The recombinant variants of SARS-CoV-2: Concerns continues amid COVID-19 pandemic.
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ABSTRACT:
SUBMITTER: Mohapatra RK
PROVIDER: S-EPMC9088633 | biostudies-literature | 2022 Aug
REPOSITORIES: biostudies-literature
Publications
The recombinant variants of SARS-CoV-2: Concerns continues amid COVID-19 pandemic.
Mohapatra Ranjan K RK Kandi Venkataramana V Tuli Hardeep S HS Chakraborty Chiranjib C Dhama Kuldeep K
Journal of medical virology 20220427 8
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Project description:BackgroundOur understanding of the cocirculation of infrequently targeted respiratory pathogens and their contribution to symptoms during the coronavirus disease 2019 (COVID-19) pandemic is currently limited. This research aims at (1) understanding the epidemiology of respiratory pathogens since the start of the pandemic, (2) assessing the contribution of non-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)/influenza/respiratory syncytial virus (RSV) respiratory pathogens to symptoms, and (3) evaluating coinfection rates in SARS-CoV-2-positive patients, both vaccinated and unvaccinated.MethodsRetrospective analysis of respiratory pathogens identified by the Johns Hopkins Diagnostic Laboratory between December 2019 and October 2021 was performed. In addition, we assessed the contribution of respiratory pathogens other than SARS-CoV-2 to symptomatic disease by retesting 2 cohorts of specimens that were (1) collected from symptomatic patients and (2) received limited respiratory pathogen testing. The first cohort was patients who tested negative by the standard-of-care SARS-CoV-2/influenza/RSV testing. The second was a cohort of SARS-CoV-2-positive, symptomatic, fully COVID-19 immunized and unimmunized patients.ResultsBetween December 2019 and October 2021, a total of 11 806, 62 829, and 579 666 specimens were tested for an extended respiratory panel, influenza/RSV with or without SARS-CoV-2 panel, or SARS-CoV-2, respectively. Positivity rates of different targets differed between different months and were impacted by the COVID-19 pandemic. The SARS-CoV-2-negative cohort had 8.5% positivity for other respiratory pathogens that included primarily enterovirus/rhinovirus (5.8%). In the SARS-CoV-2-positive cohort, no other respiratory pathogens were detected.ConclusionsThe COVID-19 pandemic impacted the circulation of certain respiratory pathogens. Other respiratory viral pathogens were associated with symptomatic infections; however, coinfections with SARS-CoV-2 were highly uncommon.
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Project description:SARS-CoV-2 virus and its variants have proven to be a threat to global health, in part due to their capacity for rapid evolution. SARS-CoV-2 variants that emerged throughout the COVID-19 pandemic exhibited variations in virulence, leading to diminished vaccine protection and modulating disease severity. Research efforts have identified the molecular changes resulting from structural protein variants of SARS-CoV-2, particularly in Spike, that have enhanced infectivity. Yet, investigating variants of nonstructural proteins is equally critical to understand viral evolution and their role in manipulating protein-protein interactions within a host. This study focuses on nonstructural protein 3 (nsp3), a viral papain-like protease (PLpro) critical for viral polyprotein cleavage, which is also implicated in host de-ubiquitylation, ISGylation, and formation of double-membrane vesicles. Using affinity-purification mass spectrometry (AP-MS), we identify differential protein interactions caused by mutations in nsp3. Included are variants identified between 2019-2024: Alpha 20I, Beta20H, Delta21I, Delta21J, Gamma20J, Kappa21B, Lambda21G, Omicron21K, Omicron21L. A small set of amino acid substitutions in the cytosolic fragment and N-terminal region of nsp3 (nsp3.1) could be traced to increased interactions with RNA binding proteins, which are vital in viral replication. Nsp3.1 variants from Omicron 21K and 21L exhibit distinct patterns of host interactor enrichment, setting them apart from five other variants. In contrast, variants of the central region of nsp3 (nsp3.2) containing the PL2pro domain were found to share interactions with protein quality control machinery, including ER-associated degradation (ERAD). In this construct, shared trends in interactor enrichment are observed between Omicron21K and Delta21I, distinguishing them from three other variants. Our study highlights that even a small number of amino acid substitutions can significantly alter the interaction partners. Our study provides a roadmap to track the interaction changes driven by SARS-CoV-2 variant evolution, which is essential for elucidating the ongoing evolutionary arms race between the host and virus.
