Epidemiology and molecular characteristics of respiratory syncytial virus (RSV) among italian community-dwelling adults, 2021/22 season.

BACKGROUND: Respiratory syncytial virus (RSV) is a leading cause of acute respiratory infections worldwide. While historically RSV research has been focused on children, data on RSV infection in adults are limited. The goal of this study was to establish the prevalence of RSV in community-dwelling Italian adults and analyze its genetic variability during the 2021/22 winter season. METHODS: In this cross-sectional study, a random sample of naso-/oropharyngeal specimens from symptomatic adults seeking for SARS-CoV-2 molecular testing between December 2021 and March 2022 were tested for RSV and other respiratory pathogens by means of reverse-transcription polymerase chain reaction. RSV-positive samples were further molecularly characterized by sequence analysis. RESULTS: Of 1,213 samples tested, 1.6% (95% CI: 0.9-2.4%) were positive for RSV and subgroups A (44.4%) and B (55.6%) were identified in similar proportions. The epidemic peak occurred in December 2021, when the RSV prevalence was as high as 4.6% (95% CI: 2.2-8.3%). The prevalence of RSV detection was similar (p = 0.64) to that of influenza virus (1.9%). All RSV A and B strains belonged to the ON1 and BA genotypes, respectively. Most (72.2%) RSV-positive samples were also positive for other pathogens being SARS-CoV-2, Streptococcus pneumoniae and rhinovirus the most frequent. RSV load was significantly higher among mono-detections than co-detections. CONCLUSION: During the 2021/22 winter season, characterized by the predominant circulation of SARS-CoV-2 and some non-pharmaceutical containment measures still in place, a substantial proportion of Italian adults tested positive for genetically diversified strains of both RSV subtypes. In view of the upcoming registration of vaccines, establishment of the National RSV surveillance system is urgently needed.

Molecular characteristics of ambient organic aerosols in Shanghai winter before and after the COVID-19 outbreak.

During the global pandemic of COVID-19, the world adopted different strategies to avoid the human and economic loss, and so does China. The reduction of human activities during this time period caused reduction in PM emissions. This study adopted a HPLC-Q-TOF-MS to compare the chemical compositions of ambient aerosol samples collected in Shanghai winter before (2018, 2019) and after (2021) the COVID-19 outbreak. The identified compositions were classified into subgroups of CHO, CHN, CHON, CHONS, CHOS and CHN compounds. Results showed that CHO compounds and CHON compounds were dominating the organic compounds in ESI- and ESI+, respectively. The average percentages of CHO- compounds were 57.97 % in 2018, 58.98 % in 2019, and 43.93 % in 2021, respectively. The average percentages of CHON+ compounds were 52.74 % in 2018, 50.34 % in 2019, and 52.02 % in 2021, respectively. The proportion of aliphatic compounds increased gradually during the three years, especially in 2021, indicating that CHO compounds were less affected by aromatic precursors after the COVID-19 outbreak. The contribution of anthropogenic emissions in Shanghai was weakened compared with the previous years. In addition, there was an enhanced emission source containing hydroxyl for CHOS compound formation in 2021. The variations of atmospheric oxidation degree among the three years were not significant.

Genetic Characteristics and Pathogenicity of a Novel Porcine Epidemic Diarrhea Virus with a Naturally Occurring Truncated ORF3 Gene.

Porcine epidemic diarrhea virus (PEDV) is the major pathogen that causes diarrhea and high mortality in newborn piglets, with devastating impact on the pig industry. To further understand the molecular epidemiology and genetic diversity of PEDV field strains, in this study the complete genomes of four PEDV variants (HN2021, CH-HNYY-2018, CH-SXWS-2018, and CH-HNKF-2016) obtained from immunized pig farms in central China between 2016 to 2021 were characterized and analyzed. Phylogenetic analysis of the genome and S gene showed that the four strains identified in the present study had evolved into the subgroup G2a, but were distant from the vaccine strain CV777. Additionally, it was noteworthy that a new PEDV strain (named HN2021) belonging to the G2a PEDV subgroup was successfully isolated in vitro and it was further confirmed by RT-PCR that this isolate had a large natural deletion at 207-373 nt of the ORF3 gene, which has never been reported before. Particularly, in terms of pathogenicity evaluation, colostrum deprivation piglets challenged with PEDV HN2021 showed severe diarrhea and high mortality, confirming that PEDV HN2021 was a virulent strain. Hence, PEDV strain HN2021 of subgroup G2a presents a promising vaccine candidate for the control of recurring porcine epidemic diarrhea (PED) in China. This study lays the foundation for better understanding of the genetic evolution and molecular pathogenesis of PEDV.

Multiomics integration-based molecular characterizations of COVID-19.

