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19 Feb 2024
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Population genetics of Glossina palpalis gambiensis in the sleeping sickness focus of Boffa (Guinea) before and after eight years of vector control: no effect of control despite a significant decrease of human exposure to the disease

Reaching the last miles for transmission interruption of sleeping sickness in Guinea: follow-up of achievements and policy making using microsatellites-based population genetics

Recommended by ORCID_LOGO based on reviews by Fabien HALKETT and 2 anonymous reviewers

Thanks to the coordinated and sustained efforts of national control programs, the World Health Organization (WHO), bilateral cooperation and nongovernmental organizations, the incidence of Human African Trypanosomiasis (HAT), better known as sleeping sickness, has drastically decreased during the last two decades (WHO, 2023a). Indeed, between 1999 and 2022, the reported number of new cases of the chronic form of sleeping sickness (Trypanosoma brucei gambiense) fell by 97% (from 27 862 to 799), and the number of newly reported cases of the acute form of HAT (Trypanosoma brucei rhodesiense) fell by 94% (from 619 to 38) (WHO, 2023b). These encouraging trends led the WHO to target this debilitating and highly fatal (if untreated) vector-borne parasitic disease for elimination as a public health problem by 2020, and for interruption of transmission (zero case) by 2030 (WHO, 2021, WHO, 2023a). However, the disease is persisting in many foci, and even some cases of resurgence have been documented after unfortunate events such as war or pandemics (Moore et al., 1999; Sah et al., 2023. Simarro et al). Although effective control measures, diagnosis and treatment are complex and require specific skills (WHO, 2023), especially in a context which animal reservoirs, including hidden reservoirs, can contribute to the maintenance/persistence of infection (Welburn and Maudlin, 2012; Camara et al., 2021). Vector control therefore appears as a viable alternative to accelerate sleeping sickness transmission interruption, and WHO has identified some critical actions for HAT elimination, including the coordination of vector control and animal trypanosomiasis management among countries, stakeholders and other sectors (e.g. tourism and wildlife) through multisectoral national bodies to maximize synergies (WHO, 2021).

The paper by Kagbadouno and Collaborators (2024) uses microsatellite markers genotyping and population genetics tools to investigate the impact of 11 years of tiny target-based vector control on the population biology of Glossina palpalis gambiensis in Boffa, one of the three active sleeping sickness foci in Guinea (Kagbadouno et al., 2012). Although vector control significantly reduced the apparent densities of tsetse flies (and therefore the human exposure to the vector) as well as the prevalence and incidence of the disease in the Boffa HAT focus (Courtin et al., 2015), no genetic signature of vector control was observed as no difference in population size, before and after the onset of the control policy, was found. The authors then provided national programs and implementing partners with indications on the actions to be taken to (i) maintain the achievements of vector control (thus avoiding rebound/resurgence as was experienced in the past (Franco et al., 2014), and (ii) accelerate the momentum towards elimination by for example combining these vector control efforts with medical surveys for case detection and treatment, in line with WHO recommendations (WHO, 2021). 


Camara M, Soumah AM, Ilboudo H, Travaillé C, Clucas C, Cooper A, Kuispond Swar NR, Camara O, Sadissou I, Calvo Alvarez E, Crouzols A, Bart JM, Jamonneau V, Camara M, MacLeod A, Bucheton B, Rotureau B. Extravascular Dermal Trypanosomes in Suspected and Confirmed Cases of gambiense Human African Trypanosomiasis. Clin Infect Dis. 2021 Jul 1;73(1):12-20.

Courtin F, Camara M, Rayaisse JB, Kagbadouno M, Dama E, Camara O, Traore IS, Rouamba J, Peylhard M, Somda MB, Leno M, Lehane MJ, Torr SJ, Solano P, Jamonneau V, Bucheton B (2015) Reducing human-tsetse contact significantly enhances the efficacy of sleeping sickness active screening campaigns: a promising result in the context of elimination. PLoS Neglected Tropical Diseases, 9.

Franco JR, Simarro PP, Diarra A, Jannin JG. (2014) Epidemiology of human African trypanosomiasis. Clin Epidemiol. 6:257-75.

Kagbadouno, M. S., Séré, M., Ségard, A., Camara, A. D., Camara, M., Bucheton, B., ... & Ravel, S. (2023). Population genetics of Glossina palpalis gambiensis in the sleeping sickness focus of Boffa (Guinea) before and after eight years of vector control: no effect of control despite a significant decrease of human exposure to the disease. bioRxiv, ver. 2 peer-reviewed and recommended by Peer Community in Infections.

Kagbadouno MS, Camara M, Rouamba J, Rayaisse JB, Traoré IS, Camara O, Onikoyamou MF, Courtin F, Ravel S, De Meeûs T, Bucheton B, Jamonneau V, Solano P (2012) Epidemiology of sleeping sickness in boffa (Guinea): where are the trypanosomes? PLoS Neglected Tropical Diseases, 6, e1949. 

Moore A, Richer M, Enrile M, Losio E, Roberts J, Levy D. Resurgence of sleeping sickness in Tambura County, Sudan. Am J Trop Med Hyg. 1999 Aug;61(2):315-8.

Sah R, Mohanty A, Rohilla R, Padhi BK. A resurgence of Sleeping sickness amidst the COVID-19 pandemic: Correspondence. Int J Surg Open. 2023 Apr;53:100604.

Welburn SC, Maudlin I. Priorities for the elimination of sleeping sickness. Adv Parasitol. 2012;79:299-337.

World Health Organization, 2021. Ending the neglect to attain the Sustainable Development Goals: a road map for neglected tropical diseases 2021–2030. World Health Organization, Geneva, Switzerland. ISBN: 978 92 4 001035 2. 196p. 

World Health Organization, 2023a. Trypanosomiasis, human African (sleeping sickness): key facts. Accessed at on February 19, 2023.

World Health Organization, 2023b. Human African Trypanosomiasis, (sleeping sickness): the global health observatory. Accessed at on February 19, 2023.

