cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14805810
title: Potential role of vector-mediated natural selection in dengue virus genotype/lineage replacements in two epidemiologically contrasted settings

description: Dengue virus (DENV) evolutionary dynamics are characterized by frequent DENV genotype/lineage replacements, potentially associated with changes in disease severity and human immunity. New Caledonia (NC) and Cambodia, two contrasted epidemiological settings, respectively experienced a DENV-1 genotype IV to I replacement in 2012 and a DENV-1 genotype I lineage 3–4 replacement in 2005–2007, both followed by a massive dengue outbreak. However, their underlying evolutionary drivers have not been elucidated. Here, we tested the hypothesis that these genotype/lineage switches reflected a higher transmission fitness of the replacing DENV genotype/lineage in the mosquito vector using <i>in vivo</i> competition experiments. For this purpose, field-derived <i>Aedes aegypti</i> from NC and Cambodia were orally challenged with epidemiologically relevant pairs of four DENV-1 genotype I and IV strains from NC or four DENV-1 genotype I lineage 3 and 4 strains from Cambodia, respectively. The relative transmission fitness of each DENV-1 genotype/lineage was measured by quantitative RT–PCR for infection, dissemination, and transmission rates. Results showed a clear transmission fitness advantage of the replacing DENV-1 genotype I from NC within the vector. A similar but more subtle pattern was observed for the DENV-1 lineage 4 replacement in Cambodia. Our results support the hypothesis that vector-driven selection contributed to the DENV-1 genotype/lineage replacements in these two contrasted epidemiological settings, and reinforce the idea that natural selection taking place within the mosquito vector plays an important role in DENV short-term evolutionary dynamics.
DOI: 10.6084/m9.figshare.14805810.v2
title: Potential role of vector-mediated natural selection in dengue virus genotype/lineage replacements in two epidemiologically contrasted settings

description: Dengue virus (DENV) evolutionary dynamics are characterized by frequent DENV genotype/lineage replacements, potentially associated with changes in disease severity and human immunity. New Caledonia (NC) and Cambodia, two contrasted epidemiological settings, respectively experienced a DENV-1 genotype IV to I replacement in 2012 and a DENV-1 genotype I lineage 3–4 replacement in 2005–2007, both followed by a massive dengue outbreak. However, their underlying evolutionary drivers have not been elucidated. Here, we tested the hypothesis that these genotype/lineage switches reflected a higher transmission fitness of the replacing DENV genotype/lineage in the mosquito vector using <i>in vivo</i> competition experiments. For this purpose, field-derived <i>Aedes aegypti</i> from NC and Cambodia were orally challenged with epidemiologically relevant pairs of four DENV-1 genotype I and IV strains from NC or four DENV-1 genotype I lineage 3 and 4 strains from Cambodia, respectively. The relative transmission fitness of each DENV-1 genotype/lineage was measured by quantitative RT–PCR for infection, dissemination, and transmission rates. Results showed a clear transmission fitness advantage of the replacing DENV-1 genotype I from NC within the vector. A similar but more subtle pattern was observed for the DENV-1 lineage 4 replacement in Cambodia. Our results support the hypothesis that vector-driven selection contributed to the DENV-1 genotype/lineage replacements in these two contrasted epidemiological settings, and reinforce the idea that natural selection taking place within the mosquito vector plays an important role in DENV short-term evolutionary dynamics.
DOI: 10.6084/m9.figshare.17113666
title: Comparing immunogenicity and protective efficacy of the yellow fever 17D vaccine in mice

