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Article: Rapid reconstruction of porcine reproductive and respiratory syndrome virus using synthetic DNA fragments

Mélade, Julien / Piorkowski, Géraldine / Bouzidi, Hawa Sophia / Medawar, Alain / Raffy, Claudine / de Lamballerie, Xavier / Nougairède, Antoine

Computational and Structural Biotechnology Journal. 2021, v. 19

2021

Abstract: Porcine reproductive and respiratory syndrome virus (PRRSV) is one of the most challenging infectious disease of pig populations causing devastating economic loss to swine industry. Reverse genetics allow to engineer modified viruses such attenuated ... ...

Abstract	Porcine reproductive and respiratory syndrome virus (PRRSV) is one of the most challenging infectious disease of pig populations causing devastating economic loss to swine industry. Reverse genetics allow to engineer modified viruses such attenuated strains for vaccine development. Some reverse genetic systems were described for PRRSVs but, due to genome complexity of PRRSVs, construction and modification of such systems remain laborious and time-consuming.In this study, we described a reverse genetics approach based on the “Infectious-Subgenomic Amplicons” (ISA) method to rescue infectious PRRSV particles. Permissive cells were transfected with 4 overlapping synthetic DNA fragments covering the entire genome of PRRSV which allowed the rapid reconstruction of the complete virus genome and the subsequent generation of infectious wild-type particles within days.The ISA method represent a rapid alternative of conventional reverse genetic systems. This method will help to generate genetically modified and attenuated strains for the development of sanitary countermeasures in the future.
Keywords	DNA ; biotechnology ; financial economics ; porcine reproductive and respiratory syndrome ; pork industry ; reverse genetics ; swine ; vaccine development ; viral genome ; viruses
Language	English
Size	p. 5108-5116.
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	2694435-2
ISSN	2001-0370
ISSN	2001-0370
DOI	10.1016/j.csbj.2021.08.040
Database	NAL-Catalogue (AGRICOLA)

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Article: Rapid reconstruction of porcine reproductive and respiratory syndrome virus using synthetic DNA fragments.

Mélade, Julien / Piorkowski, Géraldine / Bouzidi, Hawa Sophia / Medawar, Alain / Raffy, Claudine / de Lamballerie, Xavier / Nougairède, Antoine

Computational and structural biotechnology journal

2021 Volume 19, Page(s) 5108–5116

Abstract	Porcine reproductive and respiratory syndrome virus (PRRSV) is one of the most challenging infectious disease of pig populations causing devastating economic loss to swine industry. Reverse genetics allow to engineer modified viruses such attenuated strains for vaccine development. Some reverse genetic systems were described for PRRSVs but, due to genome complexity of PRRSVs, construction and modification of such systems remain laborious and time-consuming. In this study, we described a reverse genetics approach based on the "Infectious-Subgenomic Amplicons" (ISA) method to rescue infectious PRRSV particles. Permissive cells were transfected with 4 overlapping synthetic DNA fragments covering the entire genome of PRRSV which allowed the rapid reconstruction of the complete virus genome and the subsequent generation of infectious wild-type particles within days. The ISA method represent a rapid alternative of conventional reverse genetic systems. This method will help to generate genetically modified and attenuated strains for the development of sanitary countermeasures in the future.
Language	English
Publishing date	2021-09-01
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2694435-2
ISSN	2001-0370
ISSN	2001-0370
DOI	10.1016/j.csbj.2021.08.040
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Article: Predicting the Presence of Leptospires in Rodents from Environmental Indicators Opens Up Opportunities for Environmental Monitoring of Human Leptospirosis

Biscornet, Leon / Révillion, Christophe / Jégo, Sylvaine / Lagadec, Erwan / Gomard, Yann / Le Minter, Gildas / Rocamora, Gérard / Guernier-Cambert, Vanina / Mélade, Julien / Dellagi, Koussay / Tortosa, Pablo / Herbreteau, Vincent

Remote Sensing. 2021 Jan. 19, v. 13, no. 2

2021

Abstract: Leptospirosis, an environmental infectious disease of bacterial origin, is the infectious disease with the highest associated mortality in Seychelles. In small island territories, the occurrence of the disease is spatially heterogeneous and a better ... ...

