Sébastien Calvignac-Spencer

Sébastien Calvignac-Spencer
Robert Koch Institut | RKI · Epidemiology of highly pathogenic microorganisms

Ph.D.

About

204
Publications
42,399
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4,041
Citations
Introduction
My work mainly focuses on virus and parasite circulation in wild primates, within and across species. In addition to that, I have also been involved in biodiversity-related research, and more particularly in the development of new tools allowing for quick and cost-effective assessment of its extent.
Additional affiliations
March 2010 - present
September 2008 - February 2010
Claude Bernard University Lyon 1
Position
  • Universite Claude Bernard Lyon 1
September 2004 - November 2007
Université Claude Bernard Lyon 1/Ecole Normale Superieure de Lyon
Position
  • PhD Student

Publications

Publications (204)
Article
Full-text available
Human herpes simplex virus 2 (HSV-2) is a ubiquitous, slowly evolving DNA virus. HSV-2 has two primary lineages, one found in West and Central Africa and the other found worldwide. Competing hypotheses have been proposed to explain how HSV-2 migrated out-of-Africa (i)HSV-2 followed human migration out-of-Africa 50-100 thousand years ago, or (ii)HSV...
Article
Full-text available
Background Comprehensive pathogen genomic surveillance represents a powerful tool to complement and advance precision vaccinology. The emergence of the Alpha variant in December 2020 and the resulting efforts to track the spread of this and other SARS-CoV-2 variants of concern led to an expansion of genomic sequencing activities in Germany. Method...
Article
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Flies are implicated in carrying and mechanically transmitting many primate pathogens. We investigated how fly associations vary across six monkey species (Cercopithecus ascanius, Cercopithecus mitis, Colobus guereza, Lophocebus albigena, Papio anubis, and Piliocolobus tephrosceles) and whether monkey group size impacts fly densities. Fly densities...
Article
Full-text available
The 1918 influenza pandemic was the deadliest respiratory pandemic of the 20th century and determined the genomic make-up of subsequent human influenza A viruses (IAV). Here, we analyze both the first 1918 IAV genomes from Europe and the first from samples prior to the autumn peak. 1918 IAV genomic diversity is consistent with a combination of loca...
Article
Full-text available
The human parasite Plasmodium malariae has relatives infecting African apes (Plasmodium rodhaini) and New World monkeys (Plasmodium brasilianum), but its origins remain unknown. Using a novel approach to characterise P. malariae-related sequences in wild and captive African apes, we found that this group comprises three distinct lineages, one of wh...
Article
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Human respiratory pathogens have repeatedly caused lethal outbreaks in wild great apes across Africa, leading to population declines. Nonetheless, our knowledge of potential genomic changes associated with pathogen introduction and spread at the human‐great ape interface remains sparse. Here, we made use of target enrichment coupled with next gener...
Article
Full-text available
In spring 2021, an increasing number of infections was observed caused by the hitherto rarely described SARS-CoV-2 variant A.27 in south-west Germany. From December 2020 to June 2021 this lineage has been detected in 31 countries. Phylogeographic analyses of A.27 sequences obtained from national and international databases reveal a global spread of...
Preprint
Full-text available
Human herpes simplex virus 2 (HSV-2) is a globally ubiquitous, slow evolving DNA virus. HSV-2 genomic diversity can be divided into two main groups: an African lineage and worldwide lineage. Competing hypotheses have been put forth to explain the history of HSV-2. HSV-2 may have originated in Africa and then followed the first wave of human migrati...
Article
Full-text available
Humans are considered as the main host for Mycobacterium leprae1, the aetiological agent of leprosy, but spillover has occurred to other mammals that are now maintenance hosts, such as nine-banded armadillos and red squirrels2,3. Although naturally acquired leprosy has also been described in captive nonhuman primates4–7, the exact origins of infect...
Preprint
Full-text available
In spring 2021, an increasing number of infections was observed caused by the hitherto rarely described SARS-CoV-2 variant A.27 in south-west Germany. From December 2020 to June 2021 this lineage has been detected in 31 countries. Phylogeographic analyses of A.27 sequences obtained from national and international databases reveal a global spread of...
Article
Full-text available
Distinct SARS-CoV-2 lineages, discovered through various genomic surveillance initiatives, have emerged during the pandemic following unprecedented reductions in worldwide human mobility. We here describe a SARS-CoV-2 lineage - designated B.1.620 - discovered in Lithuania and carrying many mutations and deletions in the spike protein shared with wi...