Population genetics of *Glossina palpalis* gambiensis in the sleeping sickness focus of Boffa (Guinea) before and after eight years of vector control: no effect of control despite a significant decrease of human exposure to the diseaseMoise S. Kagbadouno, Modou Séré, Adeline Ségard, Abdoulaye Dansy Camara, Mamadou Camara, Bruno Bucheton, Jean-Mathieu Bart, Fabrice Courtin, Thierry de Meeûs, Sophie Ravel<p style="text-align: justify;">Human African trypanosomosis (HAT), also known as sleeping sickness, is still a major concern in endemic countries. Its cyclical vector are biting insects of the genus Glossina or tsetse flies. In Guinea, the mangro...Disease Ecology/Evolution, Ecology of hosts, infectious agents, or vectors, Evolution of hosts, infectious agents, or vectors, Parasites, Population genetics of hosts, infectious agents, or vectorsHugues Nana Djeunga2023-07-29 13:24:52 View
17 Jan 2024
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Assessing the dynamics of Mycobacterium bovis infection in three French badger populations

From disease surveillance to public action. Re-inforcing both epidemiological surveillance and data analysis: an illustration with Mycobacterium bovis

Recommended by based on reviews by Rowland Kao and 1 anonymous reviewer

Mycobacterium bovis, also called M. tuberculosis var. bovis, is a bacterium belonging to the M. tuberculosis complex (i.e., MTBC) and which can cause through zoonotic transmission another form of human tuberculosis (Tb). It is above all the agent of bovine tuberculosis (i.e., bTb) which affects not only cattle (wild or farmed) but also a large diversity of other wild mammals worldwide. An increasing number of infected animal cases are being discovered in many regions of the world, thus raising the problem of tuberculosis transmission, including to humans, more complex than previously thought. Efforts have been made in terms of vaccination or culling of populations of host carrier species, such as the badger for example, however leading to consequences of greater dispersion of the infectious agent. M. bovis shows a more or less significant capacity to persist outside its hosts, particularly in the environment under certain abiotic and biotic conditions. This bacillus can be transmitted and spread in many ways, including through aerosol, mucus and sputum, urine and feces, by direct contact with infected animals, their dead bodies or rather via their excreta or by inhalation of aerosols, depending on the host species concerned.

In this paper, Calenge and his collaborators (Callenge et al. 2024) benefited from a national surveillance program on M. bovis cases in wild species, set up in 2011 in France, i.e., Sylvatub, for detecting and monitoring M. bovis infection in European badger (Meles meles) populations. Sylvatub is a participatory program involving both national and local stakeholder systems in order to determine changes in bTb infection levels in domestic and wild animal species. This original work had two aims: to describe spatial disease dynamics in the three clusters under scrutiny using a complex Bayesian model; and to develop indicators for the monitoring of the M. bovis infection by stakeholders and decision-makers of the program. This paper is timely and very comprehensive.

In this cogent study, the authors illustrate this point by using epidemiological surveillance to obtain large amounts of data (which is generally lacking in human epidemiology, but more dramatically lacking in animal epidemiology) and a highly sophisticated biostatistical analysis (Callenge et al. 2024). It is in itself a demonstration of the current capabilities of population dynamics applied to infectious disease situations, in this case animal, in the rapidly developing discipline of disease ecology and evolution. One of the aims of the study is to propose statistical models that can be used by the different stakeholders in charge, for instance, of wildlife conservation or the regional or State veterinary services to assess disease risk in the most affected regions.


Assel AKHMETOVA​, Jimena GUERRERO​, Paul McADAM, Liliana CM SALVADOR​, Joseph CRISPELL​, John LAVERY​, Eleanor PRESHO​, Rowland R KAO​, Roman BIEK​, Fraser MENZIES​, Nigel TRIMBLE​, Roland HARWOOD​, P Theo PEPLER, Katarina ORAVCOVA​, Jordon GRAHAM​, Robin SKUCE​, Louis DU PLESSIS​, Suzan THOMPSON​, Lorraine WRIGHT​, Andrew W BYRNE​, Adrian R ALLEN. 2023. Genomic epidemiology of Mycobacterium bovis infection in sympatric badger and cattle populations in Northern Ireland. Microbial Genomics 9: mgen001023.

Roman BIEK, Anthony O’HARE, David WRIGHT, Tom MALLON, Carl McCORMICK, Richard J ORTON, Stanley McDOWELL, Hannah TREWBY, Robin A SKUCE, Rowland R KAO. 2012. Whole genome sequencing reveals local transmission patterns of Mycobacterium bovis in sympatric cattle and badger populations. PLoS Pathogens 8: e1003008.

Clément CALENGE, Ariane PAYNE, Edouard REVEILLAUD, Céline RICHOMME, Sébastien GIRARD, Stephanie DESVAUX. 2024. Assessing the dynamics of Mycobacterium bovis infection in three French badger populations. bioRxiv, ver. 3 peer-reviewed and recommended by Peer Community In Infections.

Marc CHOISY, Pejman ROHANI. 2006. Harvesting can increase severity of wildlife disease epidemics. Proceedings of the Royal Society, London, Ser. B 273: 2025-2034.

Shannon C DUFFY, Sreenidhi SRINIVASAN, Megan A SCHILLING, Tod STUBER, Sarah N DANCHUK, Joy S MICHAEL, Manigandan VENKATESAN, Nitish BANSAL, Sushila MAAN, Naresh JINDAL, Deepika CHAUDHARY, Premanshu DANDAPAT, Robab KATANI, Shubhada CHOTHE, Maroudam VEERASAMI, Suelee ROBBE-AUSTERMAN, Nicholas JULEFF, Vivek KAPUR, Marcel A BEHR. 2020. Reconsidering Mycobacterium bovis as a proxy for zoonotic tuberculosis: a molecular epidemiological surveillance study. Lancet Microbe 1: e66-e73.

Jean-François GUEGAN. 2019. The nature of ecology of infectious disease. The Lancet Infectious Diseases 19.

Brandon H HAYES, Timothée VERGNE, Mathieu ANDRAUD, Nicolas ROSE. 2023. Mathematical modeling at the livestock-wildlife interface: scoping review of drivers of disease transmission between species. Frontiers in Veterinary Science 10: 1225446.

David KING, Tim ROPER, Douglas YOUNG, Mark EJ WOOLHOUSE, Dan COLLINS, Paul WOOD. 2007. Bovine tuberculosis in cattle and badgers. Report to Secretary of State about tuberculosis in cattle and badgers. London, UK.  

