Reprint of: Coronavirus reverse genetic systems: infectious clones and replicons

Impact of COVID-19 Pandemic on Mental Health and Socioeconomic Aspects in Greece

The global outbreak of the COVID-19 pandemic has spread worldwide, affecting almost all countries and territories. COVID-19 continues to impact various spheres of our life, such as the economy, industries, global market, agriculture, human health, health care, and many others. The aim of this study was to investigate the impact of the COVID-lockdowns on people's mental health in Greece. A descriptive, cross-sectional study was conducted in several urban, semi-urban and rural areas. The survey of 252 Greek people was conducted in spring 2022, and 46.8% of them were female and the other 53.2% were male. Ages were between 19 and 60 years old. Some of the main findings were that most of the participants feel their mental health got worse than before (about 80%), participants with kids were more affected than those who did not have any kids because they had bigger responsibilities and the pandemic might have caused them a lot of problems to deal with. The higher the income, the less they are affected, and people whose jobs did not change dramatically were also less likely to not be much mentally affected. Moreover, the percentage of smokers whose mental health became worse was greater than that among those who did not smoke. The same happened with those who consumed alcohol. Finally, we used the GBM algorithm to find three important predictors and we applied k-means to have a clear picture of the different clusters and how a number of participants are connected according to their answers.

Forensic Analysis of Novel SARS2r-CoV Identified in Game Animal Datasets in China Shows Evolutionary Relationship to Pangolin GX CoV Clade and Apparent Genetic Experimentation

Pangolins are the only animals other than bats proposed to have been infected with SARS-CoV-2 related coronaviruses (SARS2r-CoVs) prior to the COVID-19 pandemic. Here, we examine the novel SARS2r-CoV we previously identified in game animal metatranscriptomic datasets sequenced by the Nanjing Agricultural University in 2022, and find that sections of the partial genome phylogenetically group with Guangxi pangolin CoVs (GX PCoVs), while the full RdRp sequence groups with bat-SL-CoVZC45. While the novel SARS2r-CoV is found in 6 pangolin datasets, it is also found in 10 additional NGS datasets from 5 separate mammalian species and is likely related to contamination by a laboratory researched virus. Absence of bat mitochondrial sequences from the datasets, the fragmentary nature of the virus sequence and the presence of a partial sequence of a cloning vector attached to a SARS2r-CoV read suggests that it has been cloned. We find that NGS datasets containing the novel SARS2r-CoV are contaminated with significant Homo sapiens genetic material, and numerous viruses not associated with the host animals sampled. We further identify the dominant human haplogroup of the contaminating H. sapiens genetic material to be F1c1a1, which is of East Asian provenance. The association of this novel SARS2r-CoV with both bat CoV and the GX PCoV clades is an important step towards identifying the origin of the GX PCoVs.

Betacoronavirus Genomes: How Genomic Information has been Used to Deal with Past Outbreaks and the COVID-19 Pandemic

In the 21st century, three highly pathogenic betacoronaviruses have emerged, with an alarming rate of human morbidity and case fatality. Genomic information has been widely used to understand the pathogenesis, animal origin and mode of transmission of coronaviruses in the aftermath of the 2002-2003 severe acute respiratory syndrome (SARS) and 2012 Middle East respiratory syndrome (MERS) outbreaks. Furthermore, genome sequencing and bioinformatic analysis have had an unprecedented relevance in the battle against the 2019-2020 coronavirus disease 2019 (COVID-19) pandemic, the newest and most devastating outbreak caused by a coronavirus in the history of mankind. Here, we review how genomic information has been used to tackle outbreaks caused by emerging, highly pathogenic, betacoronavirus strains, emphasizing on SARS-CoV, MERS-CoV and SARS-CoV-2. We focus on shared genomic features of the betacoronaviruses and the application of genomic information to phylogenetic analysis, molecular epidemiology and the design of diagnostic systems, potential drugs and vaccine candidates.

Viral metagenomics, protein structure, and reverse genetics: Key strategies for investigating coronaviruses

Viral metagenomics, modeling of protein structure, and manipulation of viral genetics are key approaches that have laid the foundations of our understanding of coronavirus biology. In this review, we discuss the major advances each method has provided and discuss how future studies should leverage these strategies synergistically to answer novel questions.