The coronavirus disease 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), rapidly became a global health challenge, leading to unprecedented social and economic consequences. The mechanisms behind the pathogenesis of SARS-CoV-2 are both unique and complex. Omics-scale studies are emerging rapidly and offer a tremendous potential to unravel the puzzle of SARS-CoV-2 pathobiology, as well as moving forward with diagnostics, potential drug targets, risk stratification, therapeutic responses, vaccine development and therapeutic innovation. This review summarizes various aspects of understanding multiomics integration-based molecular characterizations of COVID-19, which to date include the integration of transcriptomics, proteomics, genomics, lipidomics, immunomics and metabolomics to explore virus targets and developing suitable therapeutic solutions through systems biology tools. Furthermore, this review also covers an abridgment of omics investigations related to disease pathogenesis and virulence, the role of host genetic variation and a broad array of immune and inflammatory phenotypes contributing to understanding COVID-19 traits. Insights into this review, which combines existing strategies and multiomics integration profiling, may help further advance our knowledge of COVID-19.

Assessment of basic reproduction number (R0), spatial and temporal epidemiological determinants, and genetic characterization of SARS-CoV-2 in Bangladesh.

Epidemiological and molecular characterization of SARS-CoV-2 is essential for identifying the source of the virus and for effective control of the spread of local strains. We estimated case fatality rate, cumulative recovery number, basic reproduction number (R0) and future incidence of COVID-19 in Bangladesh. We illustrated the spatial distribution of cases throughout the country. We performed phylogenetic and mutation analysis of SARS-CoV-2 sequences from Bangladesh. As of July 31, 2020, Bangladesh had a case fatality rate of 1.32%. The cases were initially clustered in Dhaka and its surrounding districts in March but spreads throughout the country over time. The R0 calculated as 1.173 in Exponential Growth method. For the projection, a 20% change in R0 with subsequent infection trend has been calculated. The genomic analysis of 292 Bangladeshi SARS-CoV-2 strains suggests diverse genomic clades L, O, S, G, GH, where predominant circulating clade was GR (83.9%; 245/292). The GR clades' phylogenetic analysis revealed distinct clusters (I to XIII) with intra-clade variations. The mutation analysis revealed 1634 mutations where 94.6% and 5.4% were non-synonymous and unique mutation, respectively. The Spike, Nucleocapsid, NSP2, and RdRP showed substantially high mutation but no mutation was recorded in NSP9 and NSP11 protein. In spike (S) protein, 355 predominant mutations were recorded, highest in D614G. Alternatively, I120F in NSP2 protein, R203K and G204R in nucleocapsid protein, and P323L in RdRp were more recurrent. The Bangladeshi genomes belonged to phylogenetic lineages A, B, B.1, B.1.1, B.1.1.23, B.1.1.25, B.1.113, and B.1.36, among which 50.0% sequences owned by the pangolin lineage B.1.1.25. The study illustrates the spatial distribution of SARS-CoV-2, and molecular epidemiology of Bangladeshi isolates. We recommend continuous monitoring of R0 and genomic surveillance to understand the transmission dynamics and detect new variants of SARS-CoV-2 for proper control of the current pandemic and evaluate the effectiveness of vaccination globally.

Severe acute respiratory syndrome coronavirus 2 for physicians: Molecular characteristics and host immunity (Review).

Recently, severe acute respiratory syndrome (SARS) coronavirus (CoV) 2 (SARS­CoV­2)­causing CoV disease 2019 (COVID­19) emerged in China and has become a global pandemic. SARS­CoV­2 is a novel CoV originating from ß­CoVs. Major distinctions in the gene sequences between SARS­CoV and SARS­CoV­2 include the spike gene, open reading frame (ORF) 3b and ORF 8. SARS­CoV­2 infection is initiated when the virus interacts with angiotensin­converting enzyme 2 (ACE2) receptors on host cells. Through this mechanism, the virus infects the alveolar, esophageal epithelial, ileum, colon and other cells on which ACE2 is highly expressed, causing damage to target organs. To date, host innate immunity may be the only identified direct factor associated with viral replication. However, increased ACE2 expression may upregulate the viral load indirectly by increasing the baseline level of infectious virus particles. The peak viral load of SARS­CoV­2 is estimated to occur ~10 days following fever onset, causing patients in the acute stage to be the primary infection source. However, patients in the recovery stage or with occult infections can also be contagious. The host immune response in patients with COVID­19 remains to be elucidated. By studying other SARS and Middle East respiratory syndrome coronaviruses, it is hypothesized that patients with COVID­19 may lack sufficient antiviral T­cell responses, which consequently present with innate immune response disorders. This may to a certain degree explain why this type of CoV triggers severe inflammatory responses and immune damage and its associated complications.