Alexandre Hassanin

Alexandre Hassanin
Sorbonne University | UPMC · Institut de SYstématique, Évolution, Biodiversité (ISYEB)

PhD

About

197
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Publications

Publications (197)
Article
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Historically, for more than one and a half centuries, only one so-called “long-legged bat tick” species, i.e., Ixodes vespertilionis Koch was known to science. However, during the past decade, it was recognized on a molecular basis that long-legged ixodid ticks associated with bats may represent at least six species. Of these, until recently, five...
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Previous studies on horseshoe bats ( Rhinolophus spp.) have described many coronaviruses related to SARS‐CoV ( SARSCoVr ) in China and only a few coronaviruses related to SARS‐CoV‐2 ( SARSCoV2r ) in Yunnan (southern China), Cambodia, Laos and Thailand. Here, we report the results of several field missions carried out in 2017, 2021 and 2022 across V...
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Swine acute diarrhoea syndrome coronavirus (SADS-CoV; Coronaviridae, Rhinacovirus) was detected in 2017 in Guangdong Province (China), where it caused high mortality rates in piglets. According to previous studies, SADS-CoV evolved from horseshoe bat reservoirs. Here, we report the first five Rhinacovirus genomes sequenced in horseshoe bats from Vi...
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Across 133 confirmed mpox zoonotic index cases reported during 1970-2021 in Africa, cases occurred year-round near the equator, where climate is consistent. However, in tropical regions of the northern hemisphere under a dry/wet season cycle, cases occurred seasonally. Our findings further support the seasonality of mpox zoonotic transmission risk.
Preprint
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Previous studies on horseshoe bats ( Rhinolophus spp .) have described many coronaviruses related to SARS-CoV (SARSCoVr) in China and only a few coronaviruses related to SARS-CoV-2 ( SARSCoV2r ) in Yunnan, Cambodia, Laos and Thailand. Here, we report the results of several field missions carried out in 2017, 2021 and 2022 across Vietnam during whic...
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This study integrates analyses of mitochondrial DNA sequences and morphological and acoustic data to re-evaluate the taxonomic status of Rhinolophus rex rex , R. r. paradoxolophus and R. schnitzleri throughout their distribution ranges. Based on a dense geographic sampling of specimens hitherto referred to these taxa and contrary to the current tax...
Article
Phylogeographies of African mammals reveal patterns that correlate with Pleistocene environmental fluctuations and geographical barriers, which may affect species differently according to their habitat preferences and dispersal capabilities. The marsh mongoose Atilax paludinosus, a widely distributed African carnivoran, is a good model to compare w...
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Several bat-associated circoviruses and circular rep-encoding single-stranded DNA (CRESS DNA) viruses have been described, but the exact diversity and host species of these viruses are often unknown. Our goal was to describe the diversity of bat-associated circoviruses and cirliviruses, thus, 424 bat samples from more than 80 species were collected...
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Previous human cases or epidemics have suggested that Monkeypox virus (MPXV) can be transmitted through contact with animals of African rainforests. Although MPXV has been identified in many mammal species, most are likely secondary hosts, and the reservoir host has yet to be discovered. In this study, we provide the full list of African mammal gen...
Article
The phylogeny of sea spiders has been debated for more than a century. Despite several molecular studies in the last twenty years, interfamilial relationships remain uncertain. In the present study, relationships within Pycnogonida are examined in the light of a new dataset composed of 160 mitochondrial genomes (including 152 new sequences) and 130...
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Phylogenetic trees of coronaviruses are difficult to interpret because they undergo frequent genomic recombination. Here, we propose a new method, coloured genomic bootstrap (CGB) barcodes, to highlight the polyphyletic origins of human sarbecoviruses and understand their host and geographic origins. The results indicate that SARS-CoV and SARS-CoV-...
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This study presents the inventory of sea spiders (Pycnogonida) sampled during the Madibenthos Expedition in Martinique (West Indies). Species were discriminated leaning on morphological and molecular data. A total of 761 specimens are classified in 72 species, 16 genera and nine families. Thirteen new species are described: Ammothella dirbergi sp....
