A serological survey unravels the atypical case of Q fever in French Guiana
Some pathogens present asymptomatic forms that complicate the study of their transmission dynamics and their determinants. Researchers from the Pasteur Network based at the Institut Pasteur de la Guyane and the Institut Pasteur (Paris), in collaboration with the Cayenne Hospital, have studied the atypical incidence of Q fever in Guyana. Their work, published in The Lancet Regional Health – Americas, estimates a high risk of infection in the general population. They highlight the important role of livestock in transmission.
Q fever, a zoonosis with limited symptoms
Q fever is a zoonosis caused by Coxiella burnetii, a bacterium that infects a majority of mammals in most parts of the world. Ruminants, the main source of human infection, can excrete the bacteria in calving products, feces, vaginal secretions, and milk. Transmission is mainly by airborne route and is manifested by clinical signs in humans in only 40% of cases. If present, clinical signs are generally flu-like and non-specific, but may sometimes be associated with pneumonia, hepatitis and, more rarely, with more severe symptoms, especially in patients with comorbidities. 60% of reported cases worldwide have been identified during epidemics centered around farms or slaughterhouses infected with the bacterium.
French Guiana, a special case
The French Guiana population has the highest incidence of Q fever in the world. 24% of hospitalized cases of community-acquired pneumonia are attributed to this region. Most of the patients hospitalized came from metropolitan France and lived in the urbanized area of Cayenne and its suburbs. However, the classic risks of exposure (slaughterhouse or livestock in the vicinity) were not found among the diagnosed cases. As no wild reservoir was clearly identified, previous studies considered transmission by livestock to be unlikely.
The atypical nature of its transmission combined with a high proportion of asymptotic cases has made it difficult to understand the epidemiology and determinants associated with Q fever in French Guyana. In order to better understand its transmission dynamics and to orient public health intervention strategies, researchers from the Pasteur Network and infectious diseases specialists from the Cayenne Hospital Center collaborated to conduct a serological survey of 2,700 individuals representative of the different communities in French Guiana.
Domestic livestock as a vector of the disease
The authors modelized serological data classified by age in order to reconstruct the history of the circulation of the bacterium in the different regions of the territory. Their results show a constant circulation of C. burnetii throughout French Guiana with an estimated annual number of cases of 579. 9.6% of the population tested had already been infected and middle-aged men and individuals living near livestock. Analysis of the data identified an epidemic that occurred between 1996 and 2003 in the communes of Remire and Matoury. This epidemic, which infected 10% of the population, explains the high proportion of people carrying antibodies against C. burnetii in the urban area of Cayenne Island.
This collaborative work has made it possible to model for the first time the transmission dynamics of Q fever in French Guiana. The highlighting of the role of domestic livestock in a context of important transmission of the bacterium argues for the reinforcement of surveillance and risk reduction activities in French Guiana’s livestock farms and underlines the interest of a “One Health” approach combining a human, animal, and environmental component.
Serological surveys, essential tools
This type of large-scale serological survey has already been conducted in Bangladesh for dengue and for Chagas disease in Colombia. It allows the study of a wide range of factors contributing to disease control such as pathogen circulation patterns, immunity levels related to vaccination or previous infection or potential areas of emergence. This multi-factorial approach with a very positive cost/benefit ratio (cost of analysis versus amount of data generated/output) is a very valuable tool to promote to public health agencies and authorities.
It is proposed that this methodology could be reused by the members of the Pasteur Network in the framework of a phase 3 of the ECOMORE project involving Cambodia, Laos, Philippines, and Vietnam, in collaboration with the Institut Pasteur in Paris, for which funding is still being sought. Indeed, its use would improve the understanding of the circulation history of a multitude of pathogens (viruses, bacteria, and parasites), representing a public health issue for these countries, and of the epidemiology of their associated diseases in order to propose appropriate interventions to the authorities of these countries.
For more information:
Transmission dynamics of Q fever in French Guiana: A population-based cross-sectional study
The Lancet Regional Health – Americas, October 2022.
Sarah Bailly†, Nathanaël Hozé†, Sylvie Bisser, Aurélien Zhu-Soubise, Camille Fritzell, Sandrine Fernandes-Pellerin, Adija Mbouangoro, Dominique Rousset, Félix Djossou, Simon Cauchemez‡, Claude Flamand‡*.
