[The identification of a novel reassortant H3N2 avian influenza virus based on nanopore sequencing technology and genetic characterization].

Objective: To identify a novel reassortant H3N2 avian influenza virus using nanopore sequencing technology and analyze its genetic characteristics. Methods: The positive samples of the H3N2 avian influenza virus, collected from the external environment in the farmers' market of Guangzhou, were cultured in chicken embryos. The whole genome was sequenced by targeted amplification and nanopore sequencing technology. The genetic characteristics were analyzed using bioinformatics software. Results: The phylogenetic trees showed that each gene fragment of the strain belonged to the Eurasian evolutionary branch, and the host source was of avian origin. The HA gene was closely related to the origin of the H3N6 virus. The NA gene was closely related to the H3N2 avian influenza virus from 2017 to 2020. The PB1 gene was closely related to the H5N6 avian influenza virus in Guangxi Zhuang Autonomous Region and Fujian Province from 2016 to 2022 and was not related to the PB1 gene of the H5N6 avian influenza epidemic strain in Guangzhou. The other internal gene fragments had complex sources with significant genetic diversity. Molecular characteristics indicated that the strain exhibited the molecular characteristics of a typical low pathogenic avian influenza virus and tended to bind to the receptors of avian origin. On important protein sites related to biological characteristics, this strain had mutations of PB2-L89V, PB1-L473V, NP-A184K, M1-N30D/T215A, and NS1-P42S/N205S. Conclusions: This study identified a novel reassortant H3N2 avian influenza virus by nanopore sequencing, with the PB1 gene derived from the H5N6 avian influenza virus. The virus had a low ability to spread across species, but further exploration was needed to determine whether its pathogenicity to the host was affected.

[Epidemiological characteristics of mpox epidemic in Guangzhou].

Objective: To understand the epidemiological characteristics of mpox epidemic in Guangzhou and provide scientific evidence for the prevention and control of the disease. Methods: Based on the mpox surveillance system in Guangzhou, suspected mpox cases with fever and rash were reported by local hospitals at all levels to centers for disease control and prevention in Guangzhou for sampling, investigation and diagnosis. Descriptive epidemiological analysis was conducted on the clinical characteristics and treatment of the mpox cases and positive detection rate reported in Guangzhou as of 24:00 on June 23. Whole genome sequencing of the virus isolates was performed using Illumina Miniseq high-throughput sequencing platform. Results: The first mpox case in Guangzhou was reported on June 10 in 2023. As of 24:00 on June 23, a total of 25 confirmed mpox cases were reported. All the mpox cases were men with a M(Q1,Q3) of 32 (26, 36) years, the majority of the cases were MSM (96.0%). The main clinical features were rash (100.0%, 25/25), lymphadenectasis (100.0%, 25/25) and fever (52.0%, 13/25). Rash usually occurred near the genitals (88.0%, 22/25). The close contacts, mainly family members (40.4%, 23/57), showed no similar symptoms, such as fever or rash. The positive rate of mpox virus in household environment samples was 30.5%. The analyses on 3 complete gene sequences of mpox virus indicated that the strains belonged to West African type Ⅱb clade, B.1.3 lineage. Conclusions: Hidden transmission of mpox virus had occurred in MSM in Guangzhou. However, the size of affected population is relatively limited, and the possibility of wide spread of the virus is low.

[Health-adjusted life expectancy in residents in Guangzhou, 2010-2019].

Objective: To analyze the spatiotemporal distribution of life expectancy (LE) and health-adjusted life expectancy (HALE) in Guangzhou from 2010 to 2019, and quantize the comprehensive impact of different causes and sequelae on health. Methods: The LE, HALE, and cause-excluded health adjusted life expectancy (CEHALE) were estimated using cause-of-death surveillance datasets from Guangzhou Municipal Center for Disease Control and Prevention from 2010 to 2019 and open data from the Global Burden of Disease Study. Joinpoint log-linear regression model was used to analyze the temporal trend and described spatial distribution. Results: In 2019, the LE in residents in Guangzhou was 82.9 years (80.1 years in men and 85.9 years in women), and the HALE was 75.6 years (74.0 years in men and 77.3 years in women). Compared with the urban fringe, the central urban area had higher LE and HALE, and the differences between LE and HALE were small. The LE and HALE in Guangzhou showed an increasing trend from 2010 to 2019. The LE increased by 2.8 years (AAPC=0.4, 95%CI: 0.3-0.4), with the increase of 2.8 years in men and 2.9 years in women. The HALE increased by 2.4 years (AAPC=0.3, 95%CI: 0.3-0.4), with the increase of 2.5 years in men and 2.2 years in women. The median healthy life lost due to communicable, maternal, neonatal, and nutritional diseases was 6.2 years (AAPC=-4.2, 95%CI: -5.3--3.1), while the median healthy life lost due to non-communicable diseases was 14.7 years (AAPC=1.6, 95%CI: 0.9-2.3), the median healthy life expectancy reduced by injury was 6.3 years (AAPC=-3.5, 95%CI: -4.5--2.6). Musculoskeletal disorders, skin and subcutaneous diseases, cardiovascular diseases, nutritional deficiencies, diabetes and kidney diseases were the top five diseases causing healthy life expectancy loss. Conclusion: The LE and HALE in residents in Guangzhou increased steadily from 2010 to 2019, but the quality of life in the urban fringe was lower than that of the central urban area. Non-communicable diseases were the leading causes of healthy life expectancy loss. Health policies and prevention measures should be developed according to area specific characteristics, and social medical resources should be rationally allocated to key diseases to reduce their disease burden.