Preprint
Phylogenetic trees of coronaviruses are difficult to interpret because they undergo frequent ge-nomic recombination. Here, we propose a new method, named coloured genomic bootstrap (CGB) barcodes, to highlight the polyphyletic origins of human sarbecoviruses and understand their host and geographic ori-gins. The results indicate that SARS-CoV and S...
Preprint
Full-text available
Background: Previous human cases or epidemics have suggested that Monkeypox virus (MPXV) can be transmitted through contacts with animals of African rainforests. Although MPXV has been identified in many mammal species, most are likely secondary hosts and the reservoir host has yet to be discovered. Methodology/Principal Findings: In this study, we...
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We analyzed monkeypox disease surveillance in Central African Republic (CAR) during 2001-2021. Surveillance data show 95 suspected outbreaks, 40 of which were confirmed as monkeypox, comprising 99 confirmed and 61 suspected monkeypox cases. After 2018, CAR's annual rate of confirmed outbreaks increased, and 65% of outbreaks occurred in 2 forested r...
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Genomic data for wild species of the genus Bubalus (Asian buffaloes) are still lacking while several whole genomes are currently available for domestic water buffaloes. To address this, we sequenced the genome of a wild endangered dwarf buffalo, the lowland anoa (Bubalus depressicornis), produced a draft genome assembly, and made comparison to publ...
Preprint
Genomic data for wild species of the genus Bubalus (Asian buffaloes) are still lacking while several whole genomes are currently available for domestic water buffaloes. To address this, we sequenced the genome of a wild endangered dwarf buffalo, the lowland anoa ( Bubalus depressicornis ), produced a draft genome assembly, and made comparison to pu...
Article
The subgenus Sarbecovirus includes two human viruses, SARS-CoV and SARS-CoV-2, respectively responsible for the SARS epidemic and COVID-19 pandemic, as well as many bat viruses and two pangolin viruses. Here, the synonymous nucleotide composition (SNC) of Sarbecovirus genomes was analysed by examining third codon-positions, dinucleotides, and degen...
Article
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Recombination creates mosaic genomes containing regions with mixed ancestry, and the accumulation of such events over time can complicate greatly many aspects of evolutionary inference. Here, we developed a sliding window bootstrap (SWB) method to generate genomic bootstrap (GB) barcodes to highlight the regions supporting phylogenetic relationship...
Article
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Bats have been recognized as an exceptional viral reservoir, especially for coronaviruses. At least three bat zoonotic coronaviruses (SARS-CoV, MERS-CoV and SARS-CoV-2) have been shown to cause severe diseases in humans and it is expected more will emerge. One of the major features of CoVs is that they are all highly prone to recombination. An extr...
Article
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Bats have been recognized as an exceptional viral reservoir, especially for coronaviruses. At least three bat zoonotic coronaviruses (SARS-CoV, MERS-CoV and SARS-CoV-2) have been shown to cause severe diseases in humans and it is expected more will emerge. One of the major features of CoVs is that they are all highly prone to recombination. An extr...
Article
Full-text available
Knowledge of the origin and reservoir of the coronavirus responsible for the ongoing COVID-19 pandemic is still fragmentary. To date, the closest relatives to SARS-CoV-2 have been detected in Rhinolophus bats sampled in the Yunnan province, China. Here we describe the identification of SARS-CoV-2 related coronaviruses in two Rhinolophus shameli bat...
Preprint
Full-text available
Viruses closely related to SARS-CoV-2, the virus responsible for the Covid-19 pandemic, have previously been identified in several Sunda pangolins (Manis javanica) seized in Guangdong and Guangxi provinces of China1-4. The virus extracted from Guangdong pangolins is particularly intriguing as the amino-acid sequence of the receptor binding domain o...
Preprint
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The subgenus Sarbecovirus includes two human viruses, SARS-CoV and SARS-CoV-2, respectively responsible for the SARS epidemic and COVID-19 pandemic, as well as many bat viruses and two pangolin viruses. Here, the synonymous nucleotide composition (SNC) of Sarbecovirus genomes was analysed by examining third codon-positions, dinucleotides, and degen...
