Face masks effectively limit the probability of SARS-CoV-2 transmission

Airborne transmission by droplets and aerosols is important for the spread of viruses. Face masks are a well-established preventive measure, but their effectiveness for mitigating SARS-CoV-2 transmission is still under debate. We show that variations in mask efficacy can be explained by different regimes of virus abundance and related to population-average infection probability and reproduction number. For SARS-CoV-2, the viral load of infectious individuals can vary by orders of magnitude. We find that most environments and contacts are under conditions of low virus abundance (virus-limited) where surgical masks are effective at preventing virus spread. More advanced masks and other protective equipment are required in potentially virus-rich indoor environments including medical centers and hospitals. Masks are particularly effective in combination with other preventive measures like ventilation and distancing.

Distinct regimes of particle and virus abundance explain face mask efficacy for COVID-19

Airborne transmission is an important transmission pathway for viruses, including SARS-CoV-2. Regions with a higher proportion of people wearing masks show better control of COVID-19, but the effectiveness of masks is still under debate due to their limited and variable efficiencies in removing respiratory particles. Here, we analyze experimental data and perform model calculations to show that this contrast can be explained by the different regimes of abundance of particles and viruses. Because of the large number of particles exhaled during human respiration and vocalization, indoor environments are usually in a particle-rich regime which means that masks cannot prevent the inhalation of large numbers of respiratory particles. Usually, however, only a small fraction of these particles contain viruses, which implies a virus-limited regime where masks can help to keep the number of inhaled viruses below the infectious dose. For SARS-CoV-2, the virus load in the respiratory tract of infectious individuals can vary by 3 to 4 orders of magnitude (5th to 95th percentile), leading to substantial variations in the abundance of airborne virus concentrations and infection risks. Nevertheless, we find that most environments are in a virus-limited regime where masks have a high efficacy in preventing the spread of COVID-19 by aerosol or droplet transmission during short-term exposure. The characteristic contrast between particle-rich and virus-limited regimes explains why face masks are highly efficient in most but not all environments, and why the largest benefits can be achieved by non-linear synergetic effects of combining masks with other preventive measures such as ventilation and social distancing to reduce airborne virus concentrations and the overall risk of infection.

Honey Bee Viruses, Colony Health, and Antiviral Defense

Honey bee colony losses are influenced by multiple abiotic and biotic factors, including viruses. To investigate the effects of RNA viruses on honey bees, we infected bees with a model virus (Sindbis-GFP) in the presence or absence of double-stranded RNA (dsRNA). In honey bees, dsRNA is the substrate for sequence-specific RNA interference (RNAi)-mediated antiviral defense and is a trigger of sequence-independent\antiviral responses. Transcriptome sequencing identified more than 200 differentially expressed genes, including genes in the RNAi, Toll, Imd, JAK-STAT, and heat shock response pathways, and many uncharacterized genes. To confirm the virus limiting role of two genes (i.e., dicer and mf116383) in honey bees, we utilized RNAi to reduce their expression in vivo and determined that the virus abundance increased. To evaluate the role of the heat shock stress response in antiviral defense, bees were heat stressed post-virus infection and the virus abundance and gene expression were assessed. Heat-stressed bees had reduced virus levels and a greater expression of several heat shock protein encoding genes (hsps) compared to the controls. To determine if these genes are universally associated with antiviral defense, bees were infected with another model virus, Flock House virus (FHV), or deformed wing virus and the gene expression was assessed. The expression of dicer was greater in bees infected with either FHV or Sindbis-GFP compared to the mock-infected bees, but not in the deformed wing virus-infected bees. To further investigate honey bee antiviral defense mechanisms and elucidate the function of key genes (dicer, ago-2, mf116383, and hsps) at the cellular level, primary honey bee larval hemocytes were transfected with dsRNA or infected with the Lake Sinai virus 2 (LSV2). These studies indicate that mf116383 and hsps mediate dsRNA detection and that MF116383 is involved in limiting LSV2 infection. Together, these results further our understanding of honey bee antiviral defense, particularly dsRNA-mediated antiviral responses, at both the individual bee and cellular levels.