Robert MM SMITH , Francis DROBNIEWSKI, Andrea GIBSON, John DE MONTAGUE, Margaret N LOGAN, David HUNT, Glyn HEWINSON, Roland L SALMON, Brian O’NEILL. 2004. Mycobacterium bovis Infection, United Kingdom. Emerging Infectious Diseases 10: 539-541. 

Assessing the dynamics of *Mycobacterium bovis* infection in three French badger populationsClement CALENGE, Ariane PAYNE, Edouard REVEILLAUD, Celine RICHOMME, Sebastien GIRARD, Stephanie DESVAUX<p>The Sylvatub system is a national surveillance program established in 2011 in France to monitor infections caused by <em>Mycobacterium bovis</em>, the main etiologic agent of bovine tuberculosis, in wild species. This participatory program, inv...Animal diseases, Ecohealth, Ecology of hosts, infectious agents, or vectors, Epidemiology, Geography of infectious diseases, Pathogenic/Symbiotic Bacteria, ZoonosesJean-Francois Guegan2023-06-05 10:50:49 View
21 Jul 2022
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Structural variation turnovers and defective genomes: key drivers for the in vitro evolution of the large double-stranded DNA koi herpesvirus (KHV)

Understanding the in vitro evolution of Cyprinid herpesvirus 3 (CyHV-3), a story of structural variations that can lead to the design of attenuated virus vaccines

Recommended by ORCID_LOGO based on reviews by Lucie Cappuccio and Veronique Hourdel

Structural variations (SVs) play a key role in viral evolution, and therefore they are also important for infection dynamics. However, the contribution of structural variations to the evolution of double-stranded viruses is limited. This knowledge can help to understand the population dynamics and might be crucial for the future development of viral attenuated vaccines.

In this study, Fuandila et al (1) use the Cyprinid herpesvirus 3 (CyHV-3), commonly known as koi herpesvirus (KHV), to investigate the variability and contribution of structural variations (SV) for viral evolution after 99 passages in vitro. This virus, with the largest genome among herperviruses, causes a lethal infection in common carp and koi associated with mortalities up to 95% (2). Interestingly, KHV infections are caused by haplotype mixtures, which possibly are a source of genome diversification, but make genomic comparisons more difficult.

The authors have used ultra-deep long-read sequencing of two passages, P78 and P99, which were previously described to have differences in virulence. They have found a surprisingly high and wide distribution of SVs along the genome, which were enriched in inversion and deletion events and that often led to defective viral genomes. Although it is known that these defective viral genomes negatively impact viral replication, their implications for virus persistence are still unclear.

Subsequently, the authors concentrated on the virulence-relevant region ORF150, which was found to be different in P78 (deletion in 100% of the reads) and P99 (reference-like haplotype). To understand this loss and gain of full ORF150, they searched for SV turn-over in 10 intermediate passages. This analysis revealed that by passage 10 deleted and inverted (attenuated) haplotypes had already appeared, steadily increased frequency until P78, and then completely disappeared between P78 and P99. This is a striking result that raises new questions as to how this clearance occurs, which is really important as these reversions may result in undesirable increases in virulence of live-attenuated vaccines.

We recommend this preprint because its use of ultra-deep long-read sequencing has permitted to better understand the role of SV diversity and dynamics in viral evolution. This study shows an unexpectedly high number of structural variations, revealing a novel source of virus diversification and confirming the different mixtures of haplotypes in different passages, including the gain of function. This research provides basic knowledge for the future design of live-attenuated vaccines, to prevent the reversion to virulent viruses. 


(1)  Fuandila NN, Gosselin-Grenet A-S, Tilak M-K, Bergmann SM, Escoubas J-M, Klafack S, Lusiastuti AM, Yuhana M, Fiston-Lavier A-S, Avarre J-C, Cherif E (2022) Structural variation turnovers and defective genomes: key drivers for the in vitro evolution of the large double-stranded DNA koi herpesvirus (KHV). bioRxiv, 2022.03.10.483410, ver. 4 peer-reviewed and recommended by Peer Community in Infections.

(2)  Sunarto A, McColl KA, Crane MStJ, Sumiati T, Hyatt AD, Barnes AC, Walker PJ. Isolation and characterization of koi herpesvirus (KHV) from Indonesia: identification of a new genetic lineage. Journal of Fish Diseases, 34, 87-101. 

Structural variation turnovers and defective genomes: key drivers for the in vitro evolution of the large double-stranded DNA koi herpesvirus (KHV)Nurul Novelia Fuandila, Anne-Sophie Gosselin-Grenet, Marie-Ka Tilak, Sven M Bergmann, Jean-Michel Escoubas, Sandro Klafack, Angela Mariana Lusiastuti, Munti Yuhana, Anna-Sophie Fiston-Lavier, Jean-Christophe Avarre, Emira Cherif<p style="text-align: justify;">Structural variations (SVs) constitute a significant source of genetic variability in virus genomes. Yet knowledge about SV variability and contribution to the evolutionary process in large double-stranded (ds)DNA v...Animal diseases, Evolution of hosts, infectious agents, or vectors, Genomics, functional genomics of hosts, infectious agents, or vectors, VirusesJorge Amich Lucie Cappuccio, 2022-03-11 10:50:50 View
07 Oct 2022
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Guidelines for the reliable use of high throughput sequencing technologies to detect plant pathogens and pests

High-throughput sequencing for the diagnostic of plant pathologies and identification of pests: recommendations and challenges

Recommended by based on reviews by Denise Altenbach and David Roquis

High-throughput sequencing (HTS) has revealed an incredible diversity of microorganisms in ecosystems and is also changing the monitoring of macroorganism biodiversity (Deiner et al. 2017; Piper et al. 2019).  

The diagnostic of plant pathogens and the identification of pests is gradually integrating the use of these techniques, but there are still obstacles. Most of them are related to the reliability of these analyses, which have long been considered insufficient because of their dependence on a succession of sophisticated operations involving parameters that are sometimes difficult to adapt to complex matrices or certain diagnostic contexts. The need to validate HTS approaches is gradually being highlighted in recent work but remains poorly documented (Bester et al. 2022).

