Endothelium Activation during Severe Yellow Fever Triggers an Intense Cytokine-Mediated Inflammatory Response in the Liver Parenchyma

Yellow fever (YF) is a pansystemic disease caused by the yellow fever virus (YFV), the prototype species of the family Flaviviridae and genus Flavivirus, and has a highly complex host-pathogen relationship, in which endothelial dysfunction reflects viral disease tropism. In this study, the in situ endothelial response was evaluated. Liver tissue samples were collected from 21 YFV-positive patients who died due to the disease and five flavivirus-negative controls who died of other causes and whose hepatic parenchyma architecture was preserved. Immunohistochemical analysis of tissues in the hepatic parenchyma of YF cases showed significantly higher expression of E-selectin, P-selectin, intercellular adhesion molecule-1, vascular cell adhesion molecule-1, and very late antigen-4 in YFV-positive cases than in flavivirus-negative controls. These results indicate that endothelium activation aggravates the inflammatory response by inducing the expression of adhesion molecules that contribute to the rolling, recruitment, migration, and construction of the inflammatory process in the hepatic parenchyma in fatal YF cases.

Semi-field evaluations of three botanically derived repellents against the blacklegged tick, Ixodes scapularis (Acari: Ixodidae)

Three compounds derived from botanicals sources, ethyl perillyl carbonate, geranyl isovalerate, and citronellyl cyclobutane carboxylate, were tested for repellent activity against Ixodes scapularis Say in a semi-field trial. Tick drags were treated with the compounds or with N, N-diethyl-m-toluamide (DEET) at high (0.25mg/cm2) or low (0.15mg/cm2) concentrations. Negative controls included untreated drags and drags treated with acetone, the carrier for all repellents. Freshly treated drags (within 20 minutes) were used to collect I. scapularis ticks at a county park in Wisconsin. To assess effectiveness, we measured tick encounter rates, detachment rate, and time to detachment. None of the repellent treatments resulted in significantly fewer encounters compared to both control treatments. However, the percentage of ticks that detached within 3 min was significantly higher on drags treated with repellents compared to controls. DEET was the most effective, repelling 69.7 - 87% of ticks by 3 min, but the effectiveness of the three test compounds was still high, ranging from 42% to 87% of ticks detaching by 3 min. For time to detachment, there were no significant differences between DEET and the three test compounds. We conclude that these botanically-derived repellents were effective against I. scapularis in a semi-field trial and could be viable alternatives to DEET.

First Report of Colletotrichum truncatum Causing Anthracnose on Oxalis corniculata in China

Oxalis corniculata L., which belongs to the family Oxalidaceae R. Br., is a very common perennial herb. It is usually planted on bare land or under the forest as landscaping plants, and the whole plant can be used for its medicinal values of clearing heat, detoxification and detumescence. In August 2019, typical symptoms of anthracnose on O. corniculata leaves were observed in the green belt on the campus of Shandong University of Technology (36.81°N, 117.99°E), Shandong Province, China. The disease incidence was above 40% by investigating more than 300 m2 of planting area. Most of O. corniculata are planted under the forest where the disease is found, mainly in the environment with high relative humidity and less ventilation. The infected leaves appeared initially as tawny oval or irregular spots, and then the lesions enlarged gradually until the leaves became dieback or wholly withered, which greatly reduced the landscape effect of O. corniculata. Diseased leaves were collected by cutting into small pieces and sterilized with 75% ethanol for 30 s and 2% sodium hypochlorite (NaClO) for 60 s, rinsed with sterile deionized water for three times. Each air-dried tissue segment was cultured on potato dextrose agar (PDA) and incubated at 25℃ for 5 to 7 days in the dark (Zhu et al. 2013). Fifteen isolates were obtained from 20 symptomatic leaves and the cultures were initially gray white, subsequently became grayish to dark green after 7 days, with copious gray aerial mycelium and black microsclerotia. Three isolates were verified by the amplification of DNA sequences of glyceraldehyde-3-phosphate dehydrogenase (GAPDH), actin (ACT), histone H3 (H3) and chitin synthase (CHS1) genes, using the primer pairs GDF1/GDR1, ACT-512F/ACT-783R, CYLH3F/CYLH3R, and CHS-79F/CHS-234R (Damn et al. 2019, Fu et al. 2019, Liu et al. 2013), respectively. The sequenced genes (GenBank accession no. OK017473, OK159078, OK159076, OK159077) shared 99.62 to 100.00% nucleotide identity with the corresponding genes of Colletotrichum truncatum strain UASB-Cc-10 (GenBank accession no. KF322064.1, KF322055.1, KF322073.1, KF319059.1), respectively, which was consistent with the morphological identification (Sawant et al. 2012). Pathogenicity test was performed with six healthy O. corniculata plants infected with mycelial plugs (about 3 mm in diameter) of three C. truncatum isolates from a 5-day-old culture, while the negative controls on the same leaves were inoculated with sterile PDA plugs. All plants were placed in a greenhouse at 25 to 30℃ with 90% relative humidity. The experiment was conducted three times. Five days later, all inoculated leaves appeared brown sunken spots, whereas no symptoms appeared on negative controls. The same pathogens, C. truncatum, were identified from the inoculated leaves on the basis of morphological and molecular characteristics as described above, confirming Koch’s postulates. To our knowledge, anthracnose caused by C. truncatum on O. corniculata is the first report in China. The discovery of this new disease is beneficial to the application and protection of O. corniculata, a popular landscape and medicinal plant. References: Damn, U., et al. 2019. Stud. Mycol. 92:1. https://doi.org/10.1016/j.simyco.2018.04.001 Fu, M., et al. 2019. Persoonia 42:1. https://doi.org/10.3767/persoonia.2019.42.01 Liu, F., et al. 2013. Mycologia 105:844. https://doi.org/10.3852/12-315 Sawant, I. S., et al. 2012. New Dis. Rep. 25:2. https://doi.org/10.5197/j.2044-0588.2012.025.002 Zhu, L., et al. 2013. J. Phytopathol. 161:59. https://doi.org/10.1111/jph.12019 The author(s) declare no conflict of interest. Acknowledgments: This research was financially supported by the Top Talents Program for One Case One Discussion of Shandong Province and Academy of Ecological Unmanned Farm (2019ZBXC200).

