SARS-COV-2/COVID-19: scenario, epidemiology, adaptive mutations, and environmental factors

Tracing Emergence of SARS-CoV-2 Variants: Insights from Comprehensive Assessment Using Reverse Transcription Polymerase Chain Reaction and Whole Genome Sequencing

The emergence and evolution of SARS-CoV-2 variants, such as Delta and Omicron, pose significant challenges to pandemic management. This study evaluated the effectiveness of reverse-transcription polymerase chain reaction (RT-PCR) and whole-genome sequencing (WGS) in detecting and characterizing SARS-CoV-2 variants using 624 samples collected in South Korea from mid-2021 to mid-2022. Two RT-PCR genotyping assays demonstrated a high concordance rate (90.4%) in identifying the Delta variant during its dominance. In contrast, WGS revealed extensive genetic diversity among Omicron sub-lineages, identifying 29 distinct sub-lineages, including two South Korea-specific variants (BA.1.1.5 and BA.2.3.8). Clustering analysis of WGS data highlighted distinct groupings of BA.1, BA.2, and BA.5 sub-lineages, with overlap in shared mutations suggesting evolutionary convergence. Sub-lineage diversity expanded during rapid transmission phases and subsequently consolidated as dominant lineages emerged. These findings highlight the complementary strengths of RT-PCR and WGS and underscore the importance of integrating these methodologies for effective variant monitoring and public health response.

Significance of Initial Chest CT Severity Score (CTSS) and Patient Characteristics in Predicting Outcomes in Hospitalized COVID-19 Patients: A Single Center Study

The aim of this study is to examine the prognostic role of initial chest computed tomography severity score index (CTSS) and its association with demographic, socio-epidemiological, and clinical parameters in COVID-19 hospitalized patients. A retrospective study included patients who were hospitalized in the COVID Hospital of the Clinical Hospital Center Kosovska Mitrovica from July 2020 to March 2022. We compared patient characteristics and outcome of their hospital stay with values of CT severity score (mild, moderate, and severe form of the disease). Patients with severe disease were statistically significantly older, they treated more days, and they presented statistically significant highest mortality rate compared to mild and moderate forms. Smokers and obese were significantly more frequent among patients with higher CT, while vaccinated patients were more common among those with a mild form. Biochemical parameters at admission also showed statistical significance between the examined groups. We can conclude that by employing the initial CT severity score as the strongest predictor of mortality, it is possible to predict the outcome in hospitalized patients. A comprehensive examination of the patient upon admission, including determining the extent of inflammatory changes in the lungs using computed tomography, the levels of oxygen saturation, and other laboratory parameters, can assist doctors in making an adequate clinical evaluation and apply appropriate therapeutic protocols in the treatment of COVID-19.

A brief overview of SARS-CoV-2 infection and its management strategies: a recent update

The COVID-19 pandemic has become a global health crisis, inflicting substantial morbidity and mortality worldwide. A diverse range of symptoms, including fever, cough, dyspnea, and fatigue, characterizes COVID-19. A cytokine surge can exacerbate the disease's severity. This phenomenon involves an increased immune response, marked by the excessive release of inflammatory cytokines like IL-6, IL-8, TNF-α, and IFNγ, leading to tissue damage and organ dysfunction. Efforts to reduce the cytokine surge and its associated complications have garnered significant attention. Standardized management protocols have incorporated treatment strategies, with corticosteroids, chloroquine, and intravenous immunoglobulin taking the forefront. The recent therapeutic intervention has also assisted in novel strategies like repurposing existing medications and the utilization of in vitro drug screening methods to choose effective molecules against viral infections. Beyond acute management, the significance of comprehensive post-COVID-19 management strategies, like remedial measures including nutritional guidance, multidisciplinary care, and follow-up, has become increasingly evident. As the understanding of COVID-19 pathogenesis deepens, it is becoming increasingly evident that a tailored approach to therapy is imperative. This review focuses on effective treatment measures aimed at mitigating COVID-19 severity and highlights the significance of comprehensive COVID-19 management strategies that show promise in the battle against COVID-19.

Risk factors for COVID-19 outbreaks in livestock slaughtering and processing facilities in Republic of Korea

BACKGROUND

The goal of this study was to help prevent and control the spread of coronavirus disease 2019 (COVID-19) by identifying transmission routes and risk factors in livestock slaughtering and processing facilities (SPFs) and establishing an optimal intervention strategy for outbreaks.

METHODS

This case series study was a demographic analysis of patients with confirmed COVID-19 associated with 5 SPFs in Korea between January and June 2021. Additionally, in a retrospective cohort study, the association between COVID-19 infection and risk factors was analyzed for SPFs at which outbreaks occurred.

