in a restaurant
or in residential care settings. Onions
that were imported from the USA
from Londrina (n=51 974), Foz do
Iguaçu (n=25 638) and Maringá
(n=16 955). Overall, Brazil has recorded
1 243 188 cases, including 437 deaths.
Ebola virus disease in DR Congo
As of Aug 7, 77 confirmed cases
of Ebola virus disease, including
33 deaths, have been reported
For more on chikungunya
in Cambodia see http://
outbreaknewstoday.com/
cambodia-chikungunya-
outbreak-tops-2000-2000
For more on salmonellosis in
Canada see https://www.canada.
ca/en/public-health/services/
public-health-notices/2020/
outbreak-salmonella-infections-
under-investigation.html

Health began awareness campaigns
that focus on seeking treatment if
symptoms are present (eg. fever and
severe joint pain), as well as the higher
risk of mortality associated with
having co-infections.
Salmonellosis in Canada
As of Aug 7, 239 cases have been
linked to a Salmonella enterica serovar
Newport outbreak in Canada; of
those, 29 have been hospitalised.
Cases have been reported in Alberta
(n=149), British Columbia (n=67),
Manitoba (n=13), Saskatchewan (n=5),
have been implicated in an ongoing
outbreak of the same salmonella
strain. There is no evidence found that
onions grown in Canada are linked to
the outbreak.
Dengue in Brazil
Health officials in the Paraná state in
Brazil have recorded 217 891 confirmed
dengue cases between July, 2019, and
July 20, 2020, including 157 deaths.
243 municipalities are in an epidemic
state because of the disease, while
30 cities are on alert. The highest
numbers of cases have been reported
in the Equateur province outbreak, For more on dengue in Brazil
see http://outbreaknewstoday.
the 11th outbreak in DR Congo. com/brazil-parana-state-
The outbreak was first detected records-more-than-200000-
in June, 2020, in the area where a dengue-cases-in-past-
year-62960/
previous outbreak was reported in
For more on Ebola in DRC see
2018, with 33 deaths reported. In https://promedmail.org/
response, 18 800 people have been promed-post/?id=7657868
vaccinated. The response is challenging
owing to a lack of resources as well
as the fact that confirmed cases in
the community were not isolated,
making it difficult to break chains of
transmission.
Ruth Zwizwai

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