†, ‡These authors contributed equally to this work.
*Corresponding author.
DOI : https://doi.org/10.1016/j.lana.2022.100385
During the Pasteur Network Annual Meeting from November 28 to 30, 2022 in Rome, Dr. Norosoa Razanajatovo, from the Institut Pasteur de Madagascar received the Pasteur Network Talent Award 2022[1] issued by the President of the Institut Pasteur, Stewart Cole.
Dr Norosoa Razanajatovo joined the National Influenza Centre (NIC) of the Virology Unit of the Institut Pasteur of Madagascar in 2013 as a research engineer. She received her doctorate with an option of applied biochemistry in medical sciences, which she obtained in 2015. Carried out under the supervision of Dr. Jean-Michel Héraud, her thesis work, which focused on the identification and molecular characterization of respiratory viruses circulating in Madagascar, has helped to implement a better prevention strategy against respiratory diseases. Norosoa Razanajatovo has notably played a role for the implementation of the program to develop national surveillance of influenza in collaboration with the Ministries of Malagasy Public Health and Livestock.
From 2016, she became technical manager and deputy chief of the National Center for Influenza. The same year, she was also appointed WHO technical advisor. Over the years, she has acquired solid experience in the field of surveillance of respiratory viruses through the management of various epidemics such as H1N1 influenza, or more recently, COVID-19. In 2022, she was promoted researcher. She coordinates laboratory surveillance of viral respiratory infections and associated research programs.
“A good surveillance system is important to master an epidemic, but an effective and up -to -date research strategy is the keystone to achieve this.”
She studies the viral causes of acute respiratory infections, the identification of a seasonal characteristics for common respiratory viruses, the development of predictive diagnostic tools and molecular biology of human and zoonotic viruses.
Her latest project focuses on the dynamics of the introduction and dissemination of respiratory viruses relevant for human and animal health for the country and worldwide. In parallel, Dr. Norosoa Razanajatovo is invested in the transmission of her knowledge by the supervision of different students, by holding training workshops for local and regional laboratories and by training the staff of regional institutions in the executive training program in field epidemiology. With regard to her commitment and her career, she received the Pasteur Network Talent Award 2022 at the Annual Meeting on November 28, 2022 in Rome.
For more information:
Article from the Institut Pasteur de Madagascar: https://www.pasteur.mg/dr-norosoa-harline-razanajatovo-laureate-du-prix-pasteur-network-talent-award-2022/
[1] Each year, the Pasteur Network Talent Award recognizes one or two Pasteur Network researchers who are the future leaders of the network.
From October 24th to October 28th, Pasteur Network’s scientists had the opportunity to promote their results pursued in the framework the ECOMORE 2, in the 20th International Congress for Tropical Medicine and Malaria (ICTMM) in Bangkok, Thailand. The event allowed to highlight several activities of the project by three Pasteur Network members: the Institut Pasteur du Cambodge, the Institut Pasteur du Laos and the National Institute of Health and Epidemiology in Vietnam. Vector management for dengue, dengue outbreak simulator and, seroprevalence and serovar distribution of leptospirosis are some examples of the topics discussed.
The 20th International Congress for Tropical Medicine and Malaria (ICTMM) was held from October 24 to October 28th in Bangkok, Thailand. This five-day congress gathered key players in the sector to unravel the latest and challenging news surrounding tropical medicine, infectious diseases, neglected diseases, malaria and zoonoses. During the opening ceremony, Associate Prof. Pratap Singhasivanon, Chairman of ICTMM, stressed that these group of diseases still affect the poorest and most vulnerable populations. As climate change-induced temperatures intensify, he pointed out the pressing needs to improve current preventive measures and to further invest in the fight against these diseases. Several Pasteur Network scientists involved in ECOMORE 2, which notably aims to evaluate the impact on climate change on local health population, has shared it results through plenary sessions, topic keynotes, symposia, oral and poster presentations.
