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Letter from Dr. Paul BREY, Director

Dr. Paul BREY

The past year has been one of the most difficult in recorded history worldwide due to the Covid-19 pandemic. Covid-19 has caused so much death and destruction that we have not seen the likes of which since the Great Influenza pandemic of 1918 and before that the Black Death decimated nearly half the population of Europe in the 14th century.

In 2020, and early 2021, we thought that the Lao PDR would be spared from the scourge because the numbers of Covid-19 were so low. In fact, some neighboring countries suspected that the medical laboratory infrastructure in Laos was incapable of conducting Covid-19 diagnostics… This of course was totally untrue and unjustified as the National Laboratory for Laboratory and Epidemiology (NCLE) and Institut Pasteur du Laos (IPL) were operational for SARS-CoV-2 detection from human samples as early as January 2020. The reason Covid numbers were low is that the Lao Government and Ministry of Health put into place a series of very stringent control measures from early 2020 restricting travel, promoting mask-wearing and social distancing closing certain entertainment venues. In the summer of 2020, a consortium of Lao research partners led by scientists from IPL carried out a country-wide SARS-CoV-2 serological survey study to determine the extent and spread of Covid-19 throughout the country in high-risk populations like health care workers, guano collectors, wildlife sellers, as well as the general public. Our study, recently published in Lancet Regional Health Western Pacific (Lancet Reg Health West Pac. 2021 Aug;13:100197. doi: 10.1016/j.lanwpc.2021.100197. Epub 2021 Jul ) showed that Covid-19 had not circulated in the high-risk or general populations in 2020 and that the prevention measures put into place to mitigate the circulation of the early variants were successful in keeping the number of Covid-19 cases extremely low and limited to imported cases. When other countries around the world were going through severe transmission, Laos was living almost normally. Then around mid-April of 2021, during the Buddhist New Year festival, several illegal cross-border travelers brought the Delta variant of Covid-19 into Laos. Concomitantly the Delta variant surged through Thailand provoking a mass exodus of Lao migrant workers back into Laos making obligatory 14-day quarantine and Covid testing extremely difficult. Spillover of the Delta variant into the Lao population through community transmission, as was predicted by IPL, occurred given the intense infectivity of the Delta variant compared to the original Wuhan variant or even the Alpha variant that IPL also detected.

Concomitant to the Covid-19 serology study, IPL embarked on a study of the origins of SARS-CoV-2 in wild animals -mainly bats. For years IPL has been engaged in pathogen discovery in arthropods and most recently from bat ectoparasites, such as bat flies. In previous annual reports, we have stated that we have found a new Reovirus in Laotian bat flies, as well as an Orthobunyavirus – Wolkberg originally discovered in fruit bats in South Africa.

These bat fly studies allowed us to establish collaborations with the Department of Environmental Science at the Lao National University. Hence, when SARS-CoV-2 emerged in China in December 2020 and its closest Sarsbecovirus relative RaTG-13 was isolated from a Rhinolophus affinis bat in Yunnan province near the Lao border, we immediately started to search for funds to carry out an investigation to see if we could find SARS-CoV-2-like viruses and other alpha and beta coronaviruses in bats from Laos. With funding from the Institut Pasteur Paris Covid Task Force, we continued our collaboration with Prof Marc Eloit of the Pathogen Discovery Laboratory at IP Paris. With our colleagues from the Lao National University, several hundred bats were captured sampled (saliva and anal swab and blood sample) and released back into nature. Collections were made in four locations (2 locations in Fueng and Meth Districts of Vientiane province – 2 locations in Oudomsay province) Five Sarsbecoviruses close to SARS-CoV-2 were found in anal swabs, some of which were clearly close relatives to SARS-CoV-2 in certain portions of their genomes. An important finding was that the genomes of the Sarsbecoviruses result from mosaicism or recombinations of certain fragments of related Sarsbecoviruses. Our findings are summarized below as indicated in our manuscript submitted to the journal Nature.

“The animal reservoir of SARS-CoV-2 is unknown despite reports of various SARS-CoV-2-related viruses in Asian Rhinolophus bats 1,2,3,4, including the closest virus from R. affinis, RaTG13 5,6. Several studies have suggested the involvement of pangolin coronaviruses in SARS-CoV-2 emergence7–9. SARS-CoV-2 presents a mosaic genome, to which different progenitors contribute. The spike sequence determines the binding affinity and accessibility of its receptor-binding domain (RBD) to the cellular angiotensin-converting enzyme 2 (ACE2) receptor and is responsible for host range10–12. SARS-CoV-2 progenitor bat viruses genetically close to SARS-CoV-2 and able to enter human cells through a human ACE2 pathway have not yet been identified, though they would be key in understanding the origin of the epidemics. Here we show that such viruses indeed circulate in cave bats living in the limestone karstic terrain in North Laos, within the Indochinese peninsula. We found that the RBDs of these viruses differ from that of SARS-CoV-2 by only one or two residues, bind as efficiently to the hACE2 protein as the SARS-CoV-2 Wuhan strain isolated in early human cases, and mediate hACE2-dependent entry into human cells, which is inhibited by antibodies neutralizing SARSCoV- 2. None of these bat viruses harbors a furin cleavage site in the spike. Our findings, therefore, indicate that batborne SARS-CoV-2-like viruses potentially infectious for humans circulate in Rhinolophus spp. in the Indochinese peninsula.” Nature manuscript under review.

In addition to our research efforts on the origins of SARSCoV- 2 research in 2021, IPL has been highly implicated in the public health activities in and around Covid-19, as a second line laboratory for SARS-CoV-2 RT-PCR testing (and genomic sequencing of SARS-CoV-2 positive samples. IPL is the only laboratory in the Lao PDR with the capacity to conduct genomic sequencing of the SARS-CoV-2 viruses and hence is the only lab that can identify variants of public health interest and concern by detecting mutations in the spike protein gene.

As I write these lines there are over 50,000 confirmed cases of Covid-19 throughout the country with the epicenter of the epidemic in Vientiane Capital. Nearly one hundred deaths have been registered most of the fatalities had comorbidities such as old age, hypertension, and/or diabetes. Approximately 50% of the Lao population has been fully vaccinated with the hope to achieve 70% by the end of 2021. A booster vaccination is also to start among healthcare workers in January 2022. The Lao government has not yet indicated when the country will reopen as
Thailand and Vietnam are now opening.

It is interesting to note that Dr. Ponmek Dalaloy in 2004 had the foresight to establish Institut Pasteur du Laos as a high technology institute capable of training young Lao scientists to be able to detect and mitigate deadly emerging viruses in the Lao PDR. IPL’s research this year exemplifies that after 10 years of activity IPL has truly fulfilled its mandate!

 

Paul Brey