Competitive fitness and homologous recombination of SARS-CoV-2 variants of concern.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants continue to emerge and cocirculate in humans and wild animals. The factors driving the emergence and replacement of novel variants and recombinants remain incompletely understood. Herein, we comprehensively characterized the competitive fitness of SARS-CoV-2 wild type (WT) and three variants of concern (VOCs), Alpha, Beta and Delta, by coinfection and serial passaging assays in different susceptible cells. Deep sequencing analyses revealed cell-specific competitive fitness: the Beta variant showed enhanced replication fitness during serial passage in Caco-2 cells, whereas the WT and Alpha variant showed elevated fitness in Vero E6 cells. Interestingly, a high level of neutralizing antibody sped up competition and completely reshaped the fitness advantages of different variants. More importantly, single clone purification identified a significant proportion of homologous recombinants that emerged during the passage history, and immune pressure reduced the frequency of recombination. Interestingly, a recombination hot region located between nucleotide sites 22,995 and 28,866 of the viral genomes could be identified in most of the detected recombinants. Our study not only profiled the variable competitive fitness of SARS-CoV-2 under different conditions, but also provided direct experimental evidence of homologous recombination between SARS-CoV-2 viruses, as well as a model for investigating SARS-CoV-2 recombination.

Population genomics study of Vibrio alginolyticus.

Vibrio alginolyticus is a Gram-negative bacillus that causes vibriosis to human and aquatic products, including fish, shrimp and shellfish. It poses a threat to public health and causes enormous economic losses to the aquaculture industry. However, research on genetic diversity and pathogenicity-related genetic elements based on whole genome is still lacking. In this study, sixty-eight strains of V. alginolyticus were collected from four provinces of China and the whole genome sequences were obtained. Combined with 113 publicly available genome sequences downloaded from NCBI, we inferred the population structure of V. alginolyticus by using fineSTRUCTURE software, and identified the virulence and antibiotic resistance factors using the VFDB, CARD and ResFinder database. The results indicated that V. alginolyticus included two main lineages, named Lineage 1 and Lineage 2. Both lineages distributed in America and Asia, but all the European genomes were classified into Lineage 1. A single cross-ocean transmission event was inferred from one of the 12 identified clonal groups in our dataset. V. alginolyticus genome contains a variety of virulence factors, such as tlh, OmpU, and IlpA, etc. The distribution of virulence factors revealed no lineage-specificity, but some of which revealed differences in their geographical distribution. A lower frequency of VP1611, vcrD, vopD, fleR/flrC and a higher frequency of IlpA were observed in genomes of Europe than other continents. In China, a lower frequency of fleR/flrC, and no IlpA were observed in genomes from Guangxi province. Among the identified antibiotic resistance genes, TxR and fos are significantly enriched in Lineage 2. In addition, TxR is more common in genomes from Asia, compared with the American and European genomes. But in China, the frequency of TxR in Sichuan genomes is much lower than in other provinces. We also found that large fragments of plasmids or ICEs that carried multiple drug resistance genes were present in five V. alginolyticus genomes (VA24, VA28, 2014V-1011, ZJ-T and Vb1833). Based on population genomics analysis, our study delineated the population structure, distribution of virulence and antibiotic resistance related factors of V. alginolyticus, which lays a foundation for future study of genetic characters and pathogenesis mechanism of this pathogen and will improve the works on monitoring, prevention and control of this pathogen.

Asperfuranones A-C, 3(2H)-furanone derivatives from the fungus Aspergillus sp. and the configuration reassignment of their eighteen analogues.

Three undescribed 3(2H)-furanone derivatives, asperfuranones A-C (1-3), along with one known compound (4) were isolated from the Aspergillus sp. strain obtained from the intestines of centipede. Their structures were determined by NMR and MS spectroscopic analyses, and the absolute configurations were established by the Snatzke's sector rules, modified Mosher's method and electronic circular dichroism (ECD) calculation. Meanwhile, the application of the sector rules led to the reassignment of the absolute configurations of 4 and other seventeen previously reported analogues (5-21).