The integrated vector management for dengue
On October 25th, Dr. Sebastien Boyer, Head of Medical Entomology Unit at the Institut Pasteur du Cambodge, member of the Pasteur Network, was invited to expose his work in the “vectors, vector control and vector-borne diseases” session. He presented the results of the integrated vector management for dengue vectors in schools with entomological and epidemiological approaches. While a decrease of the core dengue virus vector, Aedes aegypti, density was observed, and toilets were detected as the main breeding sites in schools, the integrated vector control did not decrease the dengue transmission in schools and in surrounding communities. This could be explained by the fact that households are usually the significant spot of transmission.
The design of the dengue outbreak simulator
The next day, Damien Philippon, representing the Institut Pasteur du Laos, had the opportunity, during the “epidemiology and transmission dynamics of dengue” session, to explain the methods for the design of the dengue outbreak simulator, a tool for predicting dengue incidence in Vientiane prefecture. Various data (GIS, epidemiological, mobility, weather, census and land cover) were aggregated into weekly data as input of the model. Although the model is complex as available datasets do not cover the same time frames and do not overlap, its precision allows the prediction of absence or presence of dengue. At present, it does not concern incidence. In near future, more tuning of the model could be performed to increase its precision.
The seroprevalence and serovar distribution of leptospirosis
Prof. Le Thi Phuong Mai, Head of Public Health at National Institute of Health and Epidemiology, one of the three Pasteur Network members in Vietnam, presented in the form of a poster, the results of the multi-center study on seroprevalence and serovar distribution of leptospirosis among healthy people in Vietnam. 600 persons in total were enrolled, from Thai Bing (North), Ha Tinh (Center) and Can Tho (South) in 2019 for testing. A relatively high rate of leptospira seropositivity was reported among this general population, with most seropositive people being farmers. Moreover, the four predominant serovars circulating were Hebdomadis, Pomona, Saxkoebing and Panama. It has been recommended to initiate health promotion program and trainings in using personal protective equipment, among farmers to reduce the risk of infection.
All in all, this congress, which occurs every four years, happened to be a perfect regional showcase to highlight the results of the Pasteur Network scientists dedicated to ECOMORE 2.
For more information:
The article published on ECOMORE website: https://ecomore.org/2022/11/14/ecomore-2-results-promoted-at-the-20th-ictmm-congress/
The article published on the Institut Pasteur du Cambodge website: https://www.pasteur-kh.org/2022/11/04/20th-international-congress-for-tropical-medicine-and-malaria-held-in-bangkok-from-24-to-28-october-2022/
From 28 to 30 November 2022 the Annual Meeting of the Pasteur Network co-organized with the Institut Pasteur Italia will take place at Sapienza University in Rome. This meeting will bring together all directors, scientific directors and researchers of more than 30 Pasteur Network members in the world, located in over 20 countries across 5 continents. The theme this year is “The Start of a New Chapter”, which reflects the recent development of the Pasteur Network aiming for a more inclusive and participative governance.
The inaugural day will take place on Monday 28 November starting at 11:30 in the Aula Magna with the participation of Prof. Antonella Polimeni, Rector of Sapienza University of Rome, Prof. Luigi Frati, President of the Istituto Pasteur Italia Cenci Bolognetti Foundation, the French Ambassador in Italy Prof. Christian Masset, Prof. Silvio Brusaferro, President of the Istituto Superiore di Sanità and Prof. Françoise Barré-Sinoussi, Nobel Prize in Medicine in 2008 and Honorary President of the Pasteur Network.
The new vision of the Pasteur Network will be presented by Dr. Rebecca F. Grais, the new Executive Director of the Pasteur Network with Prof. Amadou Sall, President of the Pasteur Network and Prof. Stewart Cole, President of the Pasteur Network Foundation.
The keynote speaker of the session “The new vision of the Pasteur Network” will be Prof. Rino Rappuoli, Scientific Director of the Siena Biotecnopolo Foundation who will deliver a lecture on “The miracle of COVID-19 vaccines and the trillion-dollar gap” to illustrate how new technologies and unprecedented public investment have transformed vaccine development and allowed fast delivery of safe and efficacious COVID-19 vaccines, mitigating the impact of the pandemic on health and the economy. A quantum change in public investment for vaccine development and widespread vaccine distribution are necessary to achieve global pandemic preparedness.
The day will end with a ceremony unveiling the winner of the Pasteur Network Talent Awards to support the career development of young scientists to become future leaders within the Pasteur Network.
