SARS-CoV-2 within-host diversity of human hosts and its implications for viral immune evasion.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is continuously evolving, bringing great challenges to the control of the virus. In the present study, we investigated the characteristics of SARS-CoV-2 within-host diversity of human hosts and its implications for immune evasion using about 2,00,000 high-depth next-generation genome sequencing data of SARS-CoV-2. A total of 44% of the samples showed within-host variations (iSNVs), and the average number of iSNVs in the samples with iSNV was 1.90. C-to-U is the dominant substitution pattern for iSNVs. C-to-U/G-to-A and A-to-G/U-to-C preferentially occur in 5'-CG-3' and 5'-AU-3' motifs, respectively. In addition, we found that SARS-CoV-2 within-host variations are under negative selection. About 15.6% iSNVs had an impact on the content of the CpG dinucleotide (CpG) in SARS-CoV-2 genomes. We detected signatures of faster loss of CpG-gaining iSNVs, possibly resulting from zinc-finger antiviral protein-mediated antiviral activities targeting CpG, which could be the major reason for CpG depletion in SARS-CoV-2 consensus genomes. The non-synonymous iSNVs in the S gene can largely alter the S protein's antigenic features, and many of these iSNVs are distributed in the amino-terminal domain (NTD) and receptor-binding domain (RBD). These results suggest that SARS-CoV-2 interacts actively with human hosts and attempts to take different evolutionary strategies to escape human innate and adaptive immunity. These new findings further deepen and widen our understanding of the within-host evolutionary features of SARS-CoV-2. IMPORTANCE Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative pathogen of the coronavirus disease 2019, has evolved rapidly since it was discovered. Recent studies have pointed out that some mutations in the SARS-CoV-2 S protein could confer SARS-CoV-2 the ability to evade the human adaptive immune system. In addition, it is observed that the content of the CpG dinucleotide in SARS-CoV-2 genome sequences has decreased over time, reflecting the adaptation to the human host. The significance of our research is revealing the characteristics of SARS-CoV-2 within-host diversity of human hosts, identifying the causes of CpG depletion in SARS-CoV-2 consensus genomes, and exploring the potential impacts of non-synonymous within-host variations in the S gene on immune escape, which could further deepen and widen our understanding of the evolutionary features of SARS-CoV-2.

Environmental behaviors and degradation methods of microplastics in different environmental media.

Microplastics, as a group of emerging contaminants, are widely present in environmental media and have the potential to endanger the ecological environment and human health. Due to the inconsistencies and difficulties inherent in the analysis of microplastic particles, global monitoring data on the distribution of microplastics in the environment are still far from sufficient. The fate and migration of microplastics in the environment are also uncertain. Therefore, there have been increasing reviews on the distribution, biological effects, migration, and health risks of microplastics. However, reports focusing on the degradation of microplastics are still rare. Understanding and commanding the environmental behavior of microplastics are of great significance to explore the treatment of microplastic pollution. Although some preliminary studies on microplastics have been carried out, there is still an urgent need to conduct a comprehensive study on environmental behaviors and degradation methods of microplastics in different environmental media. This article summarizes the recent advances on microplastics, basically includes the distribution and ecological impact of microplastics in soil and water environments, then elaborates the migration behavior and influencing factors of microplastics, and focuses on the research progress of microplastics degradation methods. On this basis, the problems existing in the current research and the future development directions have been proposed. This review could provide a more systematic reference for the development and research of microplastics in the future.

Analyses of Long-Term Epidemic Trends and Evolution Characteristics of Haplotype Subtypes Reveal the Dynamic Selection on SARS-CoV-2.

