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Background: The whitefly Bemisia tabaci (Hemiptera: Aleyrodidae) is among the 100 worst invasive species in the world. As one of the most important crop pests and virus vectors, B. tabaci causes substantial crop losses and poses a serious threat to global food security. Results: We report the 615-Mb high-quality genome sequence of B. tabaci Middle East-Asia Minor 1 (MEAM1), the first genome sequence in the Aleyrodidae family, which contains 15,664 protein-coding genes. The B. tabaci genome is highly divergent from other sequenced hemipteran genomes, sharing no detectable synteny. A number of known detoxification gene families, including cytochrome P450s and UDP-glucuronosyltransferases, are significantly expanded in B. tabaci. Other expanded gene families, including cathepsins, large clusters of tandemly duplicated B. tabaci-specific genes, and phosphatidylethanolamine-binding proteins (PEBPs), were found to be associated with virus acquisition and transmission and/or insecticide resistance, likely contributing to the global invasiveness and efficient virus transmission capacity of B. tabaci. The presence of 142 horizontally transferred genes from bacteria or fungi in the B. tabaci genome, including genes encoding hopanoid/sterol synthesis and xenobiotic detoxification enzymes that are not present in other insects, offers novel insights into the unique biological adaptations of this insect such as polyphagy and insecticide resistance. Interestingly, two adjacent bacterial pantothenate biosynthesis genes, panB and panC, have been co-transferred into B. tabaci and fused into a single gene that has acquired introns during its evolution. Conclusions: The B. tabaci genome contains numerous genetic novelties, including expansions in gene families associated with insecticide resistance, detoxification and virus transmission, as well as numerous horizontally transferred genes from bacteria and fungi. We believe these novelties likely have shaped B. tabaci as a highly invasive polyphagous crop pest and efficient vector of plant viruses. The genome serves as a reference for resolving the B. tabaci cryptic species complex, understanding fundamental biological novelties, and providing valuable genetic information to assist the development of novel strategies for controlling whiteflies and the viruses they transmit.

Human immunodeficiency virus type 1 (HIV-1) is a human retrovirus of the lentivirus subgroup which primarily infects T cells and macrophages, and causes acquired immune deficiency syndrome (AIDS). Since its emergence in the early 1980s, HIV-1 has caused a global pandemic which is still responsible for over one million deaths per year, primarily in sub-Saharan Africa. HIV-1 has been the subject of intense study for over three decades, which has resulted not only in major advances in cell biology, but also in numerous drug treatments that effectively control the infection. However, cessation of treatment always results in reemergence of the infection due to the ability of HIV-1 (and other lentiviruses) to establish a persistent quiescent infection known as latency. The elimination of latently-infected cells is the primary goal of current research towards a cure for HIV-1, alongside efforts to develop vaccines, which have thus far been fruitless. The spread of HIV-1 to susceptible target cells (which express the receptor CD4 and a co-receptor; CXCR4 or CCR5) can take place when antigen-presenting cells, such as dendritic cells, capture virus particles and then pass them on to target cells, without themselves becoming infected. Alternatively, productively infected T cells or macrophages can spread HIV-1 either by shedding virus particles to the milieu, which are then stochastically acquired by target cells, or through transient contacts between infected and uninfected cells known as virological synapses (VSs). VS-mediated cell-to-cell transmission is thought to be highly efficient due to the release of virus directly onto (or very near to) a target cell, and some evidence suggests that the VS is a privileged site which allows the virus to evade neutralizing antibodies and drugs. However, and most importantly, it is of central interest to us because the same transient cell adhesions that facilitate virus transfer can also result in the fusion of the two cells to form a syncytium, due to the presence of the viral fusogen Env and its receptor and co-receptor on either side of the VS. While T cell syncytia can be found in vivo, they remain small, and it appears that the majority of VSs resolve without fusion. The regulation of HIV-1-induced cell-cell fusion and the fate of those syncytia are the focus of the work presented here. A family of host transmembrane proteins, the tetraspanins, which regulate cell-cell fusion in other contexts (e.g. the fusion of myoblasts to form and maintain myotubes), were found to inhibit HIV-1-induced cell-cell fusion. Our investigations have further characterized this regulation, concluding that tetraspanins allow cells to reach the fusion intermediate known as hemifusion before their ability to repress fusion takes effect. In parallel, because syncytia are nevertheless found both in infected individuals and in a humanized mouse model for HIV-1, we also became interested in whether small T cell-based syncytia were able to participate in HIV-1 spread by transmitting virus to target cells. Using a simple three dimensional in vitro culture system which closely recapitulates those in situ observations, we found that small syncytia can contact target cells and transmit virus without fusing with them. Overall, these studies further our understanding of HIV-1-induced syncytia and reveal a previously unrecognized role for these entities as active participants in HIV-1 spread.

