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.

The flora of south-eastern Mato Grosso State (Brazil): a review of herbarium collections

The diversity and richness of the Brazilian flora are documented in herbarium collections. When areas are deforested, but not documented, we lose both flora and the opportunity to know which species occupied those areas. The south-eastern mesoregion of Mato Grosso State, comprising 22 municipalities, has undergone the loss of native vegetation cover, accelerated by the substantial expansion of agribusiness. For an in-depth look at the consequences and the current state of the flora in that mesoregion, we consulted both speciesLink and JABOT databases. More specifically, we carried out a comprehensive study of herbarium collections by municipality and compiled data including scientific name, collection date, collection locality, collector name and observations made during collection. We obtained 5,861 records of angiosperms, ferns and lycophytes of 160 families, 770 genera and 1,792 species. The specimens are deposited in 80 herbaria of which the Herbarium of Universidade Federal de Mato Grosso (UFMT) hosts the largest collection. Rondonópolis was the most sampled municipality, whereas 50% of the municipalities were poorly sampled and one showed no collection records at all. Amongst the species occurring only in Mato Grosso, eleven were collected only in that mesoregion and twenty species were under some degree of threat. Our study recommends increasing collection and identification efforts to enable effective conservation actions and improve richness estimates for the State of Mato Grosso and the Cerrado, in general, before more of the flora is lost to deforestation.

Effectiveness of mRNA-1273 against Delta, Mu, and other emerging variants

ABSTRACTBackgroundReal-world studies have found high vaccine effectiveness (VE) of mRNA-based COVID-19 vaccines, but reduced VE against the Delta variant and waning protection have been reported, with few studies examining mRNA-1273 variant-specific VE.MethodsWe conducted a test-negative case-control study at Kaiser Permanente Southern California. Whole genome sequencing was conducted for SARS-CoV-2 positive specimens collected from 3/1/2021 to 7/27/2021. Test-positive cases were matched 1:5 to test-negative controls on age, sex, race/ethnicity, and specimen collection date. Outcomes included SARS-CoV-2 infection and hospitalization. Exposures were 2 doses or 1 dose of mRNA-1273 ≥14 days prior to specimen collection versus no COVID-19 vaccination. Conditional logistic regression was used to compare odds of vaccination among cases versus controls, adjusting for confounders. VE was calculated as (1-odds ratio)x100%.ResultsThe study included 8,153 cases and their matched controls. Two-dose VE (95% confidence interval) was 86.7% (84.3-88.7%) against Delta infection, 98.4% (96.9-99.1%) against Alpha, 90.4% (73.9-96.5%) against Mu, 96-98% against other identified variants, and 79.9% (76.9-82.5%) against unidentified variants. VE against Delta declined from 94.1% (90.5-96.3%) 14-60 days after vaccination to 80.0% (70.2-86.6%) 151-180 days after vaccination. Waning was less pronounced for non-Delta variants. VE against Delta was lower among individuals aged ≥65 years (75.2% [59.6-84.8%]) than those aged 18-64 years (87.9% [85.5-89.9%]). VE against Delta hospitalization was 97.6% (92.8-99.2%). One-dose VE was 77.0% (60.7-86.5%) against Delta infection.ConclusionsTwo doses of mRNA-1273 were highly effective against all SARS-CoV-2 variants. However, VE against Delta moderately declined with increasing time since vaccination.Trial Registration NumberNot applicableFundingModerna Inc.

Annotated catalogue of type specimens of helminths

This catalog contains basic information on the helminth type specimens stored in the Institute's Collection, namely, inventory numbers, inventory and status of a type material; the type host, type localization and type location are also indicated. Information is also given on the collection date and collector name, as well as material amount and its preservation quality. For each species, bibliographical references to the original publication and illustrations of type specimens taken from the original sources are given. Where necessary, the descriptions were supplemented with notes regarding the name taxonomic status, fairness or reliability of the published data, the need for nomenclature amendments, etc.