Article
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The Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) is the causal agent of the coronavirus disease 2019 (COVID-19) pandemic. To date, viruses closely related to SARS-CoV-2 have been reported in four bat species: Rhinolophus acuminatus , Rhinolophus affinis , Rhinolophus malayanus , and Rhinolophus shameli . Here, we analysed 343 sequen...
Article
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Monkeypox is an emerging infectious disease, which has a clinical presentation similar to smallpox. In the two past decades, Central Africa has seen an increase in the frequency of cases, with many monkeypox virus (MPXV) isolates detected in the Democratic Republic of Congo (DRC) and the Central African Republic (CAR). To date, no complete MPXV vir...
Preprint
Full-text available
To date, viruses closely related to SARS-CoV-2 have been reported in four bat species: Rhinolophus acuminatus, Rhinolophus affinis, Rhinolophus malayanus, and Rhinolophus shameli. Here, we analysed 343 sequences of the mitochondrial cytochrome c oxidase subunit 1 gene (CO1) from georeferenced bats of the four Rhinolophus species identified as reser...
Article
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To date, viruses closely related to SARS-CoV-2 have been reported in four bat species: Rhi-nolophus acuminatus, Rhinolophus affinis, Rhinolophus malayanus, and Rhinolophus shameli. Here, we analysed 343 sequences of the mitochondrial cytochrome c oxidase subunit 1 gene (CO1) from georeferenced bats of the four Rhinolophus species identified as rese...
Article
Two types of domestic water buffalo are currently recognized: the river buffalo from the Indian subcontinent and Mediterranean countries and the swamp buffalo from China and Southeast Asia. To test the hypothesis of two separate species of water buffalo, we sequenced the genome of the lowland anoa, Bubalus depressicornis, which is a dwarf wild buff...
Article
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The order Carnivora, which currently includes 296 species classified into 16 families, is distributed across all continents. The phylogeny and the timing of diversification of members of the order are still a matter of debate. Here, complete mitochondrial genomes were analysed to reconstruct the phylogenetic relationships and to estimate divergence...
Preprint
Full-text available
Knowledge of the origin and reservoir of the coronavirus responsible for the ongoing COVID-19 pandemic is still fragmentary. To date, the closest relatives to SARS-CoV-2 have been detected in Rhinolophus bats sampled in the Yunnan province, China. Here we describe the identification of SARS-CoV-2 related coronaviruses in two Rhinolophus shameli bat...
Article
Full-text available
Viruses similar to the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) have been discovered in bats of the genus Rhinolophus and in the Sunda pangolin, Manis javanica Desmarest, 1822, suggesting that these animals have played a key role in the emergence of the Covid-19 outbreak in the city of Wuhan, China. In this paper, we review the...
Article
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Yellow house bats (Scotophilus) have been known for centuries as a widespread genus of vesper bats in the Indomalayan Region. Despite this, their taxonomic status and phylogeographical patterns remain unclear due to differing criteria employed by early taxonomists and inconsistencies between morphological and molecular assessments. To address these...
Article
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Here, we sequenced the complete mitochondrial genome of 29 Egyptian river buffaloes collected in two breeding stations of Egypt. The genome is 16,357–16,359 base pairs in length and contains the 37 genes found in a typical mammalian genome. The overall base composition is A: 33.1%, C: 26.6%, G: 13.9%, and T: 26.4%. Our analyses confirm that the mit...
Preprint
Full-text available
The order Carnivora, which currently includes 296 species classified into 16 families, is distributed across all continents. The phylogeny and the timing of diversifications are still a matter of debate. Here, complete mitochondrial genomes were analysed to reconstruct the phylogenetic relationships and to estimate divergence times among species of...