In this paper, a large community of experts presents and discusses the key steps for optimal control of HTS performance and reliability in a diagnostic context (Massart et al. 2022). It also addresses the issue of costs. The article provides recommendations that closely combine the quality control requirements commonly used in conventional diagnostics with newer or HTS-specific control elements and concepts that are not yet widely used. It discusses the value of these for the use of the various techniques currently covered by the terms "High Throughput Sequencing" in diagnostic activities. The elements presented are intended to limit false positive or false negative results but will also optimise the interpretation of contentious results close to the limits of analytical sensitivity or unexpected results, both of which appear to be frequent when using HTS.

Furthermore, the need for risk analysis, verification and validation of methods is well illustrated with numerous examples for each of the steps considered crucial to ensure reliable use of HTS. The clear contextualisation of the proposals made by the authors complements and clarifies the need for user expertise according to the experimental objectives. Some unanswered questions that will require further development and validation are also presented.

This article should benefit a large audience including researchers with some level of expertise in HTS but unfamiliar with the recent concepts of controls common in the diagnostic world as well as scientists with strong diagnostic expertise but less at ease with the numerous and complex procedures associated with HTS.


Bester R, Steyn C, Breytenbach JHJ, de Bruyn R, Cook G, Maree HJ (2022) Reproducibility and Sensitivity of High-Throughput Sequencing (HTS)-Based Detection of Citrus Tristeza Virus and Three Citrus Viroids. Plants, 11, 1939.

Deiner K, Bik HM, Mächler E, Seymour M, Lacoursière-Roussel A, Altermatt F, Creer S, Bista I, Lodge DM, de Vere N, Pfrender ME, Bernatchez L (2017) Environmental DNA metabarcoding: Transforming how we survey animal and plant communities. Molecular Ecology, 26, 5872–5895.

Massart, S et al. (2022) Guidelines for the reliable use of high throughput sequencing technologies to detect plant pathogens and pests. Zenodo, 6637519, ver. 3  peer-reviewed and recommended by Peer Community in Infections.

Piper AM, Batovska J, Cogan NOI, Weiss J, Cunningham JP, Rodoni BC, Blacket MJ (2019) Prospects and challenges of implementing DNA metabarcoding for high-throughput insect surveillance. GigaScience, 8, giz092.

Guidelines for the reliable use of high throughput sequencing technologies to detect plant pathogens and pestsS. Massart, I. Adams, M. Al Rwahnih, S. Baeyen, G. J. Bilodeau, A. G. Blouin, N. Boonham, T. Candresse, A. Chandelier, K. De Jonghe, A. Fox, Y.Z.A. Gaafar, P. Gentit, A. Haegeman, W. Ho, O. Hurtado-Gonzales, W. Jonkers, J. Kreuze, D. Kutjnak, B. B...<p style="text-align: justify;">High-throughput sequencing (HTS) technologies have the potential to become one of the most significant advances in molecular diagnostics. Their use by researchers to detect and characterize plant pathogens and pests...Diagnosis, Pest management, Phytopathology, Plant diseasesOlivier Schumpp2022-06-13 11:26:18 View
06 Apr 2023
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Evolution within a given virulence phenotype (pathotype) is driven by changes in aggressiveness: a case study of French wheat leaf rust populations

Changes in aggressiveness in pathotypes of wheat leaf rust

Recommended by based on reviews by 2 anonymous reviewers

Understanding the ecological and evolutionary factors underlying the spread of new fungal pathogen populations can inform the development of more effective management strategies. In plant pathology, pathogenicity is generally presented as having two components: ‘virulence’ (qualitative pathogenicity) and aggressiveness (quantitative pathogenicity). Changes in virulence in response to the deployment of new resistant varieties are a major driver of the spread of new populations (called pathotypes, or races) in modern agrosystems, and the genomic (i.e. proximal) and eco-evolutionary (i.e. ultimate) factors underlying these changes are well-documented [1,2,3]. By contrast, the role of changes in aggressiveness in the spread of pathotypes remains little known [4].

The study by Cécilia Fontyn and collaborators [5] set out to characterize changes in aggressiveness for isolates of two pathotypes of the wheat leaf rust (Puccinia triticina) that have been dominant in France during the 2005-2016 period. Isolates were genetically characterized using multilocus microsatellite typing and phenotypically characterized for three components of aggressiveness on wheat varieties: infection efficiency, latency period, and sporulation capacity. Using experiments that represent quite a remarkable amount of work and effort, Fontyn et al. showed that each dominant pathotype consisted of several genotypes, including common genotypes whose frequency changed over time. For each pathotype, the genotypes that were more common initially were replaced by a more aggressive genotype. Together, these results show that changes in the genetic composition of populations of fungal plant pathogens can be associated with, and may be caused by, changes in the quantitative components of pathogenicity. This study also illustrates how extensive, decade-long monitoring of fungal pathogen populations, such as the one conducted for wheat leaf rust in France, represents a very valuable resource for research.


[1] Brown, J. K. (1994). Chance and selection in the evolution of barley mildew. Trends in Microbiology, 2(12), 470-475.

[2] Daverdin, G., Rouxel, T., Gout, L., Aubertot, J. N., Fudal, I., Meyer, M., Parlange, F., Carpezat, J., & Balesdent, M. H. (2012). Genome structure and reproductive behaviour influence the evolutionary potential of a fungal phytopathogen. PLoS Pathogens, 8(11), e1003020.

[3] Gladieux, P., Feurtey, A., Hood, M. E., Snirc, A., Clavel, J., Dutech, C., Roy, M., & Giraud, T. (2015). The population biology of fungal invasions.Molecular Ecology, 24(9), 1969-86.

[4] Fontyn, C., Zippert, A. C., Delestre, G., Marcel, T. C., Suffert, F., & Goyeau, H. (2022). Is virulence phenotype evolution driven exclusively by Lr gene deployment in French Puccinia triticina populations?. Plant Pathology, 71(7), 1511-1524.

[5] Fontyn, C., Meyer, K. J., Boixel, A. L., Delestre, G., Piaget, E., Picard, C., Suffer, F., Marcel, T.C., & Goyeau, H. (2022). Evolution within a given virulence phenotype (pathotype) is driven by changes in aggressiveness: a case study of French wheat leaf rust populations. bioRxiv, 2022.08.29.505401, ver. 3 peer-reviewed and recommended by Peer Community in Infections.

