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Pneumoconiosis is a common occupational disease that can worsen with accompanying infection. Torque teno virus (TTV) is a prevalent human virus with multiple genotypes that can chronically and persistently infect individuals. However, the prevalence of TTV in pneumoconiosis patients is still unclear. This research aims to detect the presence and prevalence of TTV in the alveolar lavage fluid of pneumoconiosis patients in the Hunan Province of China using PCR. As a result, a 65.5% positive rate (19 out of 29) of TTV was detected. The TTV detection rate varies among different stages of silicosis and different pneumoconiosis patient ages. Nine novel TTV genomes ranging in size from 3719 to 3908 nt, named TTV HNPP1, HNPP2, HNPP3, HNPP4, HNPP5, HNPP6-1, HNPP6-2, HNPP7-1 and HNPP7-2, were identified. A genomic comparison and phylogenetic analysis indicated that these nine TTVs represent five different species with high genetic diversity which belong to the genus Alphatorquevirus. HNPP6-1 and HNPP6-2 belong to TTV3, HNPP5 belongs to TTV13, HNPP1 belongs to TTV24, HNPP4 belongs to TTV20, and the others belong to TTV19. The genomes of TTV HNPP1, HNPP6-1, and HNPP6-2 contain three putative open reading frames (ORFs) coding for proteins, ORF1, ORF2, and ORF3, while the other six TTV genomes contain two ORFs coding for proteins, ORF1 and ORF2. These results provide the first description of TTV epidemiology in pneumoconiosis patients in China. The newly identified TTV genome sequences reveal the high genetic diversity of TTV in pneumoconiosis patients and could contribute to a deeper understanding of TTV retention and infection in humans. [ABSTRACT FROM AUTHOR]

This study aimed to improve the mechanical properties of predisintegrated carbonaceous mudstone (PCM) used as an embankment fill. The four factors used in the orthogonal design test were nano-Al2O3 content, cement content, water content and compaction. After the tests were completed the strength characteristics and micromechanisms of PCM modified by nano-Al2O3 and cement were studied using triaxial compression tests, X-ray diffraction analysis and SEM observations. The results show that the failure mode of PCM changes from bulging failure to shear failure when the nano-Al2O3 and cement contents are increased. The order in which the factors affected the cohesion of PCM is cement content, nano-Al2O3 content, water content and compaction. At a given cement content, the cohesion of PCM with an optimal compaction of 96% and a water content of 8% increases and then decreases with increasing nano-Al2O3 content. The increase in the internal friction angle is proportional to the nano-Al2O3 content when the cement content is between 0 and 4%. Controlling the nano-Al2O3 and cement contents to 0.3 and 8%, respectively, results in a synergistic effect of both materials on the shear strength. Nano-Al2O3 improves the cohesion and friction strength of PCM by accelerating the hydration of cement and optimizing the structure of the hydration products. [ABSTRACT FROM AUTHOR]

To control the ongoing COVID‐19 pandemic, a variety of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) vaccines have been developed. However, the rapid mutations of SARS‐CoV‐2 spike (S) protein may reduce the protective efficacy of the existing vaccines which is mainly determined by the level of neutralizing antibodies targeting S. In this study, we screened prevalent S mutations and constructed 124 pseudotyped lentiviral particles carrying these mutants. We challenged these pseudoviruses with sera vaccinated by Sinovac CoronaVac and ZF2001 vaccines, two popular vaccines designed for the initial strain of SARS‐CoV‐2, and then systematically assessed the susceptivity of these SARS‐CoV‐2 variants to the immune sera of vaccines. As a result, 14 S mutants (H146Y, V320I + S477N, V382L, K444R, L455F + S477N, L452M + F486L, F486L, Y508H, P521R, A626S, S477N + S698L, A701V, S477N + T778I, E1144Q) were found to be significantly resistant to neutralization, indicating reduced protective efficacy of the vaccines against these SARS‐CoV‐2 variants. In addition, F486L and Y508H significantly enhanced the utilization of human angiotensin‐converting enzyme 2, suggesting a potentially elevated infectivity of these two mutants. In conclusion, our results show that some prevalent S mutations of SARS‐CoV‐2 reduced the protective efficacy of current vaccines and enhance the infectivity of the virus, indicating the necessity of vaccine renewal and providing direction for the development of new vaccines. [ABSTRACT FROM AUTHOR]

Genomic recombination is an important driving force for viral evolution, and recombination events have been reported for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during the Coronavirus Disease 2019 pandemic, which significantly alter viral infectivity and transmissibility. However, it is difficult to identify viral recombination, especially for low-divergence viruses such as SARS-CoV-2, since it is hard to distinguish recombination from in situ mutation. Herein, we applied information theory to viral recombination analysis and developed VirusRecom, a program for efficiently screening recombination events on viral genome. In principle, we considered a recombination event as a transmission process of ''information'' and introduced weighted information content (WIC) to quantify the contribution of recombination to a certain region on viral genome; then, we identified the recombination regions by comparing WICs of different regions. In the benchmark using simulated data, VirusRecom showed a good balance between precision and recall compared to two competing tools, RDP5 and 3SEQ. In the detection of SARS-CoV-2 XE, XD and XF recombinants, VirusRecom providing more accurate positions of recombination regions than RDP5 and 3SEQ. In addition, we encapsulated the VirusRecom program into a command-line-interface software for convenient operation by users. In summary, we developed a novel approach based on information theory to identify viral recombination within highly similar sequences, providing a useful tool for monitoring viral evolution and epidemic control. [ABSTRACT FROM AUTHOR]