Is a highly pathogenic avian influenza virus H5N1 fragment recombined in PB1 the key for the epidemic of the novel AIV H7N9 in China, 2013?

SummaryBackgroundA novel avian influenza A H7N9 virus that infects humans was identified in China in 2013. This study is the first to comprehensively investigate the characteristics of genomic recombination, rather than reassortment, which has been the subject of investigation in previously reported studies.MethodsNovel avian influenza virus (AIV) H7N9 genome sequences were obtained from the NCBI Influenza Virus Sequence Database and the Global Initiative on Sharing Avian Influenza Database (GISAID) and a representative isolate was subjected to homogeneity analysis. A phylogenetic tree was constructed. Eight segments of the isolate were analyzed to identify segments with recombination events, the corresponding recombination fragments, and breakpoints. The evolutionary history of the recombined fragments was tracked by constructing phylogenetic trees of the recombination fragments.ResultsAmong the eight segments of the novel AIV H7N9 analyzed, only the PB1 segment showed a marked recombination phenomenon, with 11 recombination events; these included five actual recombination events and six possible misalignment artifact recombination events. The most notable was the recombination of a 291-nucleotide (nt) fragment at the 490–780 nt site that was affiliated to a highly pathogenic avian influenza virus (HPAIV) H5N1 (A/tree sparrow/Thailand/VSMU-16-RBR/2005). The phylogenetic tree of the 291-nt recombination fragment on the PB1 segment showed that the novel AIV H7N9 had a close genetic relationship to H9N2 and H5N1.ConclusionsThe novel AIV H7N9 might have reassorted its PB1 segment from H9N2 circulating in China, and this H9N2 PB1 might have been recombined into a highly pathogenic fragment from HPAIV H5N1, which could be the reason for the high fatality rate among patients with AIV H7N9 influenza

Nonparametric Evaluation of Dynamic Disease Risk: A Spatio-Temporal Kernel Approach

Quantifying the distributions of disease risk in space and time jointly is a key element for understanding spatio-temporal phenomena while also having the potential to enhance our understanding of epidemiologic trajectories. However, most studies to date have neglected time dimension and focus instead on the “average” spatial pattern of disease risk, thereby masking time trajectories of disease risk. In this study we propose a new idea titled “spatio-temporal kernel density estimation (stKDE)” that employs hybrid kernel (i.e., weight) functions to evaluate the spatio-temporal disease risks. This approach not only can make full use of sample data but also “borrows” information in a particular manner from neighboring points both in space and time via appropriate choice of kernel functions. Monte Carlo simulations show that the proposed method performs substantially better than the traditional (i.e., frequency-based) kernel density estimation (trKDE) which has been used in applied settings while two illustrative examples demonstrate that the proposed approach can yield superior results compared to the popular trKDE approach. In addition, there exist various possibilities for improving and extending this method

Enhanced Continental Weathering as a Trigger for the End‐Devonian Hangenberg Crisis

The Hangenberg Crisis coincided with a large decline of biodiversity and widespread anoxia in the end-Devonian ocean. Previous research attributed marine anoxia to the spread of deeply-rooted plants and/or increased volcanism on the continents, but crucial links have not been thoroughly explored. Herein, we propose enhanced weathering as a key trigger, as evidenced by a negative shift (∼8‰) in lithium isotopes and a coupled response in carbon isotopes of marine carbonates in South China. Our findings imply that rapid weathering of crustal rocks increased nutrient delivery to the ocean, as indicated by an increase in the carbonate-associated phosphate levels, contributing to oceanic eutrophication. In the absence of massive volcanic emissions and intense orogeny, the cause of enhanced continental weathering was likely the expansion of the terrestrial rhizosphere, highlighting the potential for land plant evolution to initiate weathering changes of sufficient severity to trigger a major bio/environmental crisis in the Earth system

Herbal formulas for detoxification and dredging collaterals in treating carotid atherosclerosis: a systematic review and meta-analysis