Evolution within a given virulence phenotype (pathotype) is driven by changes in aggressiveness: a case study of French wheat leaf rust populationsCécilia FONTYN, Kevin JG MEYER, Anne-Lise BOIXEL, Ghislain DELESTRE, Emma PIAGET, Corentin PICARD, Frédéric SUFFERT, Thierry C MARCEL, Henriette GOYEAU<p style="text-align: justify;">Plant pathogens are constantly evolving and adapting to their environment, including their host. Virulence alleles emerge, and then increase, and sometimes decrease in frequency within pathogen populations in respon...Coevolution, Epidemiology, Evolution of hosts, infectious agents, or vectors, Interactions between hosts and infectious agents/vectors, Pathogenic/Symbiotic Fungi, Phytopathology, Plant diseases, Population dynamics of hosts, infectious agents, or...Pierre Gladieux, Jacqui Shykoff, , 2022-09-29 20:01:57 View
08 Aug 2023
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A global Corynebacterium diphtheriae genomic framework sheds light on current diphtheria reemergence

DIPHTOSCAN : A new tool for the genomic surveillance of diphtheria

Recommended by based on reviews by Ankur Mutreja and 2 anonymous reviewers

One of the greatest achievements of health sciences is the eradication of infectious diseases such as smallpox that in the past imposed a severe burden on humankind, through global vaccination campaigns. Moreover, progress towards the eradication of others such as poliomyelitis, dracunculiasis, and yaws is being made.

In contrast, other infections that were previously contained are reemerging, due to several factors, including lack of access to vaccines due to geopolitical reasons, the rise of anti-vaccine movements, and the constant mobility of infected persons from the endemic sites.

One of such disease is diphtheria, caused by Corynebacterium diphtheriae and a few other related species such as C. ulcerans and C. pseudotuberculosis. Importantly, in France, diphtheria cases reported in 2022 increased 7-fold from the average of previously recorded cases per year in the previous 4 years and the situation in other European countries is similar.

Hence, as reported here, Hennart et al. (2023) developed DIPHTOSCAN, a free access bioinformatics tool with user-friendly interphase, aimed to easily identify, extract and interpret important genomic features such as the sublineage of the strain, the presence of the tox gene (as a string predictor for toxigenic disease) as well as genes coding other virulence factors such as fimbriae, and the presence of know resistant mechanisms towards antibiotics like penicillin and erythromycin currently used in the clinic to treat this infection.

The authors validated the performance of their tool with a large collection of genomes, including those obtained from the isolates of the 2022 outbreak in France, more than 1,200 other genomes isolated from France, Algeria, and Yemen, and more than 500 genomes from several countries from Europe, America, Africa, Asia, and Oceania that are available through the NCBI site.

DIPHTOSCAN will allow the rapid identification and surveillance of potentially dangerous strains such as those being tox-positive isolates and resistant to multiple drugs and/or first-line treatments and a better understanding of the epidemiology and evolution of this important reemerging disease.


Hennart M., Crestani C., Bridel S., Armatys N., Brémont S., Carmi-Leroy A., Landier A., Passet V., Fonteneau L., Vaux S., Toubiana J., Badell E. and Brisse S. (2023). A global Corynebacterium diphtheriae genomic framework sheds light on current diphtheria reemergence. bioRxiv, 2023.02.20.529124, ver 3 peer-reviewed and recommended by PCI Infections.

A global *Corynebacterium diphtheriae* genomic framework sheds light on current diphtheria reemergenceMelanie Hennart, Chiara Crestani, Sebastien Bridel, Nathalie Armatys, Sylvie Brémont, Annick Carmi-Leroy, Annie Landier, Virginie Passet, Laure Fonteneau, Sophie Vaux, Julie Toubiana, Edgar Badell, Sylvain Brisse<p style="text-align: justify;"><strong>Background</strong></p> <p style="text-align: justify;">Diphtheria, caused by <em>Corynebacterium diphtheriae</em>, reemerges in Europe since 2022. Genomic sequencing can inform on transmission routes and g...Drug resistance, tolerance and persistence, Epidemiology, Evolution of hosts, infectious agents, or vectors, Genomics, functional genomics of hosts, infectious agents, or vectors, Microbiology of infections, Population genetics of hosts, infectiou...Rodolfo García-Contreras Ankur Mutreja 2023-03-09 16:02:27 View
21 Sep 2023
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Chikungunya intra-vector dynamics in Aedes albopictus from Lyon (France) upon exposure to a human viremia-like dose range reveals vector barrier permissiveness and supports local epidemic potential

Fill in one gap in our understanding of CHIKV intra-vector dynamics

Recommended by based on reviews by 2 anonymous reviewers

Mosquitoes are first vector of pathogen worldwide and transmit several arbovirus, most of them leading to major outbreaks (1). Chikungunya virus (CHIKV) is a perfect example of the “explosive type” of arbovirus, as observed in La Réunion Island in 2005-2006 (2-6) and also in the outbreak of 2007 in Italy (7), both vectorized by Ae. albopictus. Being able to better understand CHIKV intra-vector dynamics is still of major interest since not all chikungunya strain are explosive ones (8). 

In this study (9), the authors have evaluated the vector competence of a local strain of Aedes albopictus (collected in Lyon, France) for CHIKV. They evaluated infection, dissemination and transmission dynamics of CHIKV using different dose of virus in individual mosquitoes from day 2 to day 20 post exposure, by titration and quantification of CHIKV RNA load in the saliva. As highlighted by both reviewers, the most innovative idea in this study was the use of three different oral doses trying to span human viraemia detected in two published studies (10-11), doses that were estimated through their model of human CHIKV viremia in the blood.  They have found that CHIKV dissemination from the Ae. albopictus midgut depends on the interaction between time post-exposure and virus dose (already highlighted by other international publications).  Then their results were implemented in the agent-based model nosoi to estimate the epidemic potential of CHIKV in a French population of Ae. albopictus, using realistic vectorial capacity parameters.

To conclude, the authors have discussed the importance of other parameters that could influence vector competence as mosquito microbiota and temperature, parameters that need also to be estimated in local mosquito population to improve the risk assessment through modelling.  

As pointed out by both reviewers, this is a nice study, well written and easy to read. These results allow filling in another gap of our understanding of CHIKV intra-vector dynamics and highlight the epidemic potential of CHIKV upon transmission by Aedes albopictus in mainland France. For all these reasons, I chose to recommend this article for Peer Community In Infections.


