NEWS | FEATURESSCIENCE science.orgTHE KINDS OF THREATS Supaporn had been
tracking became catastrophically real at
the beginning of 2020. On 8 January, a
passenger arriving from Wuhan at Bang-
kok’s international airport registered hot
on thermal scanning equipment. An ear
check showed her temperature was 38.1°C.
Rome Buathong, a field epidemiologist for
the Thai Ministry of Public Health who had
set up the scanners 5 days earlier when
news arrived about the outbreak in Wuhan,
promptly sent the woman to the hospital.
All viral tests were negative, so Rome con-
tacted Supaporn, who had worked with him
years earlier to screen air passengers for
Ebola and Zika viruses.
On 9 January—the day before Chinese
researchers first publicly reported SARS-
CoV-2’s genome—Supaporn discovered the
genetic signature of a novel virus in that
Wuhan visitor, becoming the first scientist
outside China to do so. A database search
showed the new virus was closest to a corona-
virus in Chinese bats that Daszak and Shi
had reported in 2017. “Ten years ago, no one
thought bats were important—we thought
only about influenza,” Rome says. “But
Supaporn was very keen to do a lot with
bats. Who knew?”
The COVID-19 pandemic in early 2020
halted field research globally, but Supaporn,
with funding from the U.S. Department of
Defense’s Biological Threat Reduction Pro-
gram, managed that June to send a team
to a large cave in western Thailand that is
home to a few million bats. The endeavor
was part of a general pathogen surveillance
effort, but the group hoped to find a clue to
SARS-CoV-2’s origin by sampling Rhinolo-
phus bats, also known as horseshoe bats forthe shape of their noses. The genus, com-
prising more than 100 species, is the main
host for SARS-related coronaviruses.
Horseshoe bats live in small colonies
that are often hard to find, and the cave
didn’t yield any. But in a water pipe drain-
ing a reservoir that’s part of the Khao Ang
Rue Nai Wildlife Sanctuary, Supaporn’s
team trapped 100 Rhinolophus acumina-
tus. Rectal swabs from 13 tested positive
for coronaviruses, including one described
in Nature Communications on 9 Febru-
ary 2021. Dubbed RacCS203, the virus
was 91.5% identical in genetic sequence
with SARS-CoV-2. That similarity implied
a common ancestor from about 140 years
ago, according to an analysis led by evo-
lutionary biologists David Robertson and
Spyros Lytras of the MRC-University of
Glasgow Centre for Virus Research, pub-
lished online on 8 February in Genome
Biology and Evolution.
Other researchers found bat corona-
viruses related to SARS-CoV-2 in China,
Laos, Vietnam, Cambodia, and Japan. One
virus from a colony in limestone caves in
Laos was 96.8% similar in sequence to the
human virus—perhaps a decade removed.
Even it is too distant to offer anything
more than crumbs on the evolutionary
path that led to the pandemic virus. But
Robertson is convinced that Asia’s bats
harbor far closer relatives to SARS-CoV-2.
“There’s definitely something that’s not
been sampled,” he says.
On the trip this January, Supaporn re-
turned to the sanctuary in search of closer
matches. RacCS203, unlike the virus from
Laos, does not infect by binding to the hu-
man cellular receptor favored by SARS-CoV-2. But antibodies in the blood of bats
in the sanctuary powerfully neutralized the
pandemic virus, suggesting they may have
been infected with a coronavirus that uses
that receptor, too.
Some researchers think the bat virus
hunt will do little to clarify the pandemic’s
origin. A distant bat precursor to SARS-
CoV-2 might have spread long ago to an
intermediate host—perhaps a rat, civet cat,
raccoon dog, or pangolin, all known to host
bat viruses—and evolved there for years
before infecting humans. But Supaporn is
betting she’ll find revealing clues in bats.
“It would be good to fill in the gaps of the
origin story in Southeast Asia because in
Thailand alone there are 23 Rhinolophus
species,” she says.
Filling in the gaps is a painstakingly
slow, expensive, risky, and often hugely
unpleasant process. “You’re looking for
something rare, and you need a ton of sam-
ples to pick up the rare thing,” Mazet says.BY THE TIME SUPAPORN’S van passed the ele-
phant and joined the rest of the team at the
field site, it was after 4 p.m. With military
efficiency, the team—two dozen grad stu-
dents, ecologists, and veterinarians—set up
a lab on the ground floor of an abandoned
traditional Thai house on stilts. The first
order of business, ironically, was to protect
the bats from human viruses, including
SARS-CoV-2: Everyone had nasal swabs,
which came back negative.
Next, team members put on hairnets,
polyethylene coveralls, nitrile gloves, and
N95 masks to protect themselves. The tem-
perature was 32°C. Sweat soon soaked every
CREDITS: (GRAPHIC K. FRANKLIN/ bit of fabric under the zipped-up suits.
SCIENCE
; (DATA DAVID ROBERTSON AND SYPROS LYTRAS/MRC UNIVERSITY OF GLASGOW
CENTRE FOR VIRUS RESEARCH; S. LYTRASET AL., GENOME BIOLOGY AND EVOLUTION, 14, 2 (20220 1500
kmCHINA JAPANTHAILANDKhao Ang Rue Nai
Wildlife SanctuaryBangkokCAMBODIALAOSHubeiBeijingWuhan To k y oHunanYunnanGuangxiGuangdongZhejiang(^16)
7
(^41110)
5
3
2
12
9
8
600 500 400 300 200 100 0 years ago
Rc-o319
RaTG15
GX-P4L/P1E/P5L/P5E/P2V
MP789/Guangdong-1
RacCS203
RshSTT182/200
HN2021G
HN2021A/B
CoVZXC21
CoVZX45
RaTG13
YN2021
PrC31
RmYN02
RpYN06
BANAL-20-236
BANAL-20-247
BANAL-20-116
BANAL-20-103
BANAL-20-52
SARS-CoV-2
4
5
5
12
2
3
7
8
9
10
11
1
6
All in the family
Coronaviruses related to SARS-CoV-2
have turned up in Rhinolophus bats
roosting all across Asia. Differences
between viral sequences have enabled
researchers to build a family tree
and estimate that the closest relatives
shared a common ancestor with
the pandemic virus a decade
ago. Supaporn Wacharapluesadee’s
team found a virus in Thailand
(No. 9) that shared a relative
about 140 years ago and has
identified but not yet published
closer relatives.
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