RESULTS

The COVID-19 attack rates were 11.2%, 24.5%, and 6.8% at 3 poultry SPFs (PSPFs) and 15.5% and 25.2% at 2 mammal SPFs (MSPFs). Regarding spatial risk factors, the COVID-19 risk levels were 12.1-, 5.2-, and 5.0-fold higher in the refrigeration/ freezing, by-product processing, and carcass cutting areas, respectively, than in the office area. The risk of COVID-19 infection was 2.1 times higher among employees of subcontractors than among employees of contractors. The COVID-19 risk levels were 5.3- and 3.0-fold higher in foreign workers than in native Korean workers in the PSPFs and MSPFs, respectively.

CONCLUSION

As the COVID-19 pandemic continues, a detailed policy for infectious disease prevention and control intervention is needed, without interrupting economic activities. Thus, we propose an ideal intervention plan to prevent COVID-19 through disinfection and preemptive testing and to block its transmission through effective contact management during outbreaks at SPFs.

Variant-specific deleterious mutations in the SARS-CoV-2 genome reveal immune responses and potentials for prophylactic vaccine development

Introduction: Coronavirus disease 2019 (COVID-19), caused by SARS-CoV-2, has had a disastrous effect worldwide during the previous three years due to widespread infections with SARS-CoV-2 and its emerging variations. More than 674 million confirmed cases and over 6.7 million deaths have been attributed to successive waves of SARS-CoV-2 infections as of 29th January 2023. Similar to other RNA viruses, SARS-CoV-2 is more susceptible to genetic evolution and spontaneous mutations over time, resulting in the continual emergence of variants with distinct characteristics. Spontaneous mutations of SARS-CoV-2 variants increase its transmissibility, virulence, and disease severity and diminish the efficacy of therapeutics and vaccines, resulting in vaccine-breakthrough infections and re-infection, leading to high mortality and morbidity rates. Materials and methods: In this study, we evaluated 10,531 whole genome sequences of all reported variants globally through a computational approach to assess the spread and emergence of the mutations in the SARS-CoV-2 genome. The available data sources of NextCladeCLI 2.3.0 (https://clades.nextstrain.org/) and NextStrain (https://nextstrain.org/) were searched for tracking SARS-CoV-2 mutations, analysed using the PROVEAN, Polyphen-2, and Predict SNP mutational analysis tools and validated by Machine Learning models. Result: Compared to the Wuhan-Hu-1 reference strain NC 045512.2, genome-wide annotations showed 16,954 mutations in the SARS-CoV-2 genome. We determined that the Omicron variant had 6,307 mutations (retrieved sequence:1947), including 67.8% unique mutations, more than any other variant evaluated in this study. The spike protein of the Omicron variant harboured 876 mutations, including 443 deleterious mutations. Among these deleterious mutations, 187 were common and 256 were unique non-synonymous mutations. In contrast, after analysing 1,884 sequences of the Delta variant, we discovered 4,468 mutations, of which 66% were unique, and not previously reported in other variants. Mutations affecting spike proteins are mostly found in RBD regions for Omicron, whereas most of the Delta variant mutations drawn to focus on amino acid regions ranging from 911 to 924 in the context of epitope prediction (B cell & T cell) and mutational stability impact analysis protruding that Omicron is more transmissible. Discussion: The pathogenesis of the Omicron variant could be prevented if the deleterious and persistent unique immunosuppressive mutations can be targeted for vaccination or small-molecule inhibitor designing. Thus, our findings will help researchers monitor and track the continuously evolving nature of SARS-CoV-2 strains, the associated genetic variants, and their implications for developing effective control and prophylaxis strategies.

Pierre Schneider B, Detrick E. SARS-CoV-2 surveillance with environmental surface sampling in public areas

Contaminated surfaces are one of the ways that coronavirus disease 2019 (COVID-19) may be transmitted. SARS-CoV-2 can be detected on environmental surfaces; however, few environmental sampling studies have been conducted in nonclinical settings. The objective of this study was to detect SARS-CoV-2 RNA on environmental surfaces in public areas in Las Vegas, Nevada. In total, 300 surface samples were collected from high-touch surfaces from high-congregate public locations and from a public health facility (PHF) that was visited by COVID-19 patients. Environmental samples were analyzed with quantitative reverse-transcriptase polymerase chain reaction (RT-qPCR) using SARS-CoV-2 specific primers and probes for three target genes. Results showed that 31 out of 300 (10.3%) surface samples tested positive for SARS-CoV-2, 24 at the PHF and 7 in high-congregate public locations. Concentrations ranged from 102 to 106 viral particles per 3 ml sample on a wide variety of materials. The data also showed that the N gene assay had greater sensitivity compared to the S and ORF gene assays. Besides frequently touched surfaces, SARS-CoV-2 was detected in restrooms, on floors and surfaces in contact with floors, as well as in a mop water sample. The results of this study describe the extent and distribution of environmental SARS-CoV-2 contamination in public areas in Las Vegas, Nevada. A method using the N gene PCR assay was developed for SARS-CoV-2 environmental monitoring in public areas. Environmental monitoring with this method can determine the specific sites of surface contamination in the community and may be beneficial for prevention of COVID-19 indirect transmission, and evaluation and improvement of infection control practices in public areas, public health facilities, universities, and businesses.