description: The live-attenuated yellow fever 17D (YF17D) vaccine is one of the most efficacious human vaccines and also employed as a vector for novel vaccines. However, in the lack of appropriate immunocompetent small animal models, mechanistic insight in YF17D-induced protective immunity remains limited. To better understand YF17D vaccination and to identify a suitable mouse model, we evaluated the immunogenicity and protective efficacy of YF17D in five complementary mouse models, i.e. wild-type (WT) BALB/c, C57BL/6, IFN-α/β receptor (<i>IFNAR<sup>-/-</sup></i>) deficient mice, and in WT mice in which type I IFN signalling was temporally ablated by an IFNAR blocking (MAR-1) antibody. Alike in <i>IFNAR<sup>-/-</sup></i> mice, YF17D induced in either WT mice strong humoral immune responses dominated by IgG2a/c isotype (Th1 type) antibodies, yet only when IFNAR was blocked. Vigorous cellular immunity characterized by CD4<sup>+</sup> T-cells producing IFN-γ and TNF-α were mounted in MAR-1 treated C57BL/6 and in <i>IFNAR<sup>-/-</sup></i> mice. Surprisingly, vaccine-induced protection was largely mouse model dependent. Full protection against lethal intracranial challenge and a massive reduction of virus loads was conferred already by a minimal dose of 2 PFU YF17D in BALB/c and <i>IFNAR<sup>-/-</sup></i> mice, but not in C57BL/6 mice. Correlation analysis of infection outcome with pre-challenge immunological markers indicates that YFV-specific IgG might suffice for protection, even in the absence of detectable levels of neutralizing antibodies. Finally, we propose that, in addition to <i>IFNAR<sup>-/-</sup></i> mice, C57BL/6 mice with temporally blocked IFN-α/β receptors represent a promising immunocompetent mouse model for the study of YF17D-induced immunity and evaluation of YF17D-derived vaccines.
DOI: 10.6084/m9.figshare.17113666.v2
title: Comparing immunogenicity and protective efficacy of the yellow fever 17D vaccine in mice

description: The live-attenuated yellow fever 17D (YF17D) vaccine is one of the most efficacious human vaccines and also employed as a vector for novel vaccines. However, in the lack of appropriate immunocompetent small animal models, mechanistic insight in YF17D-induced protective immunity remains limited. To better understand YF17D vaccination and to identify a suitable mouse model, we evaluated the immunogenicity and protective efficacy of YF17D in five complementary mouse models, i.e. wild-type (WT) BALB/c, C57BL/6, IFN-α/β receptor (<i>IFNAR<sup>-/-</sup></i>) deficient mice, and in WT mice in which type I IFN signalling was temporally ablated by an IFNAR blocking (MAR-1) antibody. Alike in <i>IFNAR<sup>-/-</sup></i> mice, YF17D induced in either WT mice strong humoral immune responses dominated by IgG2a/c isotype (Th1 type) antibodies, yet only when IFNAR was blocked. Vigorous cellular immunity characterized by CD4<sup>+</sup> T-cells producing IFN-γ and TNF-α were mounted in MAR-1 treated C57BL/6 and in <i>IFNAR<sup>-/-</sup></i> mice. Surprisingly, vaccine-induced protection was largely mouse model dependent. Full protection against lethal intracranial challenge and a massive reduction of virus loads was conferred already by a minimal dose of 2 PFU YF17D in BALB/c and <i>IFNAR<sup>-/-</sup></i> mice, but not in C57BL/6 mice. Correlation analysis of infection outcome with pre-challenge immunological markers indicates that YFV-specific IgG might suffice for protection, even in the absence of detectable levels of neutralizing antibodies. Finally, we propose that, in addition to <i>IFNAR<sup>-/-</sup></i> mice, C57BL/6 mice with temporally blocked IFN-α/β receptors represent a promising immunocompetent mouse model for the study of YF17D-induced immunity and evaluation of YF17D-derived vaccines.
DOI: 10.6084/m9.figshare.17125431
title: Colistin-phage combinations decrease antibiotic resistance in <i>Acinetobacter baumannii</i> via changes in envelope architecture