1.       Marine Viglietta, Rachel Bellone, Adrien Albert Blisnick, Anna-Bella Failloux. (2021). Vector Specificity of Arbovirus Transmission. Front Microbiol Dec 9;12:773211.

2.       Schuffenecker I, Iteman I, Michault A, Murri S, Frangeul L, Vaney M-C, Lavenir R, Pardigon N, Reynes J-M, Pettinelli F, Biscornet L, Diancourt L, Michel S, Duquerroy S, Guigon G, Frenkiel M-P, Bréhin A-C, Cubito N, Desprès P, Kunst F, Rey FA, Zeller H, Brisse S. (2006). Genome Microevolution of Chikungunya viruses Causing the Indian Ocean Outbreak. 2006. PLoS Medicine, 3, e263.

3.       Bonilauri P, Bellini R, Calzolari M, Angelini R, Venturi L, Fallacara F, Cordioli P, 687 Angelini P, Venturelli C, Merialdi G, Dottori M. (2008). Chikungunya Virus in Aedes albopictus, Italy. Emerging Infectious 689 Diseases, 14, 852–854.

4.       Pagès F, Peyrefitte CN, Mve MT, Jarjaval F, Brisse S, Iteman I, Gravier P, Tolou H, Nkoghe D, Grandadam M. (2009). Aedes albopictus Mosquito: The Main Vector of the 2007 Chikungunya Outbreak in Gabon. PLoS ONE, 4, e4691.

5.       Paupy C, Kassa FK, Caron M, Nkoghé D, Leroy EM (2012) A Chikungunya Outbreak Associated with the Vector Aedes albopictus in Remote Villages of Gabon. Vector-Borne and Zoonotic Diseases, 12, 167–169.

6.       Mombouli J-V, Bitsindou P, Elion DOA, Grolla A, Feldmann H, Niama FR, Parra H-J, Munster VJ. (2013). Chikungunya Virus Infection, Brazzaville, Republic of Congo, 2011. Emerging Infectious Diseases, 19, 1542–1543.

7.       Venturi G, Luca MD, Fortuna C, Remoli ME, Riccardo F, Severini F, Toma L, Manso MD, Benedetti E, Caporali MG, Amendola A, Fiorentini C, Liberato CD, Giammattei R, Romi R, Pezzotti P, Rezza G, Rizzo C. (2017). Detection of a chikungunya outbreak in Central Italy, August to September 2017. Eurosurveillance, 22, 17–00646.

8.       de Lima Cavalcanti, T.Y.V.; Pereira, M.R.; de Paula, S.O.; Franca, R.F.d.O. (2022). A Review on Chikungunya Virus Epidemiology, Pathogenesis and Current Vaccine Development. Viruses 2022, 14, 969.

9.       Barbara Viginier, Lucie Cappuccio, Celine Garnier, Edwige Martin, Carine Maisse, Claire Valiente Moro, Guillaume Minard, Albin Fontaine, Sebastian Lequime, Maxime Ratinier, Frederick Arnaud, Vincent Raquin. (2023). Chikungunya intra-vector dynamics in Aedes albopictus from Lyon (France) upon exposure to a human viremia-like dose range reveals vector barrier permissiveness and supports local epidemic potential. medRxiv, ver.3, peer-reviewed and recommended by Peer Community In Infections.

10.     Appassakij H, Khuntikij P, Kemapunmanus M, Wutthanarungsan R, Silpapojakul K (2013) Viremic profiles in CHIKV-infected cases. Transfusion, 53, 2567–2574.

11.     Riswari SF, Ma’roef CN, Djauhari H, Kosasih H, Perkasa A, Yudhaputri FA, Artika IM, Williams M, Ven A van der, Myint KS, Alisjahbana B, Ledermann JP, Powers AM, Jaya UA (2015) Study of viremic profile in febrile specimens of chikungunya in Bandung, Indonesia. Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology, 74, 61–5.

Chikungunya intra-vector dynamics in *Aedes albopictus* from Lyon (France) upon exposure to a human viremia-like dose range reveals vector barrier permissiveness and supports local epidemic potentialBarbara Viginier, Lucie Cappuccio, Celine Garnier, Edwige Martin, Carine Maisse, Claire Valiente Moro, Guillaume Minard, Albin Fontaine, Sebastian Lequime, Maxime Ratinier, Frederick Arnaud, Vincent Raquin<p>Arbovirus emergence and epidemic potential, as approximated by the vectorial capacity formula, depends on host and vector parameters, including the vector intrinsic ability to replicate then transmit the pathogen known as vector competence. Vec...Epidemiology, Vectors, VirusesSara Moutailler2023-06-17 15:59:17 View
14 Dec 2022
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Transcriptome responses of the aphid vector Myzus persicae are shaped by identities of the host plant and the virus

How do multiple host plants and virus species challenge aphid molecular machinery?

Recommended by based on reviews by Juan José Lopez Moya and Michelle Heck

The impact of virus infection of a plant on an aphid’s behaviour has been observed in many studies [1]. Indeed, virus infection can alter plant biochemistry through the emission of volatile organic compounds and plant tissue content modification. These alterations can further impact the interactions between plants and aphids. However, although it is a well-known phenomenon, very few studies have explored the consequences of plant virus infection on the gene expression of aphids to understand better the aphid’s manipulation by the plant virus. In this context, the recommended study [2] reports a comprehensive transcriptomic analysis of the genes expressed by one aphid species, Myzus persicae, a vector of several plant viruses, when feeding on plants. Michelle Heck underlined how significant this study is for comprehending the molecular bases of aphid-vector manipulation by plant viruses (see below).

Interestingly, the study design has integrated several factors that might influence the gene expression of M. persicae when feeding on the plant. Indeed, the authors investigated the effect of two plant species (Arabidopsis thaliana and Camelia sativa) and two virus species [turnip yellows virus (TuYV) and cauliflower mosaic virus (CaMV)]. Noteworthy, the transmission mode of TuYV is circulative and persistent, while CaMV is transmitted by a semi-persistent non-circulative mode. As Juan José Lopez Moya mentioned, multiple comparisons allowed the identification of the different responses of aphids in front of different host plants infected or not by different viruses (see below). This publication is complementary to a previous publication from the same team focusing on plant transcriptome analysis [3].