The scale of SARS-CoV-2 infection and death is so enormous that further study of the molecular and evolutionary characteristics of SARS-CoV-2 will help us better understand and respond to SARS-CoV-2 outbreaks. The present study analyzed the epidemic and evolutionary characteristics of haplotype subtypes or regions based on 1.8 million high-quality SARS-CoV-2 genomic data. The estimated ratio of the rates of non-synonymous to synonymous changes (Ka/Ks) in North America and the United States were always more than 1.0, while the Ka/Ks in other continents and countries showed a sharp decline, then a slow increase to 1.0, and a dramatic increase over time. H1 (B.1) with the highest substitution rate has become the most dominant haplotype subtype since March 2020 and has evolved into multiple haplotype subtypes with smaller substitution rates. Many evolutionary characteristics of early SARS-CoV-2, such as H3 being the only early haplotype subtype that existed for the shortest time, the global prevalence of H1 and H1-5 (B.1.1) within a month after being detected, and many high divergent genome sequences early in February 2020, indicate the missing of early SARS-CoV-2 genomic data. SARS-CoV-2 experienced dynamic selection from December 2019 to August 2021 and has been under strong positive selection since May 2021. Its transmissibility and the ability of immune escape may be greatly enhanced over time. This will bring greater challenges to the control of the pandemic.

Rapid and accurate detection of SARS-CoV-2 mutations using a Cas12a-based sensing platform.

The increasing prevalence of SARS-CoV-2 variants with spike mutations has raised concerns owing to higher transmission rates, disease severity, and escape from neutralizing antibodies. Rapid and accurate detection of SARS-CoV-2 variants provides crucial information concerning the outbreaks of SARS-CoV-2 variants and possible lines of transmission. This information is vital for infection prevention and control. We used a Cas12a-based RT-PCR combined with CRISPR on-site rapid detection system (RT-CORDS) platform to detect the key mutations in SARS-CoV-2 variants, such as 69/70 deletion, N501Y, and D614G. We used type-specific CRISPR RNAs (crRNAs) to identify wild-type (crRNA-W) and mutant (crRNA-M) sequences of SARS-CoV-2. We successfully differentiated mutant variants from wild-type SARS-CoV-2 with a sensitivity of 10-17 M (approximately 6 copies/µL). The assay took just 10 min with the Cas12a/crRNA reaction after a simple RT-PCR using a fluorescence reporting system. In addition, a sensitivity of 10-16 M could be achieved when lateral flow strips were used as readouts. The accuracy of RT-CORDS for SARS-CoV-2 variant detection was 100% consistent with the sequencing data. In conclusion, using the RT-CORDS platform, we accurately, sensitively, specifically, and rapidly detected SARS-CoV-2 variants. This method may be used in clinical diagnosis.

AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus.

In our previous work, we developed an automated tool, AutoVEM, for real-time monitoring the candidate key mutations and epidemic trends of SARS-CoV-2. In this research, we further developed AutoVEM into AutoVEM2. AutoVEM2 is composed of three modules, including call module, analysis module, and plot module, which can be used modularly or as a whole for any virus, as long as the corresponding reference genome is provided. Therefore, it's much more flexible than AutoVEM. Here, we analyzed three existing viruses by AutoVEM2, including SARS-CoV-2, HBV and HPV-16, to show the functions, effectiveness and flexibility of AutoVEM2. We found that the N501Y locus was almost completely linked to the other 16 loci in SARS-CoV-2 genomes from the UK and Europe. Among the 17 loci, 5 loci were on the S protein and all of the five mutations cause amino acid changes, which may influence the epidemic traits of SARS-CoV-2. And some candidate key mutations of HBV and HPV-16, including T350G of HPV-16 and C659T of HBV, were detected. In brief, we developed a flexible automated tool to analyze candidate key mutations and epidemic trends for any virus, which would become a standard process for virus analysis based on genome sequences in the future.

AutoVEM: An automated tool to real-time monitor epidemic trends and key mutations in SARS-CoV-2 evolution.

