The human oral and gut commensal microbes play vital roles in the development and maintenance of immune homeostasis, while its association with susceptibility and severity of SARS-CoV-2 infection is barely understood. In this study, we investigated the dynamics of the oral and intestinal flora before and after the clearance of SARS-CoV-2 in 53 COVID-19 patients, and then examined their microbiome alterations in comparison to 76 healthy individuals. A total of 140 throat swab samples and 81 fecal samples from these COVID-19 patients during hospitalization, and 44 throat swab samples and 32 fecal samples from sex and age-matched healthy individuals were collected and then subjected to 16S rRNA sequencing and viral load inspection. We found that SARS-CoV-2 infection was associated with alterations of the microbiome community in patients as indicated by both alpha and beta diversity indexes. Several bacterial taxa were identified related to SARS-CoV-2 infection, wherein elevated Granulicatella and Rothia mucilaginosa were found in both oral and gut microbiome. The SARS-CoV-2 viral load in those samples was also calculated to identify potential dynamics between COVID-19 and the microbiome. These findings provide a meaningful baseline for microbes in the digestive tract of COVID-19 patients and will shed light on new dimensions for disease pathophysiology, potential microbial biomarkers, and treatment strategies for COVID-19.

Background: Dozens of studies have demonstrated gut dysbiosis in COVID-19 patients during the acute and recovery phases. However, a consensus on the specific COVID-19 associated bacteria is missing. In this study, we performed a meta-analysis to explore whether robust and reproducible alterations in the gut microbiota of COVID-19 patients exist across different populations. Methods: A systematic review was conducted for studies published prior to May 2022 in electronic databases. After review, we included 16 studies that comparing the gut microbiota in COVID-19 patients to those of controls. The 16S rRNA sequence data of these studies were then re-analyzed using a standardized workflow and synthesized by meta-analysis. Results: We found that gut bacterial diversity of COVID-19 patients in both the acute and recovery phases was consistently lower than non-COVID-19 individuals. Microbial differential abundance analysis showed depletion of anti-inflammatory butyrate-producing bacteria and enrichment of taxa with pro-inflammatory properties in COVID-19 patients during the acute phase compared to non-COVID-19 individuals. Analysis of microbial communities showed that the gut microbiota of COVID-19 recovered patients were still in unhealthy ecostates. Conclusions: Our results provided a comprehensive synthesis to better understand gut microbial perturbations associated with COVID-19 and identified underlying biomarkers for microbiome-based diagnostics and therapeutics.

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Existing tools for the aggregation and visualization of differential expression data have discrete functionality and require that end-users rely on multiple software packages with complex dependencies or manually manipulate data for analysis and interpretation. Furthermore, at present, data aggregation and visualization are laborious, time consuming, and subject to human error. This is a serious limitation on the current state of differential transcriptomic analysis, which makes it necessary to expend extensive time and resources to reach the point where biological meaning can be interpreted. Such an approach for analysis also leads to scattered and non-standardized code, unsystematic project management and non-reproducible result sets. Here, we present a differential expression analysis toolkit, DEvis, that provides a powerful, integrated solution for the analysis of differential expression data with a rapid turnaround time. DEvis has simple installation requirements and provides a convenient, user-friendly R package that addresses the issues inherent to complex multi-factor experiments, such as multiple contrast aggregation and integration, result sorting and selection, visualization, project management, and reproducibility. This tool increases the capabilities of differential expression analysis while reducing workload and the potential for manual error. Furthermore, it provides a much-needed encapsulation of scattered functionality, making large and complex analysis more efficient and reproducible. DEvis provides a wide range of powerful visualization, data aggregation, and project management tools that provide flexibility and speed in analysis. The functionality provided by DEVis increases efficiency of analysis and supplies researchers with new and relevant means for the analysis of large and complicated transcriptomic experiments. DEvis furthermore incorporates automatic project management capabilities, which standardizes analysis and ensures the reproducibility of results. After the establishment of statistical frameworks that identify differentially expressed genes, this package is the next logical step for differential transcriptomic analysis, establishing the critical framework necessary to manipulate, explore, and extract biologically relevant meaning from differential expression data.

Background: Establishing a comprehensive and coordinated mechanism for rabies management is essential for achieving the goal of eliminating the disease. It requires the involvement of multiple disciplines and departments, as well as the implementation of necessary policies and measures. The recent COVID-19 pandemic has added further challenges to the goal, particularly for developing countries like China. However, certain regions in China are leveraging local advantages and departmental strengths to actively explore effective strategies. Principal findings: This review provides an overview of the global prevalence of rabies, international cooperation efforts, and specific measures. Of particular significance is the analysis of the transformation of the rabies situation in China as well as an exemplar management of a rabies case in the Baiyun District of Guangzhou, Guangdong Province. We also discuss the hopeful action plan based on the One Health concept, aimed at achieving the goal of rabies elimination by 2030. Conclusions: Rabies remains a significant threat to public health and economies across most countries worldwide. Despite this, eliminating rabies is increasingly feasible, with China showcasing notable progress, including the adoption of the One Health approach in disease prevention and control strategies. Synopsis: The distinction between disease eradication and elimination lies in their scope and permanence. Eradication involves globally reducing the incidence of infection caused by a specific agent to zero, requiring no further intervention measures once achieved. In contrast, disease elimination focuses on reducing the incidence of infection within a specific geographic area to zero, necessitating ongoing actions to prevent its transmission or re-emergence. In the long history of humans’ battle against infectious diseases, the complete eradication of smallpox has undoubtedly been an inspiring achievement. However, emerging and re-emerging infectious diseases have remained in the forefront of people’s minds, causing significant morbidity, mortality, and potential economic burdens in impoverished countries and regions worldwide. It is disappointing that rabies has not been eradicated globally. While high-income countries have achieved the elimination of canine-mediated rabies through dog vaccination and population management programs, there are fewer examples of successful large-scale elimination of canine rabies in low- and middle-income countries, primarily limited to Latin America.

Hepatitis E virus (HEV) causes infections in humans and animals. HEV have been identified in pig farms, markets and swine workers, but studies with parallel observations along the poultry and pork supply chains remains limited. This study aimed to characterize HEV infection risks in workers along the meat supply chain. Two rounds of cross-sectional surveys were performed among swine and poultry workers in pig and poultry farms, slaughterhouses, wholesale and retail live poultry markets, live pig markets and pork markets. Human sera from the workers and the general population were collected and tested for HEV specific IgM/IgG antibodies by commercial indirect-ELISA test kits. Risk factors of HEV seropositivity associated with different occupational settings were identified using logistic regression. 47.0% (156/332) of the swine workers and 40.2% (119/296) of the poultry workers were seropositive, compared to 26.1% (35/134) in the general population. Multivariable analysis showed that human HEV infection risk increased along the pork supply chain, with the highest risk at pig slaughterhouses (adjusted OR = 3.19, 95% CI = 1.49–6.88) and pork markets (adjusted OR = 2.02, 95% CI = 1.04–3.97), but no significant higher risk was observed among poultry workers. Swine occupational exposure is associated with HEV infection, especially in workers in pig slaughterhouses and pork markets. Strengthening control measures in these settings is important for HEV control and long term HEV elimination.