Article
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Seven years after the declaration of the first epidemic of Ebola virus disease in Guinea, the country faced a new outbreak—between 14 February and 19 June 2021—near the epicentre of the previous epidemic1,2. Here we use next-generation sequencing to generate complete or near-complete genomes of Zaire ebolavirus from samples obtained from 12 differe...
Chapter
The evolution of human-virus associations is usually reconstructed from contemporary patterns of genomic diversity. An intriguing, though still rarely implemented, alternative is to search for the genetic material of viruses in archeological and medical archive specimens to document evolution as it happened. In this chapter, we present lessons from...
Article
Full-text available
Here, we report on the increasing frequency of the SARS-CoV-2 lineage A.27 in Germany during the first months of 2021. Genomic surveillance identified 710 A.27 genomes in Germany as of 2 May 2021, with a vast majority identified in laboratories from a single German state (Baden-Wuerttemberg, n = 572; 80.5%). Baden-Wuerttemberg is located near the b...
Preprint
Full-text available
The 1918 influenza pandemic was the deadliest respiratory pandemic of the 20th century and determined the genomic make-up of subsequent human influenza A viruses (IAV). Here, we analyze the first 1918 IAV genomes from Europe and from the first, milder wave of the pandemic. 1918 IAV genomic diversity is consistent with local transmission and frequen...
Preprint
Full-text available
Many high-income countries have met the SARS-CoV-2 pandemic with overwhelming sequencing resources and have identified numerous distinct lineages, including some with notably altered biology. Over a year into the pandemic following unprecedented reductions in worldwide human mobility, distinct introduced lineages of SARS-CoV-2 without sequenced ant...
Preprint
SARS-CoV-2 variants of concern (VOC) and variants of interest (VOI) are heavily altering the COVID-19 pandemic's course due to their increased transmissibility, virulence and immune escape abilities. Data on their spread in western sub-Saharan Africa is however still scarce. We therefore sequenced viral genomes from SARS-CoV-2 cases identified in c...
Article
Full-text available
Significance Mammals harbor diverse communities of gut microbes. The assembly and evolution of the bacterial components of these communities are influenced by host evolutionary histories and social behavior. Little is known about the ecological and evolutionary origins of the phages infecting these bacteria. We explore drivers of phage community as...
Preprint
Full-text available
We determined near complete and complete monkeypox virus genomes in a shrew ( Crocidura littoralis ), two squirrels ( Funisciurus anerythrus, Funisciurus bayonii ), and produced shorter sequences from two rats ( Stochomys longicaudatus, Cricetomys sp. 2) originating from the Democratic Republic of the Congo. This suggests that a number of rodents b...
Article
Full-text available
Viruses closely related to human pathogens can reveal the origins of human infectious diseases. Human herpes simplexvirus type 1 (HSV-1) and type 2 (HSV-2) are hypothesized to have arisen via host-virus co-divergence and cross-species transmission. We report the discovery of novel herpes simplexviruses during a large-scale screening of fecal sample...
Article
Das Betacoronavirus SARS-CoV-2 gelangte höchstwahrscheinlich als zoonotischer Erreger gegen Ende 2019 in die menschliche Bevölkerung, vermutlich in Form einer einzelnen Transmission (monophyletischer Ursprung) aus einem noch immer unbekannten Tierreservoir (1, 2). Ebenso wie zum Beispiel bei Influenzaviren und HIV handelt es sich bei SARS-CoV-2 um...
Chapter
Full-text available
Over the last two decades, the viromes of our closest relatives, the African great apes (AGA), have been intensively studied. Comparative approaches have unveiled diverse evolutionary patterns, highlighting both stable host-virus associations over extended evolutionary timescales and much more recent viral emergence events. In this chapter, we summ...
Preprint
Full-text available
Humans are considered the main host for Mycobacterium leprae , the aetiologic agent of leprosy, but spill-over to other mammals such as nine-banded armadillos and red squirrels occurs. Although naturally acquired leprosy has also been described in captive nonhuman primates, the exact origins of infection remain unclear. Here, we report on leprosy-l...
Article
Full-text available
In ancient DNA research, the degraded nature of the samples generally results in poor yields of highly fragmented DNA; targeted DNA enrichment is thus required to maximize research outcomes. The three commonly used methods-array-based hybridization capture and in-solution capture using either RNA or DNA baits-have different characteristics that may...