Diversity of edaphic Gamasina mites (Acari: Mesostigmata) in different ecosystems of the Caatinga biome in northeast Brazil

Knowledge of the fauna of soil mites in Brazilian soils is still scarce and limited to a few regions, referring almost exclusively to areas of natural vegetation. The purpose of this research was to evaluate the abundance and diversity of edaphic Gamasina mites (Mesostigmata) on ecosystems of natural vegetation and cultivations of prickly pear, cassava and pasture located in the Caatinga biome in the state of Alagoas, northeast Brazil. Collections were carried out every three months between December 2018 and August 2019. In each collection date and in each ecosystem, 16 soil samples were collected. During the study, a total of 2,979 Gamasina were collected. Representatives of 10 families were identified, one of which, new to science. The largest number of Gamasina collected belonged to Ascidae (60%), followed by Laelapidae (14.3%) and Rhodacaridae (10%). Forty-four morphospecies were found, of which 25 new to science, distributed in 22 genera, two new to science. Protogamasellus mica Athias-Henriot, Protogamasellus sigillophorus Mineiro, Lindquist & Moraes and a new species of Protogamasellus (Ascidae) were the most abundant species. Mean abundance and richness were highest in the natural vegetation (respectively 38.2 mites and 12.6 species per sample), followed by prickly pear (29.6 and 8.6), pasture (20.8 and 8.6) and cassava (10.9 and 5.7). The Shannon-Weaver’s index diversity was highest for pasture (2.6) and lowest for the natural vegetation (2.2). The equitability indexes were quite similar in the different ecosystems though slightly lower in the natural vegetation (0.7 in the natural vegetation and 0.8 in other ecosystems). A cluster analysis indicated that the area of natural vegetation was the most distant from the others. Several of the species collected belong to Laelapidae and Macrochelidae, families with species used in the applied biological pest control. Thus, it is hoped that this work will serve as a basis for future applied research, aimed at prospecting Gamasina potentially useful for use in biological control programs.

CoVizu: Rapid analysis and visualization of the global diversity of SARS-CoV-2 genomes

Phylogenetics has played a pivotal role in the genomic epidemiology of SARS-CoV-2, such as tracking the emergence and global spread of variants, and scientific communication. However, the rapid accumulation of genomic data from around the world - with over two million genomes currently available in the GISAID database - is testing the limits of standard phylogenetic methods. Here, we describe a new approach to rapidly analyze and visualize large numbers of SARS-CoV-2 genomes. Using Python, genomes are filtered for problematic sites, incomplete coverage, and excessive divergence from a strict molecular clock. All differences from the reference genome, including indels, are extracted using minimap2, and compactly stored as a set of features for each genome. For each Pango lineage (https://cov-lineages.org), we collapse genomes with identical features into 'variants', generate 100 bootstrap samples of the feature set union to generate weights, and compute the symmetric differences between the weighted feature sets for every pair of variants. The resulting distance matrices are used to generate neigihbor-joining trees in RapidNJ and converted into a majority-rule consensus tree for the lineage. Branches with support values below 50% or mean lengths below 0.5 differences are collapsed, and tip labels on affected branches are mapped to internal nodes as directly-sampled ancestral variants. Currently, we process about 1.6 million genomes in approximately nine hours on 34 cores. The resulting trees are visualized using the JavaScript framework D3.js as 'beadplots', in which variants are represented by horizontal line segments, annotated with beads representing samples by collection date. Variants are linked by vertical edges to represent branches in the consensus tree. These visualizations are published at https://filogeneti.ca/CoVizu. All source code was released under an MIT license at https://github.com/PoonLab/covizu.

Evaluation of hemolysis during storage of red blood cell concentrates processed by centrifugation and settling method by simple gravity in Burkina Faso

Background: Hemolysis is one of the red blood cell concentrates (RCCs) storage concerns. In Burkina Faso, hemolysis rate was not routinely assessed in RCCs. Our study aimed at assessing the degree of hemolysis in RCCs processed by centrifugation (centrifuged RCCs) and whole blood settling by simple gravity (Sedimented RCCs) in Burkina Faso. Methods: We conducted a cross-sectional comparative study on 46 prepared by centrifugation and 46 prepared by sedimentation, matched on their collection date and initial volume of whole blood. The hemolysis percent was measured on Days 0, 7, 14, 21, 28 and 32. Results: In the centrifuged RCCs, the hemolysis percent on D0 was 0.232% versus 0.199% for the sedimented RCCs (p = 0.046). At D32, the average hemolysis percent was 835% for the sedimented RCCs and 0.779% for the centrifuged RCCs (p = 0.042). The degree of hemolysis increased gradually between D0 and D32 with an average increase of 0.120% for centrifuged RCCs and 0.116% for sedimented RCCs. Conclusion: The degree of hemolysis at D32 in both centrifuged RCCs and sedimented RCCs falls below standards. Therefore, it necessary to revisit blood components processing procedures, focusing on the centrifugation parameters and the handling conditions.