Comparison of the physical and thermodynamic stability of amorphous azelnidipine and its coamorphous phase with piperazine.

A major challenge in drug development is that the majority of drugs are water insoluble, and a powerful method to conquer this obstacle is to transfer a crystalline drug into its amorphous phase (AP) or coamorphous phase (CAP) with a coformer. In the present study, the physical and chemical stabilities of an AP and a CAP based on the dihydropyridine calcium ion antagonist azelnidipine (AZE) were investigated using thermal analysis and a solution chemistry method. The identification of two APs (named α-AP and ß-AP, from crystalline α-AZE and ß-AZE, respectively) and one AZE-piperazine CAP was attempted using powder X-ray diffraction, temperature modulated differential scanning calorimetry and Fourier-transform infrared spectroscopy. The transition thermodynamics from the two APs and the CAP to stable crystalline ß-AZE (ß-Cry) were investigated using a solubility method. The solubility of the two APs, the CAP and ß-Cry in 0.01 M HCl medium at 298, 304, 310, 316 and 322 K was investigated; the values obtained were used to calculate the thermodynamic parameters of the transition reaction. The transition temperatures of α-AP, ß-AP and the CAP to form ß-Cry in 0.01 M HCl were 237.7, 400.3, and 231.4 K, respectively. The glass transition temperature (T g) values of α-AP, ß-AP and the CAP were 365.5, 358.9 and 347.6 K, respectively, indicating a high physical stability for α-AP. However, ß-AP proved to be the most thermodynamically stable form at room temperature compared with α-AP and CAP in the 0.01 M HCl medium. As evidenced by those observations, no general relationship occurred between the solid physical stability and the solution chemical stability for AP and CAP. The kinetics of the solid-state decomposition, studied using DSC analysis, showed that the activation energies for decomposition of α-AP, ß-AP and CAP at high temperatures were 133.0, 114.2 and 131.6 kJ mol-1, respectively.

Citrifurans A-D, Four Dimeric Aromatic Polyketides with New Carbon Skeletons from the Fungus Aspergillus sp.

Citrifurans A-D (1-4), metabolized by an Aspergillus sp., are unusual dimers of azaphilone and furanone derivatives. Michael addition was thought to be the pivotal procedure in their biosynthesis, and different addition sites generated two new different carbon skeletons. Their structures were elucidated on the basis of spectroscopic methods, single-crystal X-ray diffraction, chemical conversion, and electronic circular dichroism analyses. Compounds 1-3 showed moderate inhibitory activities against LPS-induced NO production in RAW 264.7 macrophages with IC50 values of 18.3, 22.6, and 25.3 µM, respectively.

Avian leukosis virus subgroup J triggers caspase-1-mediated inflammatory response in chick livers.

Many pathogens trigger caspase-1-mediated innate immune responses. Avian leukosis virus subgroup J (ALV-J) causes serious immunosuppression and diverse tumors in chicks. The caspase-1 inflammasome mechanism of response to ALV-J invading remains unclear. Here we investigated the expression of caspase-1, the inflammasome adaptor NLRP3, IL-1ß and IL-18 in response to ALV-J infection in the liver of chick. We found caspase-1 mRNA expression was elevated at 5 dpi and peaked at 7 dpi in ALV-J infected animals. Corresponding to this, the expressions of NLRP3 and proinflammatory cytokines IL-1ß and IL-18 were significantly increased at 5 or 7 dpi. In addition, caspase-1 protein expression and inflammatory cell infiltration were induced after virus infection. These results indicated that ALV-J infection could trigger the caspase-1- mediated inflammatory response in chicks. Thus, an understanding of the inflammatory responses can provide a better insight into the pathogenicity of ALV-J and a possible anti-virus target for ALV-J infection.