Abstract	Leptospirosis, an environmental infectious disease of bacterial origin, is the infectious disease with the highest associated mortality in Seychelles. In small island territories, the occurrence of the disease is spatially heterogeneous and a better understanding of the environmental factors that contribute to the presence of the bacteria would help implement targeted control. The present study aimed at identifying the main environmental parameters correlated with animal reservoirs distribution and Leptospira infection in order to delineate habitats with highest prevalence. We used a previously published dataset produced from a large collection of rodents trapped during the dry and wet seasons in most habitats of Mahé, the main island of Seychelles. A land use/land cover analysis was realized in order to describe the various environments using SPOT-5 images by remote sensing (object-based image analysis). At each sampling site, landscape indices were calculated and combined with other geographical parameters together with rainfall records to be used in a multivariate statistical analysis. Several environmental factors were found to be associated with the carriage of leptospires in Rattus rattus and Rattus norvegicus, namely low elevations, fragmented landscapes, the proximity of urbanized areas, an increased distance from forests and, above all, increased precipitation in the three months preceding trapping. The analysis indicated that Leptospira renal carriage could be predicted using the species identification and a description of landscape fragmentation and rainfall, with infection prevalence being positively correlated with these two environmental variables. This model may help decision makers in implementing policies affecting urban landscapes and/or in balancing conservation efforts when designing pest control strategies that should also aim at reducing human contact with Leptospira-laden rats while limiting their impact on the autochthonous fauna.
Keywords	Leptospira ; Rattus norvegicus ; Rattus rattus ; altitude ; bacteria ; correlation ; data collection ; decision making ; environmental indicators ; environmental monitoring ; fauna ; forests ; habitat fragmentation ; habitats ; humans ; image analysis ; infection ; issues and policy ; land cover ; land use ; landscapes ; leptospirosis ; models ; mortality ; multivariate analysis ; occurrence ; pest control ; prediction ; prevalence ; rain ; rats ; remote sensing ; sampling ; species identification ; trapping ; urban areas ; wet season ; Seychelles
Language	English
Dates of publication	2021-0119
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
Note	NAL-light
ZDB-ID	2513863-7
ISSN	2072-4292
ISSN	2072-4292
DOI	10.3390/rs13020325
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Extracellular Vesicles Are Conveyors of the NS1 Toxin during Dengue Virus and Zika Virus Infection.

Safadi, Daed El / Lebeau, Grégorie / Lagrave, Alisé / Mélade, Julien / Grondin, Lauriane / Rosanaly, Sarah / Begue, Floran / Hoareau, Mathilde / Veeren, Bryan / Roche, Marjolaine / Hoarau, Jean-Jacques / Meilhac, Olivier / Mavingui, Patrick / Desprès, Philippe / Viranaïcken, Wildriss / Krejbich-Trotot, Pascale

Viruses

2023 Volume 15, Issue 2

Abstract: Extracellular vesicles (EVs), produced during viral infections, are of emerging interest in understanding infectious processes and host-pathogen interactions. EVs and exosomes in particular have the natural ability to transport nucleic acids, proteins, ... ...

Abstract	Extracellular vesicles (EVs), produced during viral infections, are of emerging interest in understanding infectious processes and host-pathogen interactions. EVs and exosomes in particular have the natural ability to transport nucleic acids, proteins, and other components of cellular or viral origin. Thus, they participate in intercellular communication, immune responses, and infectious and pathophysiological processes. Some viruses are known to hijack the cell production and content of EVs for their benefit. Here, we investigate whether two pathogenic flaviviruses i.e., Zika Virus (ZIKV) and Dengue virus (DENV2) could have an impact on the features of EVs. The analysis of EVs produced by infected cells allowed us to identify that the non-structural protein 1 (NS1), described as a viral toxin, is associated with exosomes. This observation could be confirmed under conditions of overexpression of recombinant NS1 from each flavivirus. Using different isolation methods (i.e., exosome isolation kit, size exclusion chromatography, Polyethylene Glycol enrichment, and ELISA capture), we showed that NS1 was present as a dimer at the surface of excreted exosomes, and that this association could occur in the extracellular compartment. This finding could be of major importance in a physiological context. Indeed, this capacity of NS1 to address EVs and its implication in the pathophysiology during Dengue or Zika diseases should be explored. Furthermore, exosomes that have demonstrated a natural capacity to vectorize NS1 could serve as useful tools for vaccine development.
MeSH term(s)	Humans ; Dengue Virus ; Exosomes ; Extracellular Vesicles ; Zika Virus ; Zika Virus Infection ; Viral Nonstructural Proteins/metabolism
Chemical Substances	NS1 protein, zika virus ; Viral Nonstructural Proteins
Language	English
Publishing date	2023-01-27
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v15020364
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Article ; Online: A simple reverse genetics method to generate recombinant coronaviruses.