An exhibition “From Louis to Pasteur: 1822-1895” will run in parallel to celebrate 200th anniversary of the birth of Louis Pasteur.
On Tuesday 29th and Wednesday 30th, working sessions organized for members of the Pasteur Network will deal with its main strategic priorities such as epidemic intelligence and preparedness, and research and development to support regional manufacturing of diagnostics, vaccines, and therapeutics. The Pasteur Network also supports thecreation of diverse collaborative multi-disciplinary communities of knowledge which will be discussed during a session called “Working Together” that illustrates the leitmotiv of the entire event.
For more information:
About Istituto Pasteur Italia
Istituto Pasteur Italia, part of the Pasteur Network, is committed to promotion of biomedical research, scientific education and dissemination. The research activity is mainly focused on understanding the mechanisms underlying the biological processes with the goal of expanding our knowledge on the molecular basis of many infectious and non-communicable diseases.
istitutopasteuritalia.it
About the Pasteur Network
The Pasteur Network is a vast human and scientific community with more than 30 members in over 20 countries who together contribute to the improvement of global health. Located in the heart of endemic areas, the Network has privileged access to a large number of pathogens that it monitors and studies on all five continents. This exceptional diversity makes the Pasteur Network a global actor in public health, science, innovation, and education, especially in the fight against infectious diseases.
pasteur-network.org
The Institut Pasteur International Network is evolving and becoming the Pasteur Network (2021)
Following the recent outbreak of monkeypox, researchers from the Pasteur Network and ANRS | Emerging Infectious Diseases have published a complete portrait of the disease in the New England Journal of Medicine. This is an opportunity to review the signs of the disease, its origin, and also the projects undertaken by the Pasteur Network, such as AFRIPOX, supported by the Institut Pasteur and in collaboration with the Institut Pasteur de Bangui.
All information on this publication can be found in the dedicated article on the Institut Pasteur website.
For more information:
Article from the Institut Pasteur: Monkeypox: a detailed profile of the disease
Review article: Monkeypox
New England Journal of Medicine, 26 octobre 2022.
Antoine Gessain, M.D., Emmanuel Nakoune, Ph.D., and Yazdan Yazdanpanah, M.D.
DOI: 10.1056/NEJMra2208860
During an epidemic, it can happen that no diagnostic test is perfectly adapted to the pathogen. In order to contain the epidemic as quickly as possible, screening is done using several tests. The interpretation of the results of the different tests becomes more complex, which can make individual diagnosis difficult and lead to an underestimation of the disease’s prevalence. Using the plague outbreak that affected Madagascar in 2017 as a case study, researchers from the Institut Pasteur and the Institut Pasteur de Madagascar propose an analytical framework to characterize the performance of different tests and estimate the true prevalence of the outbreak. Published in the journal Plos Biology, these results will help improve the quality of diagnosis during future epidemics.
Between August and November 2017, 2,414 cases clinically suspected of carrying Yersinia pestis, the plague bacillus, were reported, with a large proportion of pulmonary plague. The samples were analyzed using three types of diagnostic tests: bacterial culture, rapid plague test, and molecular biology or qPCR. Significant discrepancies were observed between the different tests, making interpretation of the results complex. The greatest uncertainty related to the extent of the pneumonic plague outbreak, with positive cases ranging from 1% to 18%. The analytical framework used in this study estimated that 7-15% of suspected cases were carriers of Yersinia pestis for this outbreak.
Estimating the performance of a diagnostic test
Two parameters, specificity and sensitivity, determine the performance of a test. Specificity is the probability of being found negative when uninfected while sensitivity is the probability of being found positive when infected. When there is a reference test with perfect sensitivity and specificity, it is easy to estimate the sensitivity and specificity of other tests by comparing them to the reference test. In the absence of a reference test, as was the case for this plague epidemic, the authors had to estimate the performance of each test and then the prevalence of the epidemic. To do this, they used the latent class method, which is based on the comparison of the results of different imperfect tests. This analysis revealed that molecular biology had the best performance; and that the rapid detection test had limited specificity during the 2017 plague outbreak. Its performance was better the following year, 2018, suggesting that the context of response to a large epidemic can impact diagnostic quality.