A dataset on type specimens of hemipteran insects in China

Type specimens are valuable resources for investigating and exploring biodiversity on Earth, which has high academic and conservation value. Hemipteran insects are one of the most important and diverse groups in Insecta and their type specimens have important reference value for many research fields. So far, the data on the type specimens of the Hemiptera in China have not been fully collated. Through extensive literature review, we have constructed a dataset of type specimens for the new species of hemipteran insects in China published from 1950 to 2017, which includes the data such as collection date, specimen gender, preservation institution and geographical distribution. A total of 6,583 type specimen records were collected, covering 3,783 new species belonging to 1,299 genera and 88 families. This dataset can support the international community in conducting research on taxonomy, biodiversity, evolution and pest management.

Determination of Sex in Ungulate Herbivores via near Infrared Spectroscopy of Hair: Growing Cattle as a Surrogate Model

Near infrared spectroscopy (NIRS) has been used in a variety of medical and veterinary science applications. In particular, NIRS calibrations have been developed in livestock for steroid content in cattle hair, and wound age or stage of healing in hot iron cattle brands. These NIRS applications also have potential utility in forensic science. Portable NIRS instruments facilitate measurements on live animals and or animal samples in the field. The objective of this study was to evaluate the efficacy of determining sex in growing cattle via NIRS of hair utilizing a portable spectrometer. In two consecutive years, log 1/R spectra (350–2500 nm) were collected using an ASD Field Spec fitted with a contact probe. Experimental subjects were Bos taurus cross calves (n = 12, yr 1; n = 14, yr 2) born to cows grazing central Arizona rangeland. Calf age was approximately 60, 90 and 210 d at branding, estrus synchronization, and weaning, respectively. As cattle were gathered for these routine working events, a total of 7 M and 19 F calves were scanned 3 times each over the left ribcage. A linear discriminant function was applied to spectral data in order to determine sample membership in M or F groups at each collection date. Chi-square procedures were used to determine differences (P < 0.05) in proportion of correct identifications per group and collection date. Overall, 86% of F and 72% of M were correctly (P < 0.05) identified. Corresponding values were 82% for F and 71% for M at branding, 100% for F and 89% for M at estrus synchronization, and 86% for F and 64% for M at weaning. Calf sex was successfully determined using portable NIRS in this proof of concept study. Efficacy of this method should be evaluated for different ungulate herbivores and under additional collection scenarios.

Harvest time affects antioxidant capacity, total polyphenol and flavonoid content of Polish St John’s wort’s (Hypericum perforatum L.) flowers

The polyphenol content and antioxidant capacity of hyperforin and hypericin-standardized H. perforatum L. extracts may vary due to the harvest time. In this work, ethanol and ethanol–water extracts of air-dried and lyophilized flowers of H. perforatum L., collected throughout a vegetation season in central Poland, were studied. Air-dried flowers extracts had higher polyphenol (371 mg GAE/g) and flavonoid (160 mg CAE/g) content, DPPH radical scavenging (1672 mg DPPH/g), ORAC (5214 µmol TE/g) and FRAP (2.54 mmol Fe2+/g) than lyophilized flowers extracts (238 mg GAE/g, 107 mg CAE/g, 1287 mg DPPH/g, 3313 µmol TE/g and 0.31 mmol Fe2+/g, respectively). Principal component analysis showed that the collection date influenced the flavonoid and polyphenol contents and FRAP of ethanol extracts, and DPPH and ORAC values of ethanol–water extracts. The ethanol extracts with the highest polyphenol and flavonoid content protected human erythrocytes against bisphenol A-induced damage. Both high field and benchtop NMR spectra of selected extracts, revealed differences in composition caused by extraction solvent and raw material collection date. Moreover, we have shown that benchtop NMR can be used to detect the compositional variation of extracts if the assignment of signals is done previously.