Mélade, Julien / Piorkowski, Géraldine / Touret, Franck / Fourié, Toscane / Driouich, Jean-Sélim / Cochin, Maxime / Bouzidi, Hawa Sophia / Coutard, Bruno / Nougairède, Antoine / de Lamballerie, Xavier

EMBO reports

2022 Volume 23, Issue 5, Page(s) e53820

Abstract: Engineering recombinant viruses is a pre-eminent tool for deciphering the biology of emerging viral pathogens such as the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, the large size of coronavirus genomes renders the current ... ...

Abstract	Engineering recombinant viruses is a pre-eminent tool for deciphering the biology of emerging viral pathogens such as the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, the large size of coronavirus genomes renders the current reverse genetics methods challenging. Here, we describe a simple method based on "infectious subgenomic amplicons" (ISA) technology to generate recombinant infectious coronaviruses with no need for reconstruction of the complete genomic cDNA and apply this method to SARS-CoV-2 and also to the feline enteric coronavirus. In both cases we rescue wild-type viruses with biological characteristics similar to original strains. Specific mutations and fluorescent red reporter genes can be readily incorporated into the SARS-CoV-2 genome enabling the generation of a genomic variants and fluorescent reporter strains for in vivo experiments, serological diagnosis, and antiviral assays. The swiftness and simplicity of the ISA method has the potential to facilitate the advance of coronavirus reverse genetics studies, to explore the molecular biological properties of the SARS-CoV-2 variants, and to accelerate the development of effective therapeutic reagents.
MeSH term(s)	Animals ; Antiviral Agents ; COVID-19/genetics ; Cats ; Reverse Genetics ; SARS-CoV-2/genetics
Chemical Substances	Antiviral Agents
Language	English
Publishing date	2022-03-03
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2020896-0
ISSN	1469-3178 ; 1469-221X
ISSN (online)	1469-3178
ISSN	1469-221X
DOI	10.15252/embr.202153820
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Article ; Online: Fatal underhanded chronic enterovirus infection associated with anti-CD20 monotherapy for central nervous system demyelinating disease.

Luciani, Léa / Ninove, Laetitia / Zandotti, Christine / Chalvignac, Virginie / Lagier, David / Baume, Julien / Mélade, Julien / Piorkowski, Géraldine / Coutard, Bruno / Lepidi, Hubert / Pelletier, Jean / Audoin, Bertrand / Rico-Lamy, Audrey / Nougairède, Antoine

Multiple sclerosis (Houndmills, Basingstoke, England)

2020 Volume 27, Issue 2, Page(s) 320–323

Abstract: We report a fatal case of coxsackievirus B4 chronic infection in a 30-year-old woman with a diagnosis of myelin oligodendrocyte glycoprotein antibody-associated disorder controlled by rituximab monotherapy for 3 years. Initially presenting as self- ... ...

Abstract	We report a fatal case of coxsackievirus B4 chronic infection in a 30-year-old woman with a diagnosis of myelin oligodendrocyte glycoprotein antibody-associated disorder controlled by rituximab monotherapy for 3 years. Initially presenting as self-limited meningitis, the infection remained silent for 8 months before the sudden onset of fulminant myocarditis. Analysis of the complete genome showed that the same virus was responsible for both episodes.
MeSH term(s)	Adult ; Autoantibodies ; Central Nervous System ; Enterovirus ; Enterovirus Infections/drug therapy ; Female ; Humans ; Myelin-Oligodendrocyte Glycoprotein ; Neuromyelitis Optica
Chemical Substances	Autoantibodies ; Myelin-Oligodendrocyte Glycoprotein
Language	English
Publishing date	2020-06-25
Publishing country	England
Document type	Case Reports ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1290669-4
ISSN	1477-0970 ; 1352-4585
ISSN (online)	1477-0970
ISSN	1352-4585
DOI	10.1177/1352458520923978
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Article ; Online: (with research data) Serological Evidence of Lyssaviruses among Bats on Southwestern Indian Ocean Islands.

Mélade, Julien / McCulloch, Stewart / Ramasindrazana, Beza / Lagadec, Erwan / Turpin, Magali / Pascalis, Hervé / Goodman, Steven M / Markotter, Wanda / Dellagi, Koussay

PloS one

2016 Volume 11, Issue 8, Page(s) e0160553

Abstract: We provide serological evidence of lyssavirus circulation among bats on southwestern Indian Ocean (SWIO) islands. A total of 572 bats belonging to 22 species were collected on Anjouan, Mayotte, La Réunion, Mauritius, Mahé and Madagascar and screened by ... ...