Objective: To systematically evaluate the efficacy and safety of the Chinese medicine detoxification and dredging collaterals in treating carotid atherosclerosis (CAS).Methods: A systematic and comprehensive search of nine relevant domestic and international databases were conducted from their inception until June 2022. The methodological quality of the included trials was evaluated, and the efficacy and safety were comprehensively analyzed. After applying the inclusion and exclusion criteria to the randomized controlled trials (RCTs), the research quality evaluation and data extraction were conducted, followed by a meta-analysis of the selected articles. The Cochrane’s Bias risk assessment was utilized to evaluate the quality of the evidence.Results: Of the 2,660 studies initially retrieved, 14 studies were included, involving a total of 1,518 patients. The results of the meta-analysis indicated that the clinical efficacy of the Detoxification and Collateral Dredging method in the treatment of CAS was superior to that of western medicine treatment alone, and the difference was statistically significant [RR = 1.23, 95% CI (1.13, 1.34)] Furthermore, carotid intima-media thickness [Mean Difference (MD) = −0.10, 95% CI (−0.13, −0.08)] and Crouse plaque score [MD = −0.54, 95% CI (−0.75, −0.32)] were significantly lower in the Detoxification and Collateral Dredging group compared to the pure western medicine treatment group. The difference was statistically significant. In addition, serum total cholesterol [MD = −0.70, 95% CI (−0.85, −0.55)] and low-density lipoprotein cholesterol [MD = −0.70, 95% CI (−0.85, −0.55)] were lower in the Detoxification and Collateral Dredging group than in the Western medicine group, with all differences being statistically significant. Serum high-density lipoprotein cholesterol was higher in the Detoxification and Collateral Dredging group compared to the pure western medicine group, and the difference was statistically significant [MD = 0.17, 95% CI (0.11, 0.23)].Conclusion: The use of Chinese medicine Detoxification and Collateral Dredging approach in the treatment of CAS may offer benefits in improving carotid atherosclerotic plaque and reducing blood lipid levels, with a safety profile superior to that of western medicine treatment alone

Spatial and temporal distribution characteristics and prediction analysis of nitrogen and phosphorus surface source pollution in Shandong Province under the climate and land use changes

The aim of this study was to explore the characteristics of non-point source pollution of nitrogen (N) and phosphorus (P) under the background of climate and land use in Shandong Province. First, using the InVEST NDR module in the model, N and P non-point source pollution in 2010 and 2020 in Shandong Province were simulated; then, based on precipitation data under three different global climate models (MRI-ESM-0, GFDL-ESM4, and Ec-Earth3) and two Shared Socioeconomic Pathways (SSP245 and SSP585), land use data under two Shared Socioeconomic Pathways (SSP245 and SSP585) were used to simulate and predict the non-point source pollution of N and P in Shandong Province in 2030. The results showed the following: (1) On the time scale, the output load and total output of N and P decreased during 2010–2020, while the output load and total output of N and P increased during 2020–2030. (2) On the spatial scale, the spatial distribution of N and P output loads in 2010, 2020, and 2030 is roughly the same, being “low in the northwest and high in the southeast”. (3) Different climate scenarios have a great influence on N and P output load and total output, and the N and P pollution in the SSP585 scenario is more serious. The total output of N and P did not change much in different climate models, while the spatial distribution of the output load of N and P varied significantly, indicating that different climate models had a greater impact on the spatial distribution of the output load of N and P. (4) The overall cold hot spot pattern of nitrogen and phosphorus pollution in Shandong Province is stable, basically showing a “band + cluster + scatter” distribution pattern; the hot spot area in the central and southern region of Shandong Province changes little regardless of the model, the northwest is basically a cold spot area, and the nitrogen and phosphorus hot spot area under the SSP245 scenario in Ec-Earth3 model had the least amount of change. According to research results, combined with the actual situation of Shandong Province, it is hoped that it can provide theoretical basis for the prevention and control of non-point source pollution in Shandong Province in the future

The impact of screening on the survival of colorectal cancer in Shanghai, China: a population based study