Article
Full-text available
Many non-human primate species in sub-Saharan Africa are infected with Treponema pallidum subsp. pertenue, the bacterium causing yaws in humans. In humans, yaws is often characterized by lesions of the extremities and face, while T. pal-lidum subsp. pallidum causes venereal syphilis and is typically characterized by primary lesions on the genital,...
Article
Full-text available
Background Emerging antimicrobial resistance (AMR) challenges gonorrhoea treatment and requires surveillance. Aim This observational study describes the genetic diversity of Neisseria gonorrhoeae isolates in Germany from 2014 to 2017 and identifies N. gonorrhoeae multi-antigen sequence typing (NG-MAST) genogroups associated with AMR or some patien...
Article
Full-text available
Background: African swine fever virus (ASFV) is a most devastating pathogen affecting swine. In 2007, ASFV was introduced into Eastern Europe where it continuously circulates and recently reached Western Europe and Asia, leading to a socioeconomic crisis of global proportion. In Africa, where ASFV was first described in 1921, it is transmitted betw...
Article
Full-text available
It has been a long time since the world has experienced a pandemic with such a rapid devastating impact as the current COVID-19 pandemic. The causative agent, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is unusual in that it appears capable of infecting many different mammal species. As a significant proportion of people worldwide...
Article
Full-text available
The multimammate mouse (Mastomys natalensis; M. natalensis) serves as the main reservoir for the zoonotic arenavirus Lassa virus (LASV), and this has led to considerable investigation into the distribution of LASV and other related arena-viruses in this host species. In contrast to the situation with arenaviruses, the presence of other viruses in M...
Article
Full-text available
After the 2017 Ebola virus (EBOV) outbreak in Likati, a district in northern Democratic Republic of the Congo, we sampled small mammals from the location where the primary case-patient presumably acquired infection. None tested positive for EBOV RNA or antibodies against EBOV, highlighting the ongoing challenge in detecting animal reservoirs for EB...
Preprint
Full-text available
In ancient DNA research, the degraded nature of the samples generally results in poor yields of highly fragmented DNA, and targeted DNA enrichment is thus required to maximize research outcomes. The three commonly used methods – (1) array-based hybridization capture and in-solution capture using either (2) RNA or (3) DNA baits – have different char...
Article
Full-text available
Monkeypox is a viral zoonotic disease on the rise across endemic habitats. Despite the growing importance of monkeypox virus, our knowledge on its host spectrum and sylvatic maintenance is limited. Here, we describe the recent repeated emergence of monkeypox virus in a wild, human-habituated western chimpanzee (Pan troglodytes verus, hereafter chim...
Article
Older origins of measles virus Animal domestication by humans is thought to have given many pathogens an opportunity to invade a new host, and measles is one example of this. However, there is controversy about when measles emerged in humans, because the historical descriptions of measles are relatively recent (late ninth century CE). The controver...
Article
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The Trypanosomatidae are protozoan parasites that infect insects, plants, and animals and have evolved complex monoxenous (single host) and dixenous (two hosts) lifestyles. A number of species of Trypanosomatidae, including Leishmania spp., have evolved the capacity to survive within intracellular niches in vertebrate hosts. The adaptations, metabo...
Article
Full-text available
Yaws-like lesions are widely reported in wild African great apes, yet the causative agent has not been confirmed in affected animals. We describe yaws-like lesions in a wild chimpanzee in Guinea for which we demonstrate infection with Treponema pallidum subsp. pertenue. Assessing the conservation implications of this pathogen requires further resea...
Preprint
Full-text available
It has been a long time since the world has experienced a pandemic with such a rapid devastating impact as the current COVID-19 pandemic. The causative agent, the Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) is further unusual in that it appears capable of infecting many different mammal species. As a significant proportion of peopl...
Preprint
Full-text available
The evolutionary origins of human-associated bacteriophage communities are poorly understood. To address this question, we examined fecal phageomes of 23 wild non-human primate taxa, including multiple representatives of all the major primate radiations, and find relatives of the majority of human-associated phages. Primate taxa have distinct phage...
Article
Full-text available
Background: Squirrels (family Sciuridae) are globally distributed members of the order Rodentia with wildlife occurrence in indigenous and non-indigenous regions (as invasive species) and frequent presence in zoological gardens and other holdings. Multiple species introductions, strong inter-species competition as well as the recent discovery of a...
Preprint
Full-text available
Background: African swine fever virus (ASFV) is the only known DNA-arbovirus and a most devastating suid pathogen that, originating from a sylvatic cycle in Africa, has spread to eastern Europe and recently reached western Europe and Asia, leading to a socio-economic crisis of global proportion. However, since neither closely related viruses nor in...