Abstract	We provide serological evidence of lyssavirus circulation among bats on southwestern Indian Ocean (SWIO) islands. A total of 572 bats belonging to 22 species were collected on Anjouan, Mayotte, La Réunion, Mauritius, Mahé and Madagascar and screened by the Rapid Fluorescent Focus Inhibition Test for the presence of neutralising antibodies against the two main rabies related lyssaviruses circulating on the African continent: Duvenhage lyssavirus (DUVV) and Lagos bat lyssavirus (LBV), representing phylogroups I and II, respectively. A total of 97 and 42 sera were able to neutralise DUVV and LBV, respectively. No serum neutralised both DUVV and LBV but most DUVV-seropositive bats (n = 32/220) also neutralised European bat lyssavirus 1 (EBLV-1) but not Rabies lyssavirus (RABV), the prototypic lyssavirus of phylogroup I. These results highlight that lyssaviruses belonging to phylogroups I and II circulate in regional bat populations and that the putative phylogroup I lyssavirus is antigenically closer to DUVV and EBLV-1 than to RABV. Variation between bat species, roost sites and bioclimatic regions were observed. All brain samples tested by RT-PCR specific for lyssavirus RNA were negative.
MeSH term(s)	Animals ; Antibodies, Neutralizing ; Chiroptera/virology ; Disease Reservoirs ; Indian Ocean Islands ; Lyssavirus/genetics ; Lyssavirus/immunology ; Lyssavirus/isolation & purification ; Rhabdoviridae Infections/veterinary ; Seroepidemiologic Studies
Chemical Substances	Antibodies, Neutralizing
Language	English
Publishing date	2016-08-08
Publishing country	United States
Document type	Journal Article
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0160553
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Article ; Online: (with research data) An eco-epidemiological study of Morbilli-related paramyxovirus infection in Madagascar bats reveals host-switching as the dominant macro-evolutionary mechanism.

Mélade, Julien / Wieseke, Nicolas / Ramasindrazana, Beza / Flores, Olivier / Lagadec, Erwan / Gomard, Yann / Goodman, Steven M / Dellagi, Koussay / Pascalis, Hervé

Scientific reports

2016 Volume 6, Page(s) 23752

Abstract: An eco-epidemiological investigation was carried out on Madagascar bat communities to better understand the evolutionary mechanisms and environmental factors that affect virus transmission among bat species in closely related members of the genus ... ...

Abstract	An eco-epidemiological investigation was carried out on Madagascar bat communities to better understand the evolutionary mechanisms and environmental factors that affect virus transmission among bat species in closely related members of the genus Morbillivirus, currently referred to as Unclassified Morbilli-related paramyxoviruses (UMRVs). A total of 947 bats were investigated originating from 52 capture sites (22 caves, 18 buildings, and 12 outdoor sites) distributed over different bioclimatic zones of the island. Using RT-PCR targeting the L-polymerase gene of the Paramyxoviridae family, we found that 10.5% of sampled bats were infected, representing six out of seven families and 15 out of 31 species analyzed. Univariate analysis indicates that both abiotic and biotic factors may promote viral infection. Using generalized linear modeling of UMRV infection overlaid on biotic and abiotic variables, we demonstrate that sympatric occurrence of bats is a major factor for virus transmission. Phylogenetic analyses revealed that all paramyxoviruses infecting Malagasy bats are UMRVs and showed little host specificity. Analyses using the maximum parsimony reconciliation tool CoRe-PA, indicate that host-switching, rather than co-speciation, is the dominant macro-evolutionary mechanism of UMRVs among Malagasy bats.
MeSH term(s)	Animals ; Biological Evolution ; Chiroptera ; Epidemiologic Studies ; Genotype ; Host Specificity ; Madagascar/epidemiology ; Paramyxoviridae/classification ; Paramyxoviridae/genetics ; Paramyxoviridae/isolation & purification ; Paramyxoviridae/physiology ; Paramyxoviridae Infections/epidemiology ; Paramyxoviridae Infections/veterinary ; Paramyxoviridae Infections/virology ; Phylogeny ; Prevalence ; RNA, Viral/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Analysis, DNA ; Viral Tropism
Chemical Substances	RNA, Viral
Keywords	covid19
Language	English
Publishing date	2016-04-12
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/srep23752
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Article ; Online: Influenza C virus high seroprevalence rates observed in 3 different population groups.

Salez, Nicolas / Mélade, Julien / Pascalis, Hervé / Aherfi, Sarah / Dellagi, Koussay / Charrel, Rémi N / Carrat, Fabrice / de Lamballerie, Xavier

The Journal of infection

2014 Volume 69, Issue 2, Page(s) 182–189

Abstract: The epidemiology of Influenza C virus (FLUCV) infections remains poorly characterised. Here, we have examined the age- and location-specific seroprevalence of antibodies against FLUCV in 1441 sera from metropolitan continental France (Marseille), South- ... ...