SARS-CoV-2 Evolution and Spike-Specific CD4+ T-Cell Response in Persistent COVID-19 with Severe HIV Immune Suppression

Intra-host evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been reported in cases with persistent coronavirus disease 2019 (COVID-19). In this study, we describe a severely immunosuppressed individual with HIV-1/SARS-CoV-2 coinfection with a long-term course of SARS-CoV-2 infection. A 28-year-old man was diagnosed with HIV-1 infection (CD4+ count: 3 cells/µL nd 563000 HIV-1 RNA copies/mL) and simultaneous Pneumocystis jirovecii pneumonia, disseminated Mycobacterium avium complex infection and SARS-CoV-2 infection. SARS-CoV-2 real-time reverse transcription polymerase chain reaction positivity from nasopharyngeal samples was prolonged for 15 weeks. SARS-CoV-2 was identified as variant Alpha (PANGO lineage B.1.1.7) with mutation S:E484K. Spike-specific T-cell response was similar to HIV-negative controls although enriched in IL-2, and showed disproportionately increased immunological exhaustion marker levels. Despite persistent SARS-CoV-2 infection, adaptive intra-host SARS-CoV-2 evolution, was not identified. Spike-specific T-cell response protected against a severe COVID-19 outcome and the increased immunological exhaustion marker levels might have favoured SARS-CoV-2 persistence.

Effectiveness of mRNA-1273 against SARS-CoV-2 omicron and delta variants

Background The recently emerged SARS-CoV-2 omicron variant raised concerns around potential escape from vaccine-elicited immunity. Limited data are available on real-world vaccine effectiveness (VE) of mRNA-1273 against omicron. Here, we report VE of 2 or 3 mRNA-1273 doses against infection and hospitalization with omicron and delta, including among immunocompromised individuals. Methods This test negative study was conducted at Kaiser Permanente Southern California. Cases were individuals aged ≥18 years testing positive by RT-PCR with specimens collected between 12/6/2021 and 12/23/2021 with variant determined by spike gene status. Randomly sampled test negative controls were 5:1 matched to cases by age, sex, race/ethnicity, and specimen collection date. Conditional logistic regression models were used to evaluate adjusted odds ratio (aOR) of vaccination with mRNA-1273 doses between cases and controls. VE(%) was calculated as (1-aOR)x100. Results 6657 test positive cases (44% delta, 56% omicron) were included. The 2-dose VE against omicron infection was 30.4% (95% CI, 5.0%-49.0%) at 14-90 days after vaccination and declined quickly thereafter. The 3-dose VE was 95.2% (93.4%-96.4%) against delta infection and 62.5% (56.2%-67.9%) against omicron infection. The 3-dose VE against omicron infection was low among immunocompromised individuals (11.5%; 0.0%-66.5%). None of the cases (delta or omicron) vaccinated with 3 doses were hospitalized compared to 53 delta and 2 omicron unvaccinated cases. Conclusions VE of 3 mRNA-1273 doses against infection with delta was high and durable, but VE against omicron infection was lower. VE against omicron infection was particularly low among immunocompromised individuals. No 3-dose recipients were hospitalized for COVID-19.