Background Shanghai is one of the earliest cities in developing countries to introduce an organized colorectal screening program for its residents to fight against the rising disease burden of colorectal cancer (CRC). This study aims to investigate the impact of the Shanghai screening program implemented in 2013 on the survival rates of CRC patients. Methods We calculated up to 5-year survival rates for 18,592 CRC patients from a representative district of Shanghai during 2002–2016, using data from the Shanghai Cancer Registry. We performed joinpoint regressions to examine temporal changes in the trends of the CRC survival rates. We then conducted Kaplan-Meier and Cox proportional hazards modelling to study the association of the survival rates with screening behaviors of the patients. In all the model specifications, we took into account the gender, age and TNM stage at diagnosis, and level of treatment hospital of the patients. Results We find that the annual percentage changes of the survival rates increased faster after somewhere around 2013, however, the differential trends were not significant. Results from the Cox multivariate regression analysis suggest that patients who did not participate in the screening program showed significantly lower cancer-specific survival (hazard ratio (HR) = 1.46; 95% confidence interval (CI): 1.12–1.91) and all-causes survival (HR = 1.37; 95% CI: 1.05–1.77), compared to those who did. Among program participants, delayed colonoscopy was associated with poor cancer-specific survival (hazard ratio (HR) = 2.93; 95% confidence interval (CI): 1.64–5.23) and all-causes survival (HR = 3.29; 95% CI: 1.85–5.84). Conclusion Screening participation and high level of colonoscopy compliance can improve the survival of CRC participants

Urban-Rural Disparity in Cancer Incidence, Mortality, and Survivals in Shanghai, China, During 2002 and 2015

Introduction: Disparities in the incidence, mortality, and survival of cancer types between urban and rural areas in China reflect the effects of different risk factor exposure, education, and different medical availability. We aimed to characterize the disparities in the incidence, mortality, and survivals of cancer types between urban and rural areas in Shanghai, China, 2002-2015.Materials and Methods: The incidence and mortality were standardized by Segi's world standard population. Trends in the incidence and mortality of cancers were compared using annual percent change. The 5-year observed and relative survivals were calculated with life table and Ederer II methods.Results: Age-standardized incidences and mortalities were 212.55/105 and 109.45/105 in urban areas and 210.14/105 and 103.99/105 in rural areas, respectively. Female breast cancer and colorectal cancer occurred more frequently in urban than in rural areas, quite in contrast to liver cancer and cervical cancer. Cancers of lung and bronchus, liver, stomach, and colon and rectum were the leading causes of cancer death in both areas. Age-standardized incidence of female breast cancer and colorectal cancer in urban areas increased while gastric cancer and liver cancer decreased in both areas. Age-standardized mortalities of cancers of breast, esophagus, stomach, colon and rectum, liver, and lung and bronchus decreased in both areas. For all cancers combined, the 5-year observed and relative survivals of cancer patients were higher in urban than in rural areas. The 5-year observed and relative survivals of cancers of liver, pancreas, stomach, brain and central nervous system (CNS), and prostate were higher in urban than in rural areas. The 5-year observed and relative survivals of cervical cancer were higher in rural than in urban areas.Conclusions: Factors promoting female breast cancer and colorectal cancer in urban areas and liver cancer and cervical cancer in rural areas should be specifically intervened in cancer prophylaxis. Improved medical services can greatly prolong the survival of major cancers in rural areas

Serotype distribution of Streptococcus pneumoniae and potential impact of pneumococcal conjugate vaccines in China: A systematic review and meta-analysis

Objective: Thirteen-valent pneumococcal conjugate vaccines (PCV13) was licensed for optional use in mainland China since 2017, but the uptake is low. To update the research evidence for the pneumococcal serotype distribution of pre-PCV era and to estimate the potential impact of PCVs, we performed a meta-analysis on the relevant publications concerning the Chinese population. Methods: This systematic review and meta-analysis were conducted on the pneumococcal serotype distribution publications in mainland China from 2000 to 2016. The literature was searched in PubMed, Ovid-EMBASE, Web of Science, CNKI and Wanfang. Heterogeneity and publication bias were tested by I2, meta-regression, Egger's and Begg's test. The pneumococcal serotype and vaccine serotype coverage rates were pooled using the random-effects model in Stata SE 12.0. Results: In total, 85 publications were included. Of all 16,945 included pneumococcal isolates, the most common serotypes/serogroups were 19F, 19A, 23F, 14, and 6B, that from children were the same as above, that from adults≥18 years were 19, 3, 6, 23, and 14. Among isolates from children <18 years, the pooled coverage for PCV10 serotypes was 52.3%, that for PCV13 was 68.4% and that for PPSV23 was 65.5%. Regarding individuals ≥18 years, the pooled coverage for PCV10 serotypes was 29.7%, that for PCV13 was 49.5% and that for PPSV23 was 50.7%. Serotype prevalence and vaccine serotype coverage varied by age group, source, and region. Conclusions: The most common pneumococcal serotype in mainland China was 19F. The serotype coverage rates of PCV13 and PPSV23 were 50%–68% in mainland China