With the global epidemic of SARS-CoV-2, it is important to effectively monitor the variation, haplotype subgroup epidemic trends and key mutations of SARS-CoV-2 over time. This is of great significance to the development of new vaccines, the update of therapeutic drugs, and the improvement of detection methods. The AutoVEM tool developed in the present study could complete all mutations detections, haplotypes classification, haplotype subgroup epidemic trends and candidate key mutations analysis for 131,576 SARS-CoV-2 genome sequences in 18 h on a 1 core CPU and 2 GB RAM computer. Through haplotype subgroup epidemic trends analysis of 131,576 genome sequences, the great significance of the previous 4 specific sites (C241T, C3037T, C14408T and A23403G) was further revealed, and 6 new mutation sites of highly linked (T445C, C6286T, C22227T, G25563T, C26801G and G29645T) were discovered for the first time that might be related to the infectivity, pathogenicity or host adaptability of SARS-CoV-2. In brief, we proposed an integrative method and developed an efficient automated tool to monitor haplotype subgroup epidemic trends and screen for the candidate key mutations in the evolution of SARS-CoV-2 over time for the first time, and all data could be updated quickly to track the prevalence of previous key mutations and new candidate key mutations because of high efficiency of the tool. In addition, the idea of combinatorial analysis in the present study can also provide a reference for the mutation monitoring of other viruses.

Design, synthesis, insecticidal activity and structure-activity relationship of 3,3-dichloro-2-propenyloxy-containing phthalic acid diamide structures.

BACKGROUND: Phthalic acid diamide derivatives are among the most important classes of synthetic insecticides. In this study, a 3,3-dichloro-2-propenyloxy group, the essential active group of pyridalyl derivatives, was incorporated into phthalic acid diamide derivatives with the aim of combining the active groups to generate more potent insecticides. RESULTS: Thirty-one new phthalic acid diamides were obtained, and these were characterised by (1) H and (13) C NMR. The structure of N(2) -[1,1-dimethyl-2-(methoxy)ethyl]-3-iodo-N(1) -[4-(3,3-dichloro-2-propenyloxy)-3-(trifluoromethyl)phenyl]-1,2-benzenedicarboxamide was determined by X-ray diffraction crystallography. The insecticidal activities of the compounds against Plutella xylostella were evaluated. The title compounds exhibited excellent larvicidal activities against P. xylostella. Structure-activity relationships revealed that varying the combination of aliphatic amide and aromatic amide moieties, or the nature and position of substituent Y on the aniline ring, could aid the design of structures with superior performance. CONCLUSION: A series of novel phthalic acid diamides containing a 3,3-dichloro-2-propenyloxy group at the 4-position of the aniline ring were designed and synthesised. Structure-activity relationships with the parent structure provided information that could direct further investigation on structure modification.

8-Thia-1,6-diaza-bicyclo-[4.3.0]nonane-7,9-dione.

There are two independent mol-ecules, A and B, in the asymmetric unit of the title compound, C(6)H(8)N(2)O(2)S. In the crystal, pairs of inter-molecular S⋯O contacts [3.286 (1) Å] link the B mol-ecules into inversion dimers.

Synthesis, insecticidal activity, and structure-activity relationship of trifluoromethyl-containing phthalic acid diamide structures.

Phthalic acid diamides have received considerable interest in agricultural chemistry due to a novel action mode, extremely high activity against a broad spectrum of lepidopterous insects, low acute toxicity to mammals, and environmentally benign characteristics. A series of phthalic acid diamides (4I-4IV) with the CF3 group at meta position on the aniline ring were synthesized. Their structures were characterized by (1)H NMR and (13)C NMR (or elemental analysis). The structure of N(2)-[1,1-dimethyl-2-(methylthio)ethyl]-3-iodo-N(1)-[3-fluoro-5-(trifluoromethyl)phenyl]-1,2-benzenedicarboxamide (4If) was determined by X-ray diffraction crystallography. Their insecticidal activities against Plutella xylostella were evaluated. The results show that some of the title compounds exhibit excellent larvicidal activities against P. xylostella, and improvement in larvicidal activity requires a reasonable combination of substituents in the parent structure, which provides some hints for further investigation on structure modification.