The architectural organization and mechanistic function of group II intron structural elements.

Group II introns are large, self-splicing RNAs and mobile genetic elements that provide good model systems for studies of RNA folding. The structures and mechanistic functions of individual domains are being elucidated, and long-range tertiary interactions between the domains are being identified, thus helping to define the three-dimensional architecture of the intron.

Antagonistic substrate binding by a group II intron ribozyme.

In this study, the thermodynamic properties of substrate-ribozyme recognition were explored using a system derived from group II intron ai5gamma. Substrate recognition by group II intron ribozymes is of interest because any nucleic ac?id sequence can be targeted, the recognition sequence can be quite long (>/=13 bp), and reaction can proceed with a very high degree of sequence specificity. Group II introns target their substrates throug?h the formation of base-pairing interactions with two regions of the intron (EBS1 and EBS2), which are usually located far apart in the secondary structure. These structures pair with adjacent, corresponding sites (IBS1 and IBS2) on the substrate. In order to understand the relative energetic contribution of each base-pairing interaction (EBS1-IBS1 or EBS2-IBS2) to substrate binding energy, the free energy of each helix was measured. The individual helices were found to have base-pairing free energies similar to those calculated for regular RNA duplexes of the same sequence, suggesting that each recognition helix derives its binding energy from base-pairing interactions alone and that each helix can form independently. Most interestingly, it was found that the sum of the measured individual free energies (approximately 20 kcal/mol) was much higher than the known free energy for substrate binding (approximately 12 kcal/mol). This indicates that certain group II intron ribozymes can bind their substrates in an antagonistic fashion, paying a net energetic penalty upon binding the full-length substrate. This loss of binding energy is not due to weakening of individual helices, but appears to be linked to ribozyme conformational changes induced by substrate binding. This coupling between substrate binding and ribozyme conformational rearrangement may provide a mechanism for lowering overall substrate binding energy while retaining the full information content of 13 bp, thus resulting in a mechanism for ensuring sequence specificity.

Guiding ribozyme cleavage through motif recognition: the mechanism of cleavage site selection by a group ii intron ribozyme.

The mechanism by which group II introns cleave the correct phosphodiester linkage was investigated by studying the reaction of mutant substrates with a ribozyme derived from intron ai5gamma. While fidelity was found to be quite high in most cases, a single mutation on the substrate (+1C) resulted in a dramatic loss of fidelity. When this mutation was combined with a second mutation that induces a bulge in the exon binding site 1/intron binding site 1 (EBS1/IBS1) duplex, the base-pairing register of the EBS1/IBS1 duplex was shifted and the cleavage site moved to a downstream position on the substrate. Conversely, when mismatches were incorporated at the EBS1/IBS1 terminus, the duplex was effectively truncated and cleavage occurred at an upstream site. Taken together, these data demonstrate that the cleavage site of a group II intron ribozyme can be tuned at will by manipulating the thermodynamic stability and structure of the EBS1/IBS1 pairing. The results are consistent with a model in which the cleavage site is not designated through recognition of specific nucleotides (such as the 5'-terminal residue of EBS1). Instead, the ribozyme detects a structure at the junction between single and double-stranded residues on the bound substrate. This finding explains the puzzling lack of phylogenetic conservation in ribozyme and substrate sequences near group II intron target sites.

Stopped-flow fluorescence spectroscopy of a group II intron ribozyme reveals that domain 1 is an independent folding unit with a requirement for specific Mg2+ ions in the tertiary structure.