Acaricide activity of Piper macedoi Yunck essential oil against Rhipicephalus sanguineus

This study evaluated the acaricide efficacy of Piper macedoi essential oil on larvae of ticks of the species Rhipicephalus sanguineus. The essential oil was extracted by hydrodistillation in a Clevenger-type apparatus. The test consisted of six treatments: from the group I to IV, samples corresponded to different concentrations of essential oil (500 μg.mL-1; 250 μg.mL-1; 100 μg.mL-1 and 50 μg.mL-1) diluted in Tween 80 at 2%. Groups V and VI corresponded to the negative controls (with distilled water and Tween 80 to 2%) and the positive control (with acaricide Amitraz at 12.5%), respectively. The essential oil was rich in apiole (39.81%) and dillapiole (26.47%). The essential oil of P. macedoi presented an activity against the larvae of R. sanguineus, with a better efficiency observed for concentrating 500 μg.mL-1, mortality of 80.67%, indicating a dose-dependent response.

Controlling Listeria monocytogenes Growth and Biofilm Formation using Flavonoids

The aim of the present study was to investigate the ability of natural plant-derivate (flavonoid compounds) products to reduce and/or inhibit the biofilm-forming ability of Listeria monocytogenes. A collection of 500 synthetic and natural flavonoids were tested on strains of L. monocytogenes for their antimicrobial and anti-biofilm activity. L. monocytogenes biofilm inhibition by flavonoid compounds was tested on i) stainless steel coupons using crystal violet staining and ii) glass slides using confocal laser scanning microscopic (CLSM) imaging. The flavonoids were tested against a L. monocytogenes cocktail of 5 strains at a concentration of 100 µM to determine their effect on planktonic growth. A total of 17 flavonoids were chosen for further study due to their ability to significantly reduce the growth of L. monocytogenes in BHI broth, while 2 flavonoids were chosen because they actually increased growth. A lower concentration of flavonoid compounds (50 µM) was selected to investigate their effects on L. monocytogenes biofilm formation using i) stainless steel coupons to quantify biomass and ii) glass coupons to observe the biofilm architecture. The 19 flavonoids showed various levels of L. monocytogenes growth inhibition, ranging from 2% to 100%, as compared to the respective positive and negative controls on stainless steel, after 48 h of incubation at 22 o C. In addition, in comparison to the control, most of the 19 flavonoids significantly (p ≤ 0.05) inhibited biofilm formation, with at least one of the L. monocytogenes strains or at one of the tested temperatures. In fact, when grown in BHI broth with 50 µM of the 19 selected flavonoid compounds for 48 h at 22 o C, there were visible reductions in L. monocytogenes biofilm formation on the glass coupons. Overall, we found multiple flavonoid compounds to be promising anti-biofilm and antimicrobial agents against L. monocytogenes .

First report of Macrophomina phaseolina causing charcoal root rot of Hebe (Veronica cupressoides, V. ochracea, and V. pinguifolia) in Oregon, U.S.A.