description: Multidrug-resistant bacterial infections are becoming increasingly common, with only few last-resort antibiotics such as colistin available for clinical therapy. An alternative therapeutic strategy gaining momentum is phage therapy, which has the advantage of not being affected by bacterial resistance to antibiotics. However, a major challenge in phage therapy is the rapid emergence of phage-resistant bacteria. In this work, our main aim was to understand the mechanisms of phage-resistance used by the top priority pathogen <i>Acinetobacter baumannii</i>. We isolated the novel phage Phab24, capable of infecting colistin-sensitive and -resistant strains of <i>A. baumannii</i>. After co-incubating Phab24 with its hosts, we obtained phage-resistant mutants which were characterized on both genotypic and phenotypic levels. Using whole genome sequencing, we identified phage-resistant strains that displayed mutations in genes that alter the architecture of the bacterial envelope at two levels: the capsule and the outer membrane. Using an adsorption assay, we confirmed that phage Phab24 uses the bacterial capsule as its primary receptor, with the outer membrane possibly serving as the secondary receptor. Interestingly, the phage-resistant isolates were less virulent compared to the parental strains in a <i>Galleria mellonella</i> infection model. Most importantly, we observed that phage-resistant bacteria that evolved in the absence of antibiotics exhibited an increased sensitivity to colistin, even though the antibiotic resistance mechanism per se remained unaltered. This increase in antibiotic sensitivity is a direct consequence of the phage-resistance mechanism, and could potentially be exploited in the clinical setting.
DOI: 10.6084/m9.figshare.14419179
title: Antigenic and molecular characterization of low pathogenic avian influenza A(H9N2) viruses in sub-Saharan Africa from 2017 through 2019

description: Sub-Saharan Africa was historically considered an animal influenza cold spot, with only sporadic highly pathogenic H5 outbreaks detected over the last 20 years. However, in 2017, low pathogenic avian influenza A(H9N2) viruses were detected in poultry in Sub-Saharan Africa. Molecular, phylogenetic, and antigenic characterization of isolates from Benin, Togo, and Uganda showed that they belonged to the G1 lineage. Isolates from Benin and Togo clustered with viruses previously described in Western Africa, whereas viruses from Uganda were genetically distant and clustered with viruses from the Middle East. Viruses from Benin exhibited decreased cross-reactivity with those from Togo and Uganda, suggesting antigenic drift associated with reduced replication in Calu-3 cells. The viruses exhibited mammalian adaptation markers similar to those of the human strain A/Senegal/0243/2019 (H9N2). Therefore, viral genetic and antigenic surveillance in Africa is of paramount importance to detect further evolution or emergence of new zoonotic strains.
DOI: 10.6084/m9.figshare.14419179.v1
title: Antigenic and molecular characterization of low pathogenic avian influenza A(H9N2) viruses in sub-Saharan Africa from 2017 through 2019

description: Sub-Saharan Africa was historically considered an animal influenza cold spot, with only sporadic highly pathogenic H5 outbreaks detected over the last 20 years. However, in 2017, low pathogenic avian influenza A(H9N2) viruses were detected in poultry in Sub-Saharan Africa. Molecular, phylogenetic, and antigenic characterization of isolates from Benin, Togo, and Uganda showed that they belonged to the G1 lineage. Isolates from Benin and Togo clustered with viruses previously described in Western Africa, whereas viruses from Uganda were genetically distant and clustered with viruses from the Middle East. Viruses from Benin exhibited decreased cross-reactivity with those from Togo and Uganda, suggesting antigenic drift associated with reduced replication in Calu-3 cells. The viruses exhibited mammalian adaptation markers similar to those of the human strain A/Senegal/0243/2019 (H9N2). Therefore, viral genetic and antigenic surveillance in Africa is of paramount importance to detect further evolution or emergence of new zoonotic strains.
DOI: 10.6084/m9.figshare.17125431.v1
title: Colistin-phage combinations decrease antibiotic resistance in <i>Acinetobacter baumannii</i> via changes in envelope architecture

description: Multidrug-resistant bacterial infections are becoming increasingly common, with only few last-resort antibiotics such as colistin available for clinical therapy. An alternative therapeutic strategy gaining momentum is phage therapy, which has the advantage of not being affected by bacterial resistance to antibiotics. However, a major challenge in phage therapy is the rapid emergence of phage-resistant bacteria. In this work, our main aim was to understand the mechanisms of phage-resistance used by the top priority pathogen <i>Acinetobacter baumannii</i>. We isolated the novel phage Phab24, capable of infecting colistin-sensitive and -resistant strains of <i>A. baumannii</i>. After co-incubating Phab24 with its hosts, we obtained phage-resistant mutants which were characterized on both genotypic and phenotypic levels. Using whole genome sequencing, we identified phage-resistant strains that displayed mutations in genes that alter the architecture of the bacterial envelope at two levels: the capsule and the outer membrane. Using an adsorption assay, we confirmed that phage Phab24 uses the bacterial capsule as its primary receptor, with the outer membrane possibly serving as the secondary receptor. Interestingly, the phage-resistant isolates were less virulent compared to the parental strains in a <i>Galleria mellonella</i> infection model. Most importantly, we observed that phage-resistant bacteria that evolved in the absence of antibiotics exhibited an increased sensitivity to colistin, even though the antibiotic resistance mechanism per se remained unaltered. This increase in antibiotic sensitivity is a direct consequence of the phage-resistance mechanism, and could potentially be exploited in the clinical setting.
DOI: 10.6084/m9.figshare.16563394
title: The emerging tick-borne pathogen <i>Neoehrlichia mikurensis</i>: first French case series and vector epidemiology