Alternation of heterotrophic bacterial and archaeal production along nitrogen and salinity gradients in coastal wetlands

Coastal wetlands are valuable ecosystems with high biological productivity and diversity, which provide ecosystem services such as a reduction in the inputs of nitrogen into coastal waters, and storage of organic carbon, thus, acting as net carbon sinks. The rise of sea level as a consequence of climatic warming will salinize many coastal wetlands, but there is considerable uncertainty about how salinization will affect microbial communities and biogeochemical processes. We analyzed prokaryotic abundance and heterotrophic bacterial and archaeal production in 112 ponds within nine coastal wetlands from the western Mediterranean coast. We determined the main drivers of prokaryotic abundance and production in these wetlands using generalized linear models (GLMs). The best GLM, including all the coastal wetlands, indicated that the concentration of total dissolved nitrogen (TDN) positively affected the abundance of heterotrophic prokaryotes and heterotrophic archaeal production. In contrast, heterotrophic bacterial production was negatively related to TDN. This negative relationship appeared to be mediated by salinity and virus abundance. Heterotrophic bacterial production declined as salinity, and virus abundance, increased. We observed a switch from heterotrophic bacterial production towards heterotrophic archaeal production as salinity and virus abundance increased. Our results imply that microbial activity will change from bacterial-dominated processes to archaeal-dominated processes along with increases of nitrogen inputs and salinity. However, more studies are required to link the mineralization rates of dissolved nitrogen and organic carbon with specific archaeal taxa, to enable more accurate predictions on future scenarios of wetlands salinization and anthropogenic nitrogen inputs.

Insights Into a Watermelon Virome Contribute to Monitoring Distribution of Whitefly-Borne Viruses

The composition of a plant virome may represent spatiotemporal patterns of plant virus abundance. Using next generation sequencing, we investigated the viromes of watermelon fruits grown in two adjacent open fields located in Eastern Israel: Kalia and Mitzpe-Shalem. The two viromes were comprised of distinct virus species and genera. Studying spatial and temporal effects on virus occurrence, we detected the crinivirus Cucurbit yellow stunting disorder virus in Kalia and not in Mitzpe-Shalem, irrespective of collection time. A spatial effect was also observed regarding the occurrence of the begomovirus Watermelon chlorotic stunt virus, which was not detected in watermelons from Kalia, but rather in watermelon fruit in Northern Israel in 2018. A temporal effect was observed on the appearance of the ipomovirus Cucumber vein yellowing virus, which was detected in watermelons from Kalia in 2017 and was absent in the 2016 virome analysis. Importantly, regardless of temporal and spatial effects, the crinivirus Cucurbit chlorotic yellows virus, which was new to Israeli landscape, was detected in all the tested watermelon plants. These changes in viral abundance were associated with an early whitefly (Bemisia tabaci) occurrence, which might be the cause for the severe disease spread in watermelons.

Single-cell transcriptional dynamics of flavivirus infection

Dengue and Zika viral infections affect millions of people annually and can be complicated by hemorrhage and shock or neurological manifestations, respectively. However, a thorough understanding of the host response to these viruses is lacking, partly because conventional approaches ignore heterogeneity in virus abundance across cells. We present viscRNA-Seq (virus-inclusive single cell RNA-Seq), an approach to probe the host transcriptome together with intracellular viral RNA at the single cell level. We applied viscRNA-Seq to monitor dengue and Zika virus infection in cultured cells and discovered extreme heterogeneity in virus abundance. We exploited this variation to identify host factors that show complex dynamics and a high degree of specificity for either virus, including proteins involved in the endoplasmic reticulum translocon, signal peptide processing, and membrane trafficking. We validated the viscRNA-Seq hits and discovered novel proviral and antiviral factors. viscRNA-Seq is a powerful approach to assess the genome-wide virus-host dynamics at single cell level.