Preprint
Full-text available
Many infectious diseases are thought to have emerged in humans after the Neolithic revolution. While it is broadly accepted that this also applies to measles, the exact date of emergence for this disease is controversial. Here, we sequenced the genome of a 1912 measles virus and used selection-aware molecular clock modeling to determine the diverge...
Article
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Research is a highly competitive profession where evaluation plays a central role; journals are ranked and individuals are evaluated based on their publication number, the number of times they are cited and their h-index. Yet such evaluations are often done in inappropriate ways that are damaging to individual careers, particularly for young schola...
Chapter
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Microbial communities impact a variety of processes including a host’s ability to access nutrients and maintain health, but can also include pathogens with a detrimental impact. Since the spread of anatomically modern humans across the planet, we have drastically changed the way we live (e.g., agriculture, antibiotic usage). These changes presumabl...
Preprint
Full-text available
Background: Increasing evidence suggests many non-human primate (NHP) species in sub-Saharan Africa are infected with Treponema pallidum subsp. pertenue (TPE), the bacterium causing yaws in humans. In humans, yaws is characterized by lesions of the extremities and face, while Treponema pallidum subsp. pallidum (TPA) causes venereal syphilis and is...
Article
Full-text available
To date, only two rodent-borne hantaviruses have been detected in sub-Saharan Africa. Here, we report the detection of a yet unknown hantavirus in a Natal mastomys (Mastomys natalensis) in Méliandou, Guinea, in 2014. The phylogenetic placement of this virus suggests that it might represent a cross-order spillover event from an unknown bat or eulipo...
Article
Full-text available
As the phylogenetic organization of mammalian polyomaviruses is complex and currently incompletely resolved, we aimed at a deeper insight into their evolution by identifying polyomaviruses in host orders and families that have either rarely or not been studied. Sixteen unknown and two known polyomaviruses were identified in animals that belong to 5...
Article
Full-text available
Despite their ubiquity, in most cases little is known about the impact of eukaryotic parasites on their mammalian hosts. Comparative approaches provide a powerful method to investigate the impact of parasites on host ecology and evolution, though two issues are critical for such efforts: controlling for variation in methods of identifying parasites...
Article
Full-text available
Metabarcoding of vertebrate DNA found in invertebrates (iDNA) represents a potentially powerful tool for monitoring biodiversity. Preliminary evidence suggests fly iDNA biodiversity assessments compare favorably with established approaches such as camera trapping or line transects. To assess whether fly-derived iDNA is consistently useful for biodi...
Article
Full-text available
Despite their ubiquity, in most cases little is known about the impact of eukaryotic parasites on their mammalian hosts. Comparative approaches provide a powerful method to investigate the impact of parasites on host ecology and evolution, though two issues are critical for such efforts: controlling for variation in methods of identifying parasites...
Article
Full-text available
Herpesviruses are thought to have evolved in very close association with their hosts. This is notably the case for cytomegaloviruses (CMVs; genus Cytomegalovirus) infecting primates, which exhibit a strong signal of co-divergence with their hosts. Some herpesviruses are however known to have crossed species barriers. Based on a limited sampling of...
Article
Full-text available
Living in groups provides benefits but incurs costs such as attracting disease vectors. For example, synanthropic flies associate with human settlements, and higher fly densities increase pathogen transmission. We investigated whether such associations also exist in highly mobile non‐human primate groups (NHP). We studied flies in a group of wild s...
Article
Full-text available
New technologies enable viral discovery in a diversity of hosts, providing insights into viral evolution. We used one such approach, the virome capture sequencing for vertebrate viruses (VirCapSeq-VERT) platform, on 21 samples originating from six dead Maxwell's duikers (Philantomba maxwellii) from Taï National Park, Côte d'Ivoire. We detected the...
Article
Bats are considered a reservoir species for Ebola viruses, but non-human primates (NHP) have represented a source of infection in several outbreaks in humans. Here we report serological screening of blood or fecal samples from monkeys (n=2,322) and apes (n=2,327). Thirty-six NHP species from Cameroon, Democratic Republic of Congo and Ivory Coast we...
Article
Full-text available
The bacterium Treponema pallidum (TP) causes human syphilis (subsp. pallidum; TPA), bejel (subsp. endemicum; TEN), and yaws (subsp. pertenue; TPE)1. Although syphilis has reached a worldwide distribution2, bejel and yaws have remained endemic diseases. Bejel affects individuals in dry areas of Sahelian Africa and Saudi Arabia, whereas yaws affects...