Article
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The present corrigendum corrects errors that occurred in: Petzold A., Magnant A.-S., Edderai D., Chardonnet B., Rigoulet J., Saint-Jalme M. & Hassanin A. 2020. First insights into past biodiversity of giraffes based on mitochondrial sequences from museum specimens. European Journal of Taxonomy 703: 1–33. https://doi.org/10.5852/ejt.2020.703
Article
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Intensified exploration of sub-Saharan Africa during the 18th and 19th centuries led to many newly described giraffe subspecies. Several populations described at that time are now extinct, which is problematic for a full understanding of giraffe taxonomy. In this study, we provide mitochondrial sequences for 41 giraffes, including 19 museum specime...
Preprint
Full-text available
Viruses closely related to SARS-CoV-2, which is the virus responsible of the Covid-19 pandemic, were sequenced in several Sunda pangolins (Manis javanica) seized in the Guangdong and Guangxi provinces of China between 2017 and 2019. These viruses belong to two lineages: one from Guangdong (GD/P) and the other from Guangxi (GX/P). The GD/P viruses a...
Article
Members of the family Pteropodidae, also known as Old World fruit bats, are represented in Africa by 14 genera and 44 species. Here, we sequenced 67 complete mitochondrial genomes from African and Asian pteropodids to better understand the evolutionary history of the subfamily Rousettinae, which includes most of the African species. An increased fr...
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Molecular data are now commonly used in taxonomy for delimiting cryptic species. In the case of giraffes, which were treated as a single species (Giraffa camelopardalis) during half of a century, several molecular studies have suggested a splitting into four to seven species, but the criteria applied for taxonomic delimitation were not fully descri...
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Domestic cattle have contributed both to the rise of civilizations and the global loss of biodiversity, but the timing and mechanism of their domestication history remain to be fully understood. Palaeogenetics, which can now explore the target of human selection in the genome, have revolutionized our understanding of cattle domestication. However,...
Preprint
Full-text available
Molecular data are now commonly used in taxonomy for delimiting cryptic species. In the case of giraffes, which were treated as a single species (Giraffa camelopardalis) during half of a century, several molecular studies have suggested a splitting into four to seven species, but the criteria applied for taxonomic delimitation were not fully descri...
Article
The marine biodiversity of the tropical northwestern Atlantic (TNWA) has been explored by many great naturalist expeditions. After more than one century of marine exploration, how well do we know its biodiversity? As a poorly studied taxon, sea spiders (Arthropoda: Pycnogonida Latreille, 1810) are excellent candidates to address this issue. Here, w...
Article
Sea spiders (Pycnogonida) are strange arthropods characterized by a unique morphology, including reduced body, egg-carrying appendages and a proboscis. This peculiar body plan dates at least as early as the first undoubted occurrence of the group, 425 million years ago in the Silurian. All extant species belong to the order Pantopoda, characterized...
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We undertook a comparative phylogeographic study using molecular, morphological and morphometric approaches to address systematic issues in bats of the Kerivoula hardwickii complex in Asia. Our phylogenetic reconstructions using DNA sequences of two mitochondrial and seven nuclear genes reveal a distinct clade containing four small-sized species (K...
Article
The bushbuck is the most widespread bovid species in Africa. Previous mitochondrial studies have revealed a polyphyletic pattern suggesting the possible existence of two distinct species. To assess this issue, we have sequenced 16 nuclear genes and one mitochondrial fragment (cytochrome b gene + control region) for most species of the tribe Tragela...
Article
The nearly cosmopolitan tribe Desmodieae (Fabaceae) includes many important genera for medicine and forage. However, the phylogenetic relationships among the infratribal groups circumscribed using morphological traits are still poorly known. In this study, we used chloroplast (rbcL, psbA-trnH) and nuclear (ITS-1) DNA sequences to investigate the mo...
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The genus Glauconycteris Dobson, 1875 currently contains 12 species of butterfly bats, all endemic to sub-Saharan Africa. Most species are rarely recorded, with half of the species known from less than six geographic localities. The taxonomic status of several species remains problematic. Here, we studied the systematics of butterfly bats using bot...
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The Malagasy carnivorans (Eupleridae) comprise seven genera and up to ten species, depending on the authority, and, within the past decades, two new taxa have been described. The family is divided into two subfamilies, the Galidiinae, mongoose-like animals, and the Euplerinae, with diverse body forms. To verify the taxonomic status of Galidiinae sp...