Combining results to reconstruct an epidemic
Once the performance of the different tests was known, the researchers determined how to improve case classification algorithms to minimize the risk of false positives and false negatives. They were also able to reconstruct, in a more refined way, the epidemiological trends of the epidemic in space and time. Better classification of cases is particularly important for the allocation of scarce resources, for example by accurately targeting contact tracing efforts where incidence is highest. This avoids deploying resources to false positives and maximizes the impact of mobile testing facilities.
While the development and availability of high quality diagnostics remains a priority, this analytical framework could be a valuable tool to reduce uncertainty for other infectious diseases that lack reference diagnostics. For example, it is already used by the Institut Pasteur de Madagascar to diagnose tuberculosis.
For more information:
Evaluating and optimizing the use of diagnostics during epidemics: Application to the 2017 plague outbreak in Madagascar
Plos Biology, August 15th, 2022.
Quirine ten Bosch†*, Voahangy Andrianaivoarimanana†, Beza Ramasindrazana†, Guillain Mikaty, Rado JL Rakotonanahary, Birgit Nikolay, Soloandry Rahajandraibe, Maxence Feher, Quentin Grassin, Juliette Paireau, Soanandrasana Rahelinirina, Rindra Randremanana, Feno Rakotoarimanana, Marie Melocco,Voahangy Rasolofo, Javier Pizarro-Cerda, Anne-Sophie Le Guern, Eric Bertherat, Maherisoa Ratsitorahina, André Spiegel, Laurence Baril†, Minoarisoa Rajerison†, Simon Cauchemez†
† These authors contributed equally to this work.
* Corresponding author.
https://doi.org/10.1371/journal.pbio.3001736
A study conducted as part of the Afriobiota project involving several members of the Pasteur Network, in collaboration with the University of Lausanne, unravels the link between the gut ecosystem and stunting that affects undernourished children. The results of this research that included nearly 1,000 children aged 2 to 5 years between 2016 and 2018 are published in the journal PNAS.
In children, undernutrition – the consumption and/or assimilation of insufficient food to cover the body’s needs – manifests itself mainly through stunted growth. According to the Food and Agriculture Organization of the United Nations, 22% of children under 5 years of age worldwide will be affected by stunting (estimate for the year 2020).
This study focuses on the role of gut microbial communities (microbiota) in undernutrition. This research was coordinated by Prof. Philippe Sansonetti and conducted within the Pasteur Network. It was conducted over a period of six years by the Institut Pasteur in collaboration with the Institut Pasteur de Madagascar and the Institut Pasteur de Bangui as part of the Afriobiota project supported by the Total Foundation.
The work, carried out in Madagascar and the Central African Republic on 1,000 children aged 2 to 5 years, showed that more than 80% of stunted children have an abnormal bacterial overgrowth in the small intestine (SIBO). More specifically, these are bacteria initially present in the mouth that proliferate in the small intestine. Using experimental models (cell cultures and mice), researchers have shown that this phenomenon slows down the assimilation of lipids. This malabsorption of fats could partly explain the growth retardation suffered by children.
For more information:
Stunted children display ectopic small intestinal colonization by oral bacteria, which cause lipid malabsorption in experimental models
PNAS, October 05th, 2022.
Pascale Vonaesch*, João R. Araújo, Jean-Chrysostome Gody, Jean-Robert Mbecko, Hugues Sanke, Lova Andrianonimiadana, Tanteliniaina Naharimanananirina, Synthia Nazita Ningatoloum, Sonia Sandrine Vondo, Privat Bolmbaye Gondje, Andre Rodriguez-Pozo, Maheninasy Rakotondrainipiana, Kaleb Jephté Estimé Kandou, Alison Nestoret, Nathalie Kapel, Serge Ghislain Djorie, B. Brett Finlay, Laura Wegener Parfrey, Jean-Marc Collard, Rindra Vatosoa Randremanana, Philippe J. Sansonetti* and The Afribiota Investigators
* Corresponding authors.
https://doi.org/10.1073/pnas.2209589119
Flash Research of the University of Lausanne
Monkeypox virus (MPXV) is a neglected tropical pathogen whose recent emergence has accelerated its study. In this context, Pasteur Network researchers have developed rapid MPXV diagnostic tests that can be viewed by the naked eye in less than 30 minutes, and are as consistent as the current PCR-based nucleic acid test used for MPXV diagnostics. This new diagnostic tool will contribute to the control and prevention of MPXV epidemics.