The cacao swollen shoot disease of Theobroma cacao L. (cacao) is caused by Cacao swollen shoot virus (CSSV; genus, Badnavirus, family, Caulimoviridae). The virus is endemic to West Africa, where it poses a serious threat to cocoa production. Despite efforts to control CSSV spread by replacement of infected trees with tolerant cultivars and mealybug vector management, the disease is widespread in West Africa. In Trinidad, leaf mosaic and vein-banding symptoms have been observed in cacao plants in the field since the 1940s, and recently at the International Cocoa Genebank (ICGT), a custodian of cacao germplasm resources. The strains A and B of the suspect Cacao Trinidad virus (CTV) caused the symptoms, and were thought to be related to CSSV, however, viral causality was not demonstrated, until now. To develop molecular detection methods for CSSV in infected plants, polymerase chain reaction (PCR) amplification of eight regions of the CSSV genome was implemented. The PCR results showed variable amplification frequencies of 19 - 42% at each region, for 124 isolates collected in Cote d'Ivoire and Ghana. Pairwise nucleotide (nt) analyses of the eight regions showed 66-99% shared identities, indicating that CSSV isolates exhibit extensive variability with respect to primer design. The results provided preliminary evidence for the existence of a CSSV complex consisting of four divergent species. The full length genome of 14 CSSV isolates from cacao determined using the Illumina HiSeq platform showed 70-99% shared nt identities. The pairwise nt identities placed CSSV sequences into a group of four distinct species, one of which represented a previously undescribed species. Moreover, the full-length genomes grouped phylogenetically with other badnaviruses and revealed two CSSV subclades with three types of genome arrangements; four, five or six open reading frames (ORFs). Predicted functional protein domains were conserved on each ORF. Two distinct, full-length genome sequences were determined using the Illumina HiSeq platform, from DNA isolated from cacao leaves exhibiting distinct symptoms in Trinidad. The sequences were validated by PCR-amplification and sequencing of overlapping viral genome fragments. Pairwise nt analysis indicated that each genome shared 52-62% nt identities with CSSV and other badnaviruses, suggesting that the two are distinct species. Phylogenetic analysis indicated that the two sequences are not strains of the same virus, as supposed, but they represent two previously undescribed species in the genus, Badnavirus, and they have been named Cacao mild mosaic virus (CaMMV) and Cacao yellow-vein-banding virus (CYVBV). Despite sharing the same host and causing similar symptoms in cacao, CSSV, CaMMV, and CYVBV are phylogenetically-distinct species. The discovery of a CSSV species complex and the identification of three new cacao-infecting badnavirus species will support the development of molecular detection tools using the partial and complete genome sequences determined in this study. The ability to develop validated molecular tools for the detection of CSSV and related viruses, CaMMV and CYVBV, in cacao will aid quarantine efforts and safe movement of germplasm from the ICGT in Trinidad to cacao-growing countries, worldwide. Also, molecular diagnostics tools are expected to be useful in efforts underway to develop CSSV-resistant planting material for countries in West Africa, which are currently experiencing continued or new disease outbreaks.