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Project description:ACE2 on epithelial cells is the SARS-CoV-2 entry receptor. Single-cell RNA-sequencing data derived from two COVID-19 cohorts revealed that MAP4K3/GLK-positive epithelial cells were increased in patients. SARS-CoV-2-induced GLK overexpression in epithelial cells correlated with COVID-19 severity and vesicle secretion. GLK overexpression induced the epithelial cell-derived exosomes containing ACE2; the GLK-induced exosomes transported ACE2 proteins to recipient cells, facilitating pseudovirus infection. Consistently, ACE2 proteins were increased in the serum exosomes from another COVID-19 cohort. Remarkably, SARS-CoV-2 spike protein stimulated GLK, and GLK stabilized ACE2 in epithelial cells. Mechanistically, GLK phosphorylated ACE2 at two serine residues (Ser776, Ser783), leading to dissociation of ACE2 from its E3 ligase UBR4. Reduction of UBR4-induced Lys48-linked ubiquitination at three lysine residues (Lys26, Lys112, Lys114) of ACE2 prevented its degradation. Furthermore, SARS-CoV-2 pseudovirus or live virus infection in humanized ACE2 mice induced GLK and ACE2 protein levels, as well as ACE2-containing exosomes. Collectively, ACE2 stabilization by SARS-CoV-2-induced MAP4K3/GLK may contribute to the pathogenesis of COVID-19.
| S-SCDT-EMM-2022-15904 | biostudies-other
Project description:ObjectivesSchool closure during the coronavirus disease 2019 (COVID-19) pandemic resulted in a negative impact on children. Serial testing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been proposed as a measure for safety school reopening. We aimed to study the usefulness of SARS-CoV-2 surveillance by saliva testing and performing wastewater surveillance for SARS-CoV-2 in a day school in a resource-limited setting.MethodsWe conducted a cluster randomized study to investigate the potential use of saliva antigen testing compared to saliva pooling for nucleic acid detection in a primary school in Thailand from December 2021 to March 2022. Wastewater surveillance in the school was also performed.ResultsA total of 484 participants attended the study. SARS-CoV-2 was detected in two participants from the tests provided by the study (one in the pool nucleic acid test arm, and another in the quantitative antigen test arm). Additional ten participants reported positive results on an additional rapid antigen test (RAT) performed by nasal swab when they had symptoms or household contact. There was no difference among arms in viral detection by intention-to-treat and per protocol analysis (p = 0.304 and 0.894, respectively). We also investigated the feasibility of wastewater surveillance to detect the virus in this setting. However, wastewater surveillance could not detect the virus.ConclusionsIn a low COVID-19 prevalence, serial saliva testing and wastewater surveillance for SARS-CoV-2 rarely detected the virus in a day school setting. Performing RAT on nasal swabs when students, teachers or staff have symptoms or household contact might be more reasonable.
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2025-03-31 | E-MTAB-14495 | biostudies-arrayexpress
Project description:Severe acute respiratory syndrome Coronavirus- 2 (SARS-CoV-2), the etiological agent of the novel coronavirus disease (COVID-19), has posed a great public health threat to the global community as a pandemic. The origin of the virus has been linked to animals, through a yet-to-be-identified intermediate host. The disease is transmitted to humans mainly through inhalation or contact with infected droplets. The variable clinical presentation of COVID-19 includes fever, cough, sore throat, breathlessness, fatigue and malaise; however, cutaneous, ocular, neurological, and gastrointestinal manifestations have also been reported. There is an urgent need to strengthen One Health surveillance, intervention, and management strategies to understand the ecology of coronaviruses and to prevent epidemics in the future. Global attention toward the development of treatments, immunotherapies, vaccines, and control options to combat the COVID-19 pandemic has been on an increasing trend. Here, we review the current epidemiological status, public health concerns, and mitigation strategies for COVID-19.
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