Hebes (Veronica spp. in the section Hebe) are ornamental perennials and shrubs grown for their flowers and symmetric, evergreen leaves. They are uncommon in U.S. horticulture and are only produced by a few nurseries regionally (Oregon and Washington). In June, July, and August (2016 to 2021), stems on 1 to 5-year-old Veronica cupressoides, V. ochracea, and V. pinguifolia in five landscape plantings around Benton County, OR (17 plants total, locations 2 to 37 km apart) began to wilt, turn brown, and die. At least nine of the plants originated from a single nursery. Initially, just one or two stems/plant were affected, but eventually the entire plant died. Stem tissues were discolored brown to black internally and the roots were dry and necrotic. Leaves turned brown and brittle, but remained attached. Stems from each plant were disinfested in 0.5% NaOCl (1 min), rinsed in 70% ethanol, and dried (2 min). Pieces (5 mm2) were then plated onto 1/2 strength potato dextrose agar amended with streptomycin (50 mg/liter) and incubated in the dark at 20°C. Three to five days later, greyish-white cultures producing black microsclerotia (75 × 110 µm, n = 50) grew out of all samples. No spores were produced. All isolates were identified as Macrophomina phaseolina by morphology and by ≥99% homology (566-570/571 nt) to the internal transcribed spacer sequence (primers ITS1 and ITS4) from the type specimen (GenBank KF766195) (Hyde et al. 2014). Three representative sequences were deposited in GenBank (MZ726450 to MZ726452). Inoculum was prepared from these isolates by growing cultures in 250 ml of potato dextrose broth on a shaker (125 rpm at 25°C). After 2 weeks, the broth was decanted and the fungal biomass was air dried for 3 days at 25°C before grinding into a powder with a mortar and pestle. Three plants each of 6-month-old V. ochracea 'James Stirling', V. cupressoides 'McKean', and V. pinguifolia 'Sutherlandii' were inoculated with each isolate by rinsing the soil off of the roots with tap water, trimming off 0.5 cm of the roots, and then soaking the rootball in a slurry of 1 g dried inoculum in 500 ml of 0.2% water agar (WA) for 10 minutes (Reyes Gaige et al. 2010). Three plants of each species that were soaked in plain 0.2% WA served as negative controls. Afterwards, plants were potted into soilless media (Metro-Mix 840, Sun Gro Horticulture, Agawam, MA) in 3.5 inch square pots and arranged in a completely randomized design in a greenhouse set at 28/24°C day/night. The experiment was conducted three times. One to three months later, inoculated plants began to turn yellow, wilt, and die whereas all control plants remained healthy. The same pathogen was reisolated from 90% of the inoculated plants, but never from negative controls. M. phaseolina was reported on strawberry in southern Oregon in 2014 (Pscheidt and Ocamb 2021), but has not been reported from locations further north in the state where soil temperatures are cooler. It is unusual that M. phaseolina was isolated from an uncommon host at five different locations in an area of the state where the pathogen was not known to occur. Based on this, and on the number of infected plants originating from a single source, it seems likely that M. phaseolina was accidentally spread on contaminated plants produced by the nursery industry, where the warmer temperatures in production greenhouses would provide a more conducive environment for the pathogen's growth and spread. Growers should keep watch for symptoms of this pathogen in their nurseries.

Differential word expression analyses highlight plague dynamics during the second pandemic

Research on the second plague pandemic that swept over Europe from the fourteenth to nineteenth centuries mainly relies on the exegesis of contemporary texts and is prone to interpretive bias. By leveraging certain bioinformatic tools routinely used in biology, we developed a quantitative lexicography of 32 texts describing two major plague outbreaks, using contemporary plague-unrelated texts as negative controls. Nested, network and category analyses of a 207-word pan-lexicome, comprising overrepresented terms in plague-related texts, indicated that ‘buboes' and ‘carbuncles' are words that were significantly associated with the plague and signalled an ectoparasite-borne plague. Moreover, plague-related words were associated with the terms ‘merchandise’, ‘movable’, ‘tatters', ‘bed’ and ‘clothes'. Analysing ancient texts using the method reported in this paper can certify plague-related historical records and indicate the particularities of each plague outbreak, which can inform on the potential sources for the causative Yersinia pestis .

Effectiveness of COVID-19 vaccines against Omicron or Delta infection

Background The incidence of SARS-CoV-2 infection, including among those who have received 2 doses of COVID-19 vaccines, has increased substantially since Omicron was first identified in the province of Ontario, Canada. Methods Applying the test-negative design to linked provincial data, we estimated vaccine effectiveness against infection (irrespective of symptoms or severity) caused by Omicron or Delta between November 22 and December 19, 2021. We included individuals who had received at least 2 COVID-19 vaccine doses (with at least 1 mRNA vaccine dose for the primary series) and used multivariable logistic regression to estimate the effectiveness of two or three doses by time since the latest dose. Results We included 3,442 Omicron-positive cases, 9,201 Delta-positive cases, and 471,545 test-negative controls. After 2 doses of COVID-19 vaccine, vaccine effectiveness against Delta infection declined steadily over time but recovered to 93% (95%CI, 92-94%) ≥7 days after receiving an mRNA vaccine for the third dose. In contrast, receipt of 2 doses of COVID-19 vaccines was not protective against Omicron. Vaccine effectiveness against Omicron was 37% (95%CI, 19-50%) ≥7 days after receiving an mRNA vaccine for the third dose. Conclusions Two doses of COVID-19 vaccines are unlikely to protect against infection by Omicron. A third dose provides some protection in the immediate term, but substantially less than against Delta. Our results may be confounded by behaviours that we were unable to account for in our analyses. Further research is needed to examine protection against severe outcomes.