In May 2022, outbreaks of monkeypox virus (MPXV) were reported simultaneously in Europe, North America and South America, outside the virus-endemic regions of Africa. Pasteur Network researchers collaborated to develop and validate tests for the rapid detection of MPXV. These newly designed tests can produce reliable fluorescence or lateral flow results on a strip in 20 to 30 minutes. Led by the teams of Emmanuel Nakouné (Institut Pasteur de Bangui) and Nicolas Berthet and Gary Wong (Institut Pasteur de Shanghai), the study presenting the results of these rapid diagnostic tests was published in the journal Viruses.
The tests are based on isothermal amplification of a targeted region of the virus genome, and are based on recombinase with or without CRISPR/Cas12. The tests gave consistent results with the reference molecular test, PCR in real time, for the 19 clinical samples used to validate the assay. In addition, the tests were specific and did not cross-react with other pox viruses, such as vaccinia.
MPXV, a neglected tropical pathogen, is closely related to smallpox, a disease that has been eradicated in humans since the 1980s. Although MPXV epidemics are regularly reported in Africa among the poorest communities, it remains understudied, even after the first MPXV epidemic was reported outside the endemic areain the USA during 2003. Rapid, sensitive and specific detection of MPXV is essential to inform health authorities of suspected cases as soon as possible, in order to monitor epidemic developments. These results therefore provide a point-of-care platform for the early diagnosis of potential MPXV cases, and will contribute to the prevention and control of current and future MPXV epidemics.
For more information:
Article from the Institut Pasteur de Bangui (in French)
Development and Characterization of Recombinase-Based Iso-thermal Amplification Assays (RPA/RAA) for the Rapid Detection of Monkeypox virus
Viruses, September 2022.
Lingjing Mao, Jiaxu Ying, Benjamin Selekon, Ella Gonofio, Xiaoxia Wang, Emmanuel Nakoune, Gary Wong*, Nicolas Berthet*
* Corresponding authors.
https://doi.org/10.3390/v14102112.
The first conference of French-speaking science journalists was held in Dakar from October 10th to 16th, 2022. It was attended by nearly 60 journalists from more than 20 countries[1]. The Pasteur Network partnered with the event with the aim of sharing the scientific knowledge of its members, all of which are experts in global health. The idea was to bring scientists and journalists together to ensure that only factually verified scientific information reaches the public. Several scientists from the Institut Pasteur de Dakar spoke at the event, demonstrating this commitment to delivering quality scientific information.
The conference was organized by the French-speaking Africa Science Journalists’ Network (RJSAF) with the French Association of Science Journalists (AJSPI), the Quebec Association of Science Communication (ACS) and the Swiss Association of Science Journalism (SASJ). It was held at the Center for Studies in Information Science and Technology (CESTI) at Cheikh Anta Diop University (UCAD).
The main theme of the conference was journalism and the climate crisis. Several of the topics proposed by the organizers were related to health, an area of expertise for Pasteur Network members like the Institut Pasteur de Dakar.
Neglected and emerging diseases in Africa
Dr. Xavier Berthet, the Institut Pasteur de Dakar’s, Scientific Director, spoke alongside Dr. Digas Ngolo Tete from DNDi during an expert panel discussion on “Neglected and emerging diseases in Africa” on Monday October 10th, the opening day of the conference. Their presentation was an opportunity to take a closer look at these diseases, caused mostly by parasites (sleeping sickness and schistosomiasis) or bacteria (trachoma and Buruli ulcer), that can be very debilitating for those affected. Dr. Xavier Berthet explained how problems affecting populations can be tackled via the initiatives implemented at the Institut Pasteur de Dakar, like the manufacture of biological products at its future vaccine facility, currently under construction in Diamniadio, and infectious disease surveillance.