description: <i>Neoehrlichia mikurensis</i> is an intracellular bacterium transmitted in Europe and Asia by ticks of the <i>Ixodes ricinus</i> complex. Interest in this bacterium has increased since it was demonstrated to be responsible for febrile syndromes in patients. To date, most clinical cases have been reported in northern Europe, but case series have also been described in central Europe and China. Notably, thrombotic events occurred during the course of the disease. We investigated the presence of <i>N. mikurensis</i> in 10,885 <i>I. ricinus</i> nymphs in two regions of France (Alsace and Brittany) collected between 2013 and 2020 and in 934 patients suspected of human granulocytic anaplasmosis in Alsace, an endemic area for Lyme borreliosis, using a specific PCR assay. <i>N. mikurensis</i> was detected in 5.42% of the ticks from Alsace, whereas only one (0.03%) tick was found to be positive in Brittany. Spatiotemporal disparities were also noticed within the Alsace region over the four collection sites investigated, and a significant increase in the prevalence of nymphs carrying <i>N. mikurensis</i> was also observed in the last three years of collection. Four out of 934 screened patients were found to be positive for <i>N. mikurensis</i>. Two had malignancies, and the other two were apparently immunocompetent. Superficial thrombosis was noticed in one patient, and long-lasting bacteremia was noted in another patient. These four patients are the first clinical cases of neoehrlichiosis described in France. We suggest including <i>N. mikurensis</i> in the differential diagnosis of post-tick bite febrile syndromes to treat patients and prevent the occurrence of thrombotic complications.
DOI: 10.6084/m9.figshare.16563394.v1
title: The emerging tick-borne pathogen <i>Neoehrlichia mikurensis</i>: first French case series and vector epidemiology

description: <i>Neoehrlichia mikurensis</i> is an intracellular bacterium transmitted in Europe and Asia by ticks of the <i>Ixodes ricinus</i> complex. Interest in this bacterium has increased since it was demonstrated to be responsible for febrile syndromes in patients. To date, most clinical cases have been reported in northern Europe, but case series have also been described in central Europe and China. Notably, thrombotic events occurred during the course of the disease. We investigated the presence of <i>N. mikurensis</i> in 10,885 <i>I. ricinus</i> nymphs in two regions of France (Alsace and Brittany) collected between 2013 and 2020 and in 934 patients suspected of human granulocytic anaplasmosis in Alsace, an endemic area for Lyme borreliosis, using a specific PCR assay. <i>N. mikurensis</i> was detected in 5.42% of the ticks from Alsace, whereas only one (0.03%) tick was found to be positive in Brittany. Spatiotemporal disparities were also noticed within the Alsace region over the four collection sites investigated, and a significant increase in the prevalence of nymphs carrying <i>N. mikurensis</i> was also observed in the last three years of collection. Four out of 934 screened patients were found to be positive for <i>N. mikurensis</i>. Two had malignancies, and the other two were apparently immunocompetent. Superficial thrombosis was noticed in one patient, and long-lasting bacteremia was noted in another patient. These four patients are the first clinical cases of neoehrlichiosis described in France. We suggest including <i>N. mikurensis</i> in the differential diagnosis of post-tick bite febrile syndromes to treat patients and prevent the occurrence of thrombotic complications.
DOI: 10.6084/m9.figshare.14562163
title: Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications

description: Mutations in the SARS-CoV-2 Membrane (M) gene are relatively uncommon. The M gene encodes the most abundant viral structural protein, and is implicated in multiple viral functions, including initial attachment to the host cell via heparin sulphate proteoglycan, viral protein assembly in conjunction with the N and E genes, and enhanced glucose transport. We have identified a recent spike in the frequency of reported SARS-CoV-2 genomes carrying M gene mutations. This is associated with emergence of a new sub-B.1 clade, B.1.I82T, defined by the previously unreported M:I82T mutation within TM3, the third of three membrane spanning helices implicated in glucose transport. The frequency of this mutation increased in the USA from 0.014% in October 2020 to 1.62% in February 2021, a 116-fold change. While constituting 0.7% of the isolates overall, M:I82T sub-B.1 lineage accounted for 14.4% of B.1 lineage isolates in February 2021, similar to the rapid initial increase previously seen with the B.1.1.7 and B.1.429 lineages, which quickly became the dominant lineages in Europe and California over a period of several months. A similar increase in incidence was also noted in another related mutation, V70L, also within the TM2 transmembrane helix. These M mutations are associated with younger patient age (4.6 to 6.3 years). The rapid emergence of this B.1.I82T clade, recently named Pangolin B.1.575 lineage, suggests that this M gene mutation is more biologically fit, perhaps related to glucose uptake during viral replication, and should be included in ongoing genomic surveillance efforts and warrants further evaluation for potentially increased pathogenic and therapeutic implications.
DOI: 10.6084/m9.figshare.14769117
title: Clinical signs and symptoms associated with WHO severe dengue classification: a systematic review and meta-analysis

description: The World Health Organization (WHO) introduced the new dengue classification in 2009. We aimed to assess the association of clinical signs and symptoms with WHO severe dengue classification in clinical practice. A systematic literature search was performed using the databases of PubMed, Embase, and Scopus between 2009 and 2018 according to PRISMA guideline. Meta-analysis was performed with the RevMan software. A random or fixed-effect model was applied to pool odds ratios and 95% confidence intervals of important signs and symptoms across studies. Thirty nine articles from 1790 records were included in this review. In our meta-analysis, signs and symptoms associated with higher risk of severe dengue were comorbidity, vomiting, persistent vomiting, abdominal pain or tenderness, pleural effusion, ascites, epistaxis, gum bleeding, GI bleeding, skin bleeding, lethargy or restlessness, hepatomegaly (&gt;2 cm), increased HCT with decreased platelets, shock, dyspnea, impaired consciousness, thrombocytopenia, elevated AST and ALT, gall bladder wall thickening and secondary infection. This review shows new factors comorbidity, epistaxis, GI and skin bleeding, dyspnea, gall bladder wall thickening and secondary infection may be useful to refine the 2009 classification to triage severe dengue patients.
DOI: 10.6084/m9.figshare.14769117.v1
title: Clinical signs and symptoms associated with WHO severe dengue classification: a systematic review and meta-analysis

description: The World Health Organization (WHO) introduced the new dengue classification in 2009. We aimed to assess the association of clinical signs and symptoms with WHO severe dengue classification in clinical practice. A systematic literature search was performed using the databases of PubMed, Embase, and Scopus between 2009 and 2018 according to PRISMA guideline. Meta-analysis was performed with the RevMan software. A random or fixed-effect model was applied to pool odds ratios and 95% confidence intervals of important signs and symptoms across studies. Thirty nine articles from 1790 records were included in this review. In our meta-analysis, signs and symptoms associated with higher risk of severe dengue were comorbidity, vomiting, persistent vomiting, abdominal pain or tenderness, pleural effusion, ascites, epistaxis, gum bleeding, GI bleeding, skin bleeding, lethargy or restlessness, hepatomegaly (&gt;2 cm), increased HCT with decreased platelets, shock, dyspnea, impaired consciousness, thrombocytopenia, elevated AST and ALT, gall bladder wall thickening and secondary infection. This review shows new factors comorbidity, epistaxis, GI and skin bleeding, dyspnea, gall bladder wall thickening and secondary infection may be useful to refine the 2009 classification to triage severe dengue patients.