Fatal Pneumonia Associated With a Novel Genotype of Human Coronavirus OC43

Since its first discovery in 1967, human coronavirus OC43 (HCoV-OC43) has been associated with mild self-limiting upper respiratory infections worldwide. Fatal primary pneumonia due to HCoV-OC43 is not frequently described. This study describes a case of fatal primary pneumonia associated with HCoV-OC43 in a 75-year-old patient with good past health. The viral loads of the respiratory tract specimens (bronchoalveolar lavage and endotracheal aspirate) from diagnosis to death were persistently high (3.49 × 106–1.10 × 1010 copies/ml). HCoV-OC43 at a 6.46 × 103 copies/ml level was also detected from his pleural fluid 2 days before his death. Complete genome sequencing and phylogenetic analysis showed that the present HCoV-OC43 forms a distinct cluster with three other HCoV-OC43 from United States, with a bootstrap value of 100% and sharing 99.9% nucleotide identities. Pairwise genetic distance between this cluster and other HCoV-OC43 genotypes ranged from 0.27 ± 0.02% to 1.25 ± 0.01%. In contrast, the lowest pairwise genetic distance between existing HCoV-OC43 genotypes was 0.26 ± 0.02%, suggesting that this cluster constitutes a novel HCoV-OC43 genotype, which we named genotype I. Unlike genotypes D, E, F, G, and H, no recombination event was observed for this novel genotype. Structural modeling revealed that the loop with the S1/S2 cleavage site was four amino acids longer than other HCoV-OC43, making it more exposed and accessible to protease, which may have resulted in its possible hypervirulence.

Life in the desert: habitat spatial complexity, gene flow, and functional connectivity in Ivesia webberi

Habitat protection, by itself, is not sufficient to conserve range-restricted species with disjunct populations. Indeed, it becomes critical to characterize gene flow among the populations and factors that influence functional connectivity in order to design effective conservation programs for such species. In this study, we genotyped 314 individuals of Ivesia webberi, a United States federally threatened Great Basin Desert perennial forb using six microsatellite loci, to estimate genetic diversity and population genetic structure, as well as rates and direction of gene flow among 16 extant I. webberi populations. We assessed the effects of Euclidean distance, landscape features, and ecological dissimilarity on the genetic structure of the sampled populations, while also testing for a relationship between I. webberi genetic diversity and diversity in the vegetative communities. The results show low levels of genetic diversity overall (He = 0.200–0.441; Ho = 0.192–0.605) and high genetic differentiation among populations. Genetic diversity was structured along a geographic gradient, congruent with patterns of isolation by distance. Populations near the species’ range core have relatively high genetic diversity, supporting a central-marginal pattern, while peripheral populations have lower genetic diversity, significantly higher genetic distances, higher relatedness, and evidence of genetic bottlenecks. Genotype cluster admixture results support a predominant west to east gene flow pattern for populations near the species’ range center, as well as smaller genotype clusters with a narrow north to south distribution and little admixture, suggesting that dispersal direction and distance vary on the landscape. Pairwise genetic distance strongly correlates with actual evapotranspiration and precipitation, indicating a role for isolation by environment, which the observed phenological mismatches among the populations also support. The significant correlation between pairwise genetic distance and dissimilarity in the soil seed bank suggest that annual regeneration of the floristic communities contributes to the maintenance of genetic diversity in I. webberi.

Genetic diversity of Turkish lathyrus L. landraces using ISSR markers

Fifty-one Lathyrus sativus L. landraces and one L. clymenum L. landrace collected from Turkey and one L. sativus cultivar, G?rb?z, were evaluated with ISSR markers in this study to molecular characterization. Three ISSR primers were used and 45 DNA fragment were evaluated, of which 44 bands were polymorphic. The frequencies of scored bands ranged from 0.009 to 0.888 and averaged 0.363. The genotypes MLT04 and NEV02 had high similarity with 0.825 according to pairwise grouping. The furthest pairwise group was G?rb?z and MLT02 with 0.244. The nearest genotype to G?rb?z was CNR03 with 0.577. The pairwise genetic distance between L. clymenum and L. sativus ranged from 0.353 (accession NEV01) to 0.637 (accession DEN04) and pairwise genetic distance to the cultivar G?rb?z was 0.375. Assessment of genetic relationships among Lathyrus genotypes made two main groups. One of them covered only G?rb?z variety and the other covered 52 Lathyrus landrace. L. sativus and L. clymenum separated prominently in the second group.

A new species of the Cyrtodactylus irregularis complex (Squamata: Gekkonidae) from Gia Lai Province, Central Highlands of Vietnam

We describe a new species of the genus Cyrtodactylus from Gia Lai Province, Central Highlands of Vietnam based on morphological and molecular differences. Cyrtodactylus gialaiensis sp. nov. is differentiated from other congeners by a unique combination of the following characters: Size small, maximum known SVL reaching 62.8 mm; dorsal pattern consisting of six or seven dark transverse bands between limb insertions; intersupranasals two or three; dorsal tubercles at midbody in 16–21 irregular rows, strongly developed on flanks; lateral folds poorly defined with interspersed tubercles; ventral scales between ventrolateral folds 38–45; precloacal pores nine or 10 in males, eight pitted scales in the adult female, in a continuous row; femoral pores absent; enlarged femoral scales present; postcloacal tubercles two or three; dorsal tubercles present to half of tail; subcaudal scales not enlarged. In molecular analyses, the new species is weakly supported as a member of the Cyrtodactylus irregularis species group with a minimum pairwise genetic distance of 13.7% from others within the group.

Variance in Estimated Pairwise Genetic Distance Under High versus Low Coverage Sequencing: the Contribution of Linkage Disequilibrium

The mean pairwise genetic distance among haplotypes is an estimator of the population mutation rate θ and a standard measure of variation in a population. With the advent of next-generation sequencing (NGS) methods, this and other population parameters can be estimated under different modes of sampling. One approach is to sequence individual genomes with high coverage, and to calculate genetic distance over all sample pairs. The second approach, typically used for microbial samples or for tumor cells, is sequencing a large number of pooled genomes with very low individual coverage. With low coverage, pairwise genetic distances are calculated across independently sampled sites rather than across individual genomes. In this study, we show that the variance in genetic distance estimates is reduced with low coverage sampling if the mean pairwise linkage disequilibrium weighted by allele frequencies is positive. Practically, this means that if on average the most frequent alleles over pairs of loci are in positive linkage disequilibrium, low coverage sequencing results in improved estimates of θ, assuming similar per-site read depths. We show that this result holds under the expected distribution of allele frequencies and linkage disequilibria for an infinite sites model at mutation-drift equilibrium. From simulations, we find that the conditions for reduced variance only fail to hold in cases where variant alleles are few and at very low frequency. These results are applied to haplotype frequencies from a lung cancer tumor to compute the weighted linkage disequilibria and the expected error in estimated genetic distance using high versus low coverage.