Zoonoses: situation and challenges in the age of climate change
A panel of virology experts from the Institut Pasteur de Dakar addressed the question “Zoonoses: situation and challenges in the age of climate change” on Wednesday October 12th. Dr. Jean-Michel Héraud pointed out that 75% of the diseases that have emerged recently are of zoonotic origin. Out of the total estimated number of viruses on the planet, known as the “virome,” few are as yet known to infect humans. Factors contributing to emergence, like demographics, uncontrolled urbanization, human-induced environmental changes and climate change, were explained to the journalists in attendance. Dr. Oumar Faye, winner of the 2019 Pasteur Network Talent Award, reiterated the role of WHO Collaborating Centers in identifying viruses. He shared his experiences of the Ebola outbreak and more recently the Zika outbreak in Brazil, which helped him to anticipate and prepare for future outbreaks, for example with a mobile laboratory facilitating access to samples and speeding up virus identification. The scientists emphasized the value of One Health approaches, methods to identify viral reservoirs and the use of genomic surveillance to rapidly detect new threats to human and animal health and better anticipate their emergence.
The conference continued for a further four days, covering other scientific fields such as agricultural models in a +1.5°C climate scenario, with events including workshops for journalists. A visit to a virology laboratory at the Institut Pasteur de Dakar and to the Diamniadio manufacturing site brought the week to a close.
Full program: https://www.cmjsf.org/programme/
[1] Countries represented: Benin, Burkina Faso, Burundi, Cameroon, Canada, Central African Republic, Côte d’Ivoire, Democratic Republic of the Congo, Egypt, France, Guinea, Haiti, Madagascar, Mali, Morocco, Niger, Rwanda, Senegal, Switzerland, Togo, Tunisia
Genomic sequencing enables live tracking of the spread of a virus. A Science paper, released on September 15th, 2022, analyzing more than 100,000 genomes, recalls the benefits of local sequencing while studying the spread dynamics of SARS-CoV-2 and its variants of interest on the African continent. More than 300 authors combined their research including 10 members of the Pasteur Network who shared locally sampled SARS-CoV-2 sequences. The results show that most of the introductions of the virus in Africa were from abroad. They also highlight the critical need to invest in diagnostics and genomic surveillance in Africa to best prepare for and respond to future emergencies and epidemics.
This study reveals a mapping of the transmission dynamics of COVID-19 on the African continent. Increased local sequencing capacity has resulted in improved turnaround times and more regular routine surveillance. Pasteur Network members have shared, via the GISAID initiative, the SARS-CoV-2 sequences in the framework of the REPAIR and AFROSCREEN projects.
The spread of the different COVID-19 variants in the continent was heterogeneous, especially for the Alpha, Beta, Delta and Omicron variants which have followed and still follow distinct patterns of dispersion. The Alpha variant that occurred on the continent emanated mainly from Europe before spreading to 43 countries. Most of the Delta variant introductions (about 72%) came from India, while introductions between African countries of the same variant represented only 7% of cases. As for the Omicron variant, its emergence came from Europe, as well as North America and Asia.
The 200 signatory institutions[1] of this study constitute the largest consortium of African scientists and public health institutions united to respond to COVID-19 using local data. The establishment of the Africa Pathogen Genomics initiatives by the Africa CDC and the continental network by the Africa CDC and WHO AFRO are testament to the intent to expand access to sequencing across the continent. Following the example of this study, sustained monitoring remains essential to maintain quality surveillance of both the circulation of COVID-19 and other emerging or re-emerging infectious diseases that may affect Africa.
For more information:
The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance
Science, September 15th, 2022.
Houriiyah Tegally†, Tulio de Oliveira*, Eduan Wilkinson†* and al.
† These authors contributed equally to this work.
* Corresponding author.
DOI: 10.1126/science.abq5358
Press release: https://africacdc.org/news-item/a-continent-wide-collaboration-on-genomics-surveillance-show-the-power-of-african-science-and-how-the-majority-of-covid-19-variants-were-introduced-into-africa/
[1] This study was conducted by the Centre for Epidemic Response and Innovation (CERI) at Stellenbosch University, and the KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP) at the University of KwaZulu-Natal, in coordination with Africa CDC, WHO AFRO, and more than 200 partner institutions, including 10 Pasteur Network members: the CERMES Niger, the Institut Pasteur, the Institut Pasteur d’Algérie, the Institut Pasteur de Bangui, the Institut Pasteur de Côte d’Ivoire, the Institut Pasteur de Dakar, the Institut Pasteur de Guinée, the Institut Pasteur de Madagascar, the Institut Pasteur de Tunis, the Pasteur Center in Cameroon.