Abstract	The epidemiology of Influenza C virus (FLUCV) infections remains poorly characterised. Here, we have examined the age- and location-specific seroprevalence of antibodies against FLUCV in 1441 sera from metropolitan continental France (Marseille), South-West Indian Ocean French territories (Reunion Island) and United-Kingdom (Edinburgh) using a combination of haemagglutination inhibition, virus neutralisation and ELISA assays. Our results show that immunity to FLUCV is common in all locations studied (global seroprevalence values >50%) and that the first immunising contacts generally occur early in life (i.e., in the 0-4 year-old age group). The latter item is further supported by the detection of FLUCV RNA by RT-PCR in naso-pharyngeal samples collected in patient attending the Emergency Room of the Public hospitals of Marseille, France with a large majority of children under 10 years-old: 17 (60.7%) in children ≤3 yo, 10 (35.7%) in the 4-10 yo age group and 1 (3.6%) in an adult (49yo). The temporal distribution of cases was atypical with regard to influenza (a large proportion of cases occurred in spring and summer) and the clinical presentation was diverse, including but being not limited to classical Influenza-like-Ilnesses. Altogether, our results indicate an intense circulation of FLUCV in the different study areas and an early occurrence of infection in human life. Flu C appears to be a widely under-diagnosed and under-studied human paediatric disease that obviously deserves further clinical and epidemiological characterisation.
MeSH term(s)	Adolescent ; Adult ; Antibodies, Viral/blood ; Child ; Child, Preschool ; Cohort Studies ; Enzyme-Linked Immunosorbent Assay ; Female ; France/epidemiology ; Hemagglutination Inhibition Tests ; Humans ; Influenza, Human/epidemiology ; Gammainfluenzavirus/isolation & purification ; Male ; Middle Aged ; Population Groups ; Reverse Transcriptase Polymerase Chain Reaction ; Seroepidemiologic Studies ; United Kingdom/epidemiology ; Young Adult
Chemical Substances	Antibodies, Viral
Language	English
Publishing date	2014-04-04
Publishing country	England
Document type	Journal Article
ZDB-ID	424417-5
ISSN	1532-2742 ; 0163-4453
ISSN (online)	1532-2742
ISSN	0163-4453
DOI	10.1016/j.jinf.2014.03.016
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Article ; Online: Insight into the global evolution of Rodentia associated Morbilli-related paramyxoviruses.

Ghawar, Wissem / Pascalis, Hervé / Bettaieb, Jihéne / Mélade, Julien / Gharbi, Adel / Snoussi, Mohamed Ali / Laouini, Dhafer / Goodman, Steven M / Ben Salah, Afif / Dellagi, Koussay

Scientific reports

2017 Volume 7, Issue 1, Page(s) 1974

Abstract: One portion of the family Paramyxoviridae is a group of Unclassified Morbilli-Related Viruses (UMRV) recently recognized in wild small mammals. At a global level, the evolutionary history of these viruses is not properly understood and the relationships ... ...

Abstract	One portion of the family Paramyxoviridae is a group of Unclassified Morbilli-Related Viruses (UMRV) recently recognized in wild small mammals. At a global level, the evolutionary history of these viruses is not properly understood and the relationships between UMRV and their hosts still remain largely unstudied. The present study revealed, for the first time, that Rodentia associated UMRV emerged from a common ancestor in southern Africa more than 4000 years ago. Sequenced UMRV originating from different regions in the world, clustered into four well-supported viral lineages, which suggest that strain diversification occurred during host dispersal and associated exchanges, with purifying selection pressure as the principal evolutionary force. In addition, multi-introductions on different continents and islands of Rodentia associated UMRV and spillover between rodent species, most probably Rattus rattus, were detected and indicate that these animals are implicated in the vectoring and in the worldwide emergence of this virus group. The natural history and the evolution dynamics of these zoonotic viruses, originating from and hosted by wild animals, are most likely shaped by commensalism related to human activities.
MeSH term(s)	Animals ; Bayes Theorem ; Biological Evolution ; Evolution, Molecular ; Host-Pathogen Interactions ; Paramyxoviridae ; Paramyxoviridae Infections/veterinary ; Phylogeny ; Rodentia/classification ; Rodentia/genetics ; Rodentia/virology ; Viral Proteins/genetics
Chemical Substances	L protein, paramyxoviridae ; Viral Proteins
Language	English
Publishing date	2017-05-16
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-017-02206-0
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