Thanks to their experimental design, the authors identified genes commonly deregulated by both viruses and/or both plant species and deregulated genes by a single virus or a single plant. Figure 4 nicely summarizes the number of deregulated genes. A thorough discussion on the putative role of deregulated genes in different conditions gave a comprehensive follow-up of the results and their impact on the current knowledge of plant-virus-vector interactions.

This study has now opened the gate to promising research focusing on the functional validation of the identified genes while also narrowing the study from the body to the tissue level.


1. Carr JP, Tungadi T, Donnelly R, Bravo-Cazar A, Rhee S-J, Watt LG, Mutuku JM, Wamonje FO, Murphy AM, Arinaitwe W, Pate AE, Cunniffe NJ, Gilligan CA (2020) Modelling and manipulation of aphid-mediated spread of non-persistently transmitted viruses. Virus Research, 277, 197845.

2. Chesnais Q, Golyaev V, Velt A, Rustenholz C, Verdier M, Brault V, Pooggin MM, Drucker M (2022) Transcriptome responses of the aphid vector Myzus persicae are shaped by identities of the host plant and the virus. bioRxiv , 2022.07.18.500449, ver. 5 peer-reviewed and recommended by Peer Community in Infections.

3. Chesnais Q, Golyaev V, Velt A, Rustenholz C, Brault V, Pooggin MM, Drucker M (2022) Comparative Plant Transcriptome Profiling of Arabidopsis thaliana Col-0 and Camelina sativa var. Celine Infested with Myzus persicae Aphids Acquiring Circulative and Noncirculative Viruses Reveals Virus- and Plant-Specific Alterations Relevant to Aphid Feeding Behavior and Transmission. Microbiology Spectrum, 10, e00136-22.

Transcriptome responses of the aphid vector *Myzus persicae* are shaped by identities of the host plant and the virusQuentin Chesnais, Victor Golyaev, Amandine Velt, Camille Rustenholz, Maxime Verdier, Véronique Brault, Mikhail M. Pooggin, Martin Drucker<p style="text-align: justify;"><strong>Background:</strong> Numerous studies have documented modifications in vector orientation behavior, settling and feeding behavior, and/or fecundity and survival due to virus infection in host plants. These a...Behaviour of hosts, infectious agents, or vectors, Cell biology of hosts, infectious agents, or vectors, Molecular biology of infections, Physiology of hosts, infectious agents, or vectors, Phytopathology, Plant diseases, Vectors, VirusesSebastien Massart2022-07-19 15:24:14 View
27 Feb 2023
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African army ants at the forefront of virome surveillance in a remote tropical forest

A groundbreaking study using ants revealed a spectacular diversity of viruses in hardly accessible ecosystems like tropical forests

Recommended by based on reviews by Mart Krupovic and 1 anonymous reviewer

Deciphering the virome (the set or assemblage of viruses) of the Earth, from individual organisms to entire ecosystems, has become a key priority. The first step to better understanding the impact of viruses on the ecology and functions of ecosystems is to describe their diversity. Such knowledge opens the gates to a better assessment of global nutrient cycling or of the threat that viruses represent to individual health. This explains the increasing number of pioneering studies that are currently sequencing the complete or partial genome of thousands of new viruses [1].

In their exciting study, Fritz and collaborators [2], authors sampled 209 army ants (Genus Dorylus) to investigate the virus diversity in dense forests that researchers cannot easily access. Indeed, these ants live in colonies (21 were sampled) that can move 1 km per day, covering a significant area and attacking many invertebrate and vertebrate preys.  Each sample was sequenced by a protocol called VANA sequencing and allowing the enrichment of the sample in viral sequences [3], so improving the detection of viruses present at low abundance in the ant (and more specifically in its gut for viruses infecting preys). 

Around 45,000 contigs presented homologies with bacterial, plant, invertebrate, and vertebrate infecting viruses. Half could be assigned to 56 families and 157 genera of the International Committee on Taxonomy of Viruses. Beyond this amazing harvest of new and known virus sequences using an original methodology, the results significantly improve the current frontiers of known viral taxonomy and diversity and raise exciting research tracks to expand them. 

As a preprint, several blogs or news of leading scientists and journals have already highlighted this study. For example, in the news section of Science magazine, Jon Cohen underlined the originality of the approach for virus hunting on Earth with the title “Armed with air samplers, rope tricks, and—yes—ants, virus hunters spot threats in new ways”[4]. Another example is the mention of the publication by Elisabeth Bik in her Microbiome Digest: she wrote, “An amazing read is a fresh preprint from Fritz and collaborator describing an exciting method of sampling in difficult-to-reach environments“ [5].

The paper from Fritz et al [2] thus represents a significant advance in virus ecology, as already recognized by early readers, and this is why I strongly recommend its publication in PCI Infections.


1. Edgar RC, Taylor J, Lin V, Altman T, Barbera P, Meleshko D, Lohr D, Novakovsky G, Buchfink B, Al-Shayeb B, Banfield JF, de la Peña M, Korobeynikov A, Chikhi R, Babaian A (2022) Petabase-scale sequence alignment catalyses viral discovery. Nature, 602, 142–147.

2. Fritz M, Reggiardo B, Filloux D, Claude L, Fernandez E, Mahé F, Kraberger S, Custer JM, Becquart P, Mebaley TN, Kombila LB, Lenguiya LH, Boundenga L, Mombo IM, Maganga GD, Niama FR, Koumba J-S, Ogliastro M, Yvon M, Martin DP, Blanc S, Varsani A, Leroy E, Roumagnac P (2023) African army ants at the forefront of virome surveillance in a remote tropical forest. bioRxiv, 2022.12.13.520061, ver. 4 peer-reviewed and recommended by Peer Community in Infections.

3. François S, Filloux D, Fernandez E, Ogliastro M, Roumagnac P (2018) Viral Metagenomics Approaches for High-Resolution Screening of Multiplexed Arthropod and Plant Viral Communities. In: Viral Metagenomics: Methods and Protocols Methods in Molecular Biology. (eds Pantaleo V, Chiumenti M), pp. 77–95. Springer, New York, NY.