Chez un individu infecté, le VHC circule sous la forme d’une population de variants viraux appelés quasi-espèce. Lors d’un évènement de transmission, certains variants viraux sont préférentiellement transmis et un effondrement de la diversité virale chez l’individu nouvellement infecté est souvent observé. Les propriétés électives de ces variants ainsi que leur rôle dans l’évolution clinique sont méconnus. L’objectif de cette étude est d’identifier si des déterminants moléculaires situés au niveau des glycoprotéines d’enveloppe du VHC sont associés à une plus grande capacité de transmission. Les propriétés fonctionnelles des variants transmis et non transmis seront étudiées, en particulier la sensibilité à la neutralisation autologue. Les échantillons étudiés proviennent de couples mère-enfant infectés chroniquement par le VHC issus de d’un essai clinique réalisé en Thaïlande. La composition des populations virales au sein de 3 paires a été étudiée à l’aide d’une technique d’amplification après dilution limite (SGA) suivie d’un séquençage profond (Illumina). Le variant majoritaire chez la mère était retrouvé majoritaire chez l’enfant pour les paires 1 et 3. Pour 2 paires (2 et 3), une moindre diversité génétique a été observée chez l’enfant par rapport à la mère témoignant d’un goulot d’étranglement génétique lors de la transmission. Après clonage des gènes E1E2, des tests d’infectivité sur cellules hépatocytaires ainsi que des tests de neutralisation par le sérum maternel sont réalisés avec le modèle de rétrovirus pseudotypés (VHCpp). Pour la 1ère paire, le variant majoritaire chez la mère (variant transmis à l’enfant) est infectieux et résistant au sérum autologue. Pour la deuxième paire, le variant minoritaire (transmis) est légèrement résistant à la neutralisation autologue. Un variant majoritaire non transmis apparait sensible à la neutralisation autologue. Des études complémentaires en système de virus réplicatifs issus de la culture cellulaire (VHCcc) sont en cours. Au final, les résultats de cette étude contribuent à comprendre les étapes précoces de l’infection par le VHC, afin de mieux appréhender de futures approches immunoprophylactiques ou vaccinales. / In infected individuals, HCV circulates as a complex mixture of genetically different, but closely related viral variants named quasispecies. In a transmission event, some viral variants are preferentially transmitted. The genetic and functional properties of these variants are still unknown. The aim of our work was to identify molecular determinants of E1E2 associates with a greater capacity of transmission. We also intend to study the functional properties of transmitted and no transmitted variants, as for example sensibility to autologous neutralization. Studied sera samples were obtained from three women and their child infected by the HCV, who were participating in HIV prevention clinical trial for the prevention of perinatal transmission of HIV in Thailand. Quasispecies were studied with single genome amplification (SGA) followed by deep sequencing (Illumina). A decrease in intra-host diversity (genetic bottleneck) was observed in the viral population of child near birth (week 6) compared with that observed in the mother (just before delivery). For 2 pairs, the major variant observed in the mother was the same as the major one identified in the child. Retroviral pseudotypes (HCVpp), bearing each transmitted and non-transmitted envelope glycoproteins were produced. For each one, the level of infectivity on HuH7 cells was measured as well as the neutralizing activity of the autologous sera. For the first pair, the major variant (transmitted) appears resistant to autologous neutralization. For the second pair, the transmitted minor variant appears slightly resistant to autologous neutralization. A non-transmitted major variant is sensitive to autologous neutralization. Complementary studies with HCV derived from cell culture (HCVcc) are in progress We hope that the results of this study may be helpful to better understand early steps of HCV infection, which is of great interest for the development of immunoprophylaxis and vaccine strategies.

The aim of this study was to examine the effect of tick infection with tick-borne encephalitis virus on its behaviour and development. The effect of infection on feeding performance, metamorphosis, locomotion or phototaxis was analysed. Despite the fact that we were not able to demonstrate any significant effect of infection on tick behaviour, the obtained results contribute to understanding transmission dynamics of the virus during tick life cycle including co-feeding and transovarial transmission.

<p>Evidence exists for the airborne transmission of contagious pathogens such as SARS-CoV-2, influenza A virus and <i>Mycobacterium</i> <i>tuberculosis</i> in indoor environments. These pathogens are carried in the respiratory droplets and transmitted through airborne route to infect individuals. An important element in risk assessment for pathogenic bioaerosol exposure is a determination of the inhaled deposited dose rate – the number of deposited pathogenic particles per minute – received by each respiratory region and the fractional reduction of dose rate by different material facemasks. This paper presents an aerosol physics-based modeling framework to estimate the fractional reduction of regional dose rate in diverse indoor healthcare environments. The fractional reduction of dose rate is a useful metric to evaluate the facemask effectiveness in reducing the inhaled dose rate. Data extraction of pathogenic bioaerosol size distributions and size-dependent facemask filtration efficiency curve combined with deposition fraction model become the baseline to calculate the fractional reduction of dose rate by 10 different facemasks. Facemask leakage is also considered for the realistic representation of its impact on reduction fraction as current studies focus on mask material filtration efficiency. This analysis considers how the fractional reduction of dose rate is influenced by the pathogenic bioaerosol size distribution, age-dependent respiratory parameters, age-specific deposition fraction, facemask filtration efficiency and mask leakage. Different factors drove variations in the reduction fraction of various sized-pathogenic bioaerosols received by each respiratory region for each age group. This framework can be a useful tool for decision-makers in evaluating the mask’s effectiveness in reducing deposition of pathogenic bioaerosols.</p>

The spread of severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) has raised major health policy questions. Direct transmission via respiratory droplets seems to be the dominant route of its transmission. However, indirect transmission via shared contact of contaminated objects may also occur. The contribution of each transmission route to epidemic spread might change during lock-down scenarios. Here, we simulate viral spread of an abstract epidemic considering both routes of transmission by use of a stochastic, agent-based SEIR model. We show that efficient contact tracing (CT) at a high level of incidence can stabilize daily cases independently of the transmission route long before effects of herd immunity become relevant. CT efficacy depends on the fraction of cases that do not show symptoms. Combining CT with lock-down scenarios that reduce agent mobility lowers the incidence for exclusive direct transmission scenarios and can even eradicate the epidemic. However, even for small fractions of indirect transmission, such lockdowns can impede CT efficacy and increase case numbers. These counterproductive effects can be reduced by applying measures that favor distancing over reduced mobility. In summary, we show that the efficacy of lock-downs depends on the transmission route. Our results point to the particular importance of hygiene measures during mobility lock-downs.