A stopped-flow fluorescence spectroscopic assay for RNA folding was used to monitor the association of a multicomponent ribozyme derived from group II intron ai5gamma. In the presence of Mg2+, association of a short fluorescein-labeled oligonucleotide substrate with intron domain 1 (D1) resulted in a unique fluorescein emission enhancement, which reflected ribozyme folding and substrate binding. It was found that substrate binding follows a simple bimolecular encounter model, with k(on) approaching the rate of simple duplex formation. The Kd between substrate and D1 was determined to be 11 nM, which is in close agreement with the Kd obtained through oligonucleotide cleavage assays requiring catalytic domain 5 (D5). Ribozyme variants D13 and D135, which contain D3 and/or D5 attached to D1 in-cis, bound substrate with very similar Kd values, suggesting that D1 can fold independently and contains all residues important for ground-state binding to substrate. Both stopped-flow fluorescence assays and chemical modification footprinting data showed that, in all three ribozymes, Mg2+ was required and sufficient for folding. The rates of substrate association and the fraction of active ribozyme showed similar [Mg2+] dependencies, indicating that folding and substrate binding in these three ribozymes are the result of similar processes involving specific, weakly bound Mg2+ ions. The apparent binding constants for the Mg2+ ions were found to be approximately 70 mM in each case. Together, these data show that D1 is an independent folding unit with respect to substrate binding and that specific Mg2+ ions are required for the formation of a distinct tertiary structure in group II introns.

Site-specific labeling of RNA with fluorophores and other structural probes.

Site-specific probes provide a powerful tool for structure and function studies of nucleic acids, especially in elucidating tertiary structures of large ribozymes and other folded RNA molecules. Among many types of extrinsic labels, fluorophores are most attractive because they can provide structural information at millisecond time resolution, thus allowing real-time observation of structural transition during biological function. Methods for introducing fluorophores in RNA molecules are summarized here. These methods are robust and readily applicable to the labeling of other types of probes. However, as each case of RNA modification is unique, fine tuning of the general methodology is beneficial.

Quantitative analysis of the isolated GAAA tetraloop/receptor interaction in solution: a site-directed spin labeling study.

The GNRA (N: any nucleotide; R: purine) tetraloop/receptor interaction is believed to be one of the most frequently occurring tertiary interaction motifs in RNAs, but an isolated tetraloop/receptor complex has not been identified in solution. In the present work, site-directed spin labeling is applied to detect tetraloop/receptor complex formation and estimate the free energy of interaction. For this purpose, the GAAA tetraloop/receptor interaction was chosen as a model system. A method was developed to place nitroxide labels at specific backbone locations in an RNA hairpin containing the GAAA tetraloop. Formation of the tetraloop/receptor complex was monitored through changes in the rotational correlation time of the tetraloop and the attached nitroxide. Results show that a hairpin containing the GAAA tetraloop forms a complex with an RNA containing the 11-nucleotide GAAA tetraloop receptor motif with an apparent Kd that is strongly dependent on Mg2+. At 125 mM MgCl2, Kd = 0.40 +/- 0.05 mM. The corresponding standard free energy of complex formation is -4.6 kcal/mol, representing the energetics of the tetraloop/receptor interaction in the absence of other tertiary constraints. The experimental strategy presented here should have broad utility in quantifying weak interactions that would otherwise be undetectable, for both nucleic acids and nucleic acid-protein complexes.

Sequence specificity of a group II intron ribozyme: multiple mechanisms for promoting unusually high discrimination against mismatched targets.

Group II intron ai5 gamma was reconstructed into a multiple-turnover ribozyme that efficiently cleaves small oligonucleotide substrates in-trans. This construct makes it possible to investigate sequence specificity, since second-order rate constants (kcat/K(m), or the specificity constant) can be obtained and compared with values for mutant substrates and with other ribozymes. The ribozyme used in this study consists of intron domains 1 and 3 connected in-cis, together with domain 5 as a separate catalytic cofactor. This ribozyme has mechanistic features similar to the first step of reverse-splicing, in which a lariat intron attacks exogenous RNA and DNA substrates, and it therefore serves as a model for the sequence specificity of group II intron mobility. To quantitatively evaluate the sequence specificity of this ribozyme, the WT kcat/Km value was compared to individual kcat/Km values for a series of mutant substrates and ribozymes containing single base changes, which were designed to create mismatches at varying positions along the two ribozyme-substrate recognition helices. These mismatches had remarkably large effects on the discrimination index (1/relative kcat/K(m)), resulting in values > 10,000 in several cases. The delta delta G++ for mismatches ranged from 2 to 6 kcal/mol depending on the mismatch and its position. The high specificity of the ribozyme is attributable to effects on duplex stabilization (1-3 kcal/mol) and unexpectedly large effects on the chemical step of reaction (0.5-2.5 kcal/mol). In addition, substrate association is accompanied by an energetic penalty that lowers the overall binding energy between ribozyme and substrate, thereby causing the off-rate to be faster than the rate of catalysis and resulting in high specificity for the cleavage of long target sequences (> or = 13 nucleotides).