4. Cohen J (2023) Virus hunters test new surveillance tools. Science, 379, 16–17.

5. Ponsero A (2023) February 18th, 2023. Microbiome Digest - Bik’s Picks.

African army ants at the forefront of virome surveillance in a remote tropical forestMatthieu Fritz, Berenice Reggiardo, Denis Filloux, Lisa Claude, Emmanuel Fernandez, Frederic Mahe, Simona Kraberger, Joy M. Custer, Pierre Becquart, Telstar Ndong Mebaley, Linda Bohou Kombila, Leadisaelle H. Lenguiya, Larson Boundenga, Illich M. M...<p style="text-align: justify;">In this study, we used a predator-enabled metagenomics strategy to sample the virome of a remote and difficult-to-access densely forested African tropical region. Specifically, we focused our study on the use of arm...Ecohealth, Ecology of hosts, infectious agents, or vectors, One Health, Reservoirs, VirusesSebastien Massart2022-12-14 11:57:40 View
24 Jan 2024
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Physiological and behavioural resistance of malaria vectors in rural West-Africa : a data mining study to address their fine-scale spatiotemporal heterogeneity, drivers, and predictability

Large and complete datasets, and modelling reveal the major determinants of physiological and behavioral insecticide resistance of malaria vectors

Recommended by ORCID_LOGO based on reviews by Haoues Alout and 1 anonymous reviewer

            Parasites represent the most diverse and adaptable ecological group of the biosphere (Timm & Clauson, 1988; De Meeûs et al., 1998; Poulin & Morand, 2000; De Meeûs & Renaud, 2002). The human species is known to considerably alter biodiversity, though it hosts, and thus sustains the maintenance of a spectacular diversity of parasites (179 species for eukaryotic species only) (De Meeûs et al., 2009). Among these, the five species of malaria agents (genus Plasmodium) remain a major public health issue around the world. Plasmodium falciparum is the most prevalent and lethal of these (Liu et al., 2010). With a pick of up to 2 million deaths due to malaria in 2004, deaths decreased to around 1 million in 2010 (Murray et al., 2012), to reach 619,000 in 2021, most of which in sub-Saharan Africa, and 79% of which were among children aged under 5 years (World Health Organization, 2022). 

            As stressed by Taconet et al. (2023), reduction in malaria deaths is attributable to control measures, in particular against its vectors (mosquitoes of the genus Anopheles). Nevertheless, the success of vector control is hampered by several factors (biological, environmental and socio-economic), and in particular by the great propensity of targeted mosquitoes to evolve physiological or behavioral avoidance of anti-vectorial measures.

            In their paper Taconet et al. (2023) aims at understanding what are the main factors that determine the evolution of insecticide resistance in several malaria vectors, in relation to the biological determinisms of behavioral resistance and how fast such evolutions take place. To tackle these objectives, authors collected an impressive amount of data in two rural areas of West Africa. With appropriate modeling, Taconet et al. discovered, among many other results, a predominant role of public health measures, as compared to agricultural practices, in the evolution of physiological resistance. They also found that mosquito foraging activities are mostly explained by host availability and climate, with a poor, if any, association with genetic markers of physiological resistance to insecticides. These findings represent an important contribution to the field and should help at designing more efficient control strategies against malaria.



De Meeûs T, Michalakis Y, Renaud F (1998) Santa Rosalia revisited: or why are there so many kinds of parasites in “the garden of earthly delights”? Parasitology Today, 14, 10–13.

De Meeûs T, Prugnolle F, Agnew P (2009) Asexual reproduction in infectious diseases. In: Lost Sex: The Evolutionary Biology of Parthenogenesis (eds Schön I, Martens K, van Dijk P), pp. 517-533. Springer, NY.

De Meeûs T, Renaud F (2002) Parasites within the new phylogeny of eukaryotes. Trends in Parasitology, 18, 247–251.

Liu W, Li Y, Learn GH, Rudicell RS, Robertson JD, Keele BF, Ndjango JB, Sanz CM, Morgan DB, Locatelli S, Gonder MK, Kranzusch PJ, Walsh PD, Delaporte E, Mpoudi-Ngole E, Georgiev AV, Muller MN, Shaw GM, Peeters M, Sharp PM, Rayner JC, Hahn BH (2010) Origin of the human malaria parasite Plasmodium falciparum in gorillas. Nature, 467, 420–425.

Murray CJ, Rosenfeld LC, Lim SS, Andrews KG, Foreman KJ, Haring D, Fullman N, Naghavi M, Lozano R, Lopez AD (2012) Global malaria mortality between 1980 and 2010: a systematic analysis. The Lancet, 379, 413–431.

Poulin R, Morand S (2000) The diversity of parasites. Quarterly Review of Biology, 75, 277–293.

Taconet P, Soma DD, Zogo B, Mouline K, Simard F, Koffi AA, Dabire RK, Pennetier C, Moiroux N (2023) Physiological and behavioural resistance of malaria vectors in rural West-Africa : a data mining study to address their fine-scale spatiotemporal heterogeneity, drivers, and predictability. bioRxiv, ver. 4 peer-reviewed and recommended by Peer Community in Infections.

Timm RM, Clauson BL (1988) Coevolution: Mammalia. In: 1988 McGraw-Hill yearbook of science & technology, pp. 212–214. McGraw-Hill Book Company, New York.

World Health Organization (2022) World malaria report 2022. Geneva: World Health Organization; 2022. Licence: CC BY-NC-SA 3.0 IGO.


Physiological and behavioural resistance of malaria vectors in rural West-Africa : a data mining study to address their fine-scale spatiotemporal heterogeneity, drivers, and predictabilityPaul Taconet, Dieudonné Diloma Soma, Barnabas Zogo, Karine Mouline, Frédéric Simard, Alphonsine Amanan Koffi, Roch Kounbobr Dabiré, Cédric Pennetier, Nicolas Moiroux<p>Insecticide resistance and behavioural adaptation of malaria mosquitoes affect the efficacy of long-lasting insecticide nets - currently the main tool for malaria vector control. To develop and deploy complementary, efficient and cost-effective...Behaviour of hosts, infectious agents, or vectors, Ecology of hosts, infectious agents, or vectors, Pesticide resistance, Population genetics of hosts, infectious agents, or vectors, VectorsThierry DE MEEÛS Haoues Alout, Anonymous2023-07-03 11:29:10 View