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The family Ammotheidae is the most diversified group of the class Pycnogonida, with 297 species described in 20 genera. Its monophyly and intergeneric relationships have been highly debated in previous studies. Here, we investigated the phylogeny of Ammotheidae using specimens from poorly studied areas. We sequenced the mitochondrial gene encoding...
Article
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Due to the difficulty in obtaining samples, the systematics of the Hemigalinae civets has not been fully resolved. The aim of this study was to clarify the relationships of the species and the intraspecific diversity within this subfamily, and to explore the environmental factors that might have affected its evolution. Using two mitochondrial and t...
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The taxonomy of sub-Saharan small insectivore bats of the family Vespertilionidae is unresolved and currently five named species of the genus Neoromicia are recognized from southern Africa, with N. melckorum considered a synonym of N. capensis. Since several years, the name “N. cf. melckorum” has been used in the literature to designate an apparent...
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In Southeast Asia, bats of the genus Tylonycteris Peters, 1872 have traditionally been classified into two wide-ranging species, T. pachypus (Temminck, 1840) and T. robustula Thomas, 1915. Our comparative phylogeographic analyses based on two mitochondrial and seven nuclear genes, combined with our multivariate morphological analyses, show that the...
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The pied butterfly bat, Glauconycteris superba, is endemic to the tropical forest zone of Africa, where it was previously known from only five specimens. Here we report the capture of 10 individuals in two localities of the Democratic Republic of the Congo (Mbiye Island and Yoko forest reserve), and we present the first acoustic data of the species...
Article
South-East Asia is a hot spot for emerging zoonotic diseases, and bats have been recognized as hosts for a large number of zoonotic viruses such as Severe Acute Respiratory Syndrome (SARS), responsible for acute respiratory syndrome outbreaks. Thus, it is important to expand our knowledge of the presence of viruses in bats which could represent a r...
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The question whether taxonomic descriptions naming new animal species without type specimen(s) deposited in collections should be accepted for publication by scientific journals and allowed by the Code has already been discussed in Zootaxa (Dubois & Nemésio 2007; Donegan 2008, 2009; Nemésio 2009a–b; Dubois 2009; Gentile & Snell 2009; Minelli 2009;...
Data
This plot is not part of the published stance but derives from it. The plot shows the number of authors by geographic region (courtesy of Dr. Diego Astua).
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Both Ebolavirus and Marburgvirus were detected in several fruit bat species of the family Pteropodidae, suggesting that this taxon plays a key role in the life cycle of filoviruses. After four decades of Zaire Ebolavirus (ZEBOV) outbreaks in Central Africa, the virus was detected for the first time in West Africa in 2014. To better understand the r...
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Significance Understanding the evolutionary history of Haemosporidian parasites would help to understand human malaria evolution. Nevertheless, Haemosporidia parasite diversity in bats remains largely unstudied. In addition, some cases of unsuccessful PCR amplification of cytochrome b , the most widely used molecular marker to characterize Haemospo...
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Abstract The complete mitochondrial genome of the Spotted Linsang, Prionodon pardicolor, was sequenced using overlapping PCR products. The genome is 16,718 base pairs in length and contains the 37 genes found in a typical mammalian genome: 13 protein-coding genes, 22 transfer RNA genes and 2 ribosomal RNA genes. The overall base composition on the...
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Abstract The complete mitochondrial genome of the boky-boky, Mungotictis decemlineata, was sequenced using overlapping PCRs. The genome is 16,910 base pairs in length and contains the 37 genes found in a typical mammalian genome: 13 protein-coding genes, 22 transfer RNA genes and 2 ribosomal RNA genes. The overall base composition on the L-strand i...
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Trident bats found in mainland Southeast Asia are currently subsumed into a single species, Aselliscus stoliczkanus. In this study, we examined morphological and genetic data from different populations from Southeast Asia, with a special focus on specimens from Vietnam. Our analyses support the existence of a further species of Aselliscus in northe...