SARS-CoV-2 Sequence Analysis during COVID-19 Case Surge, Liberia, 2021.
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ABSTRACT:
SUBMITTER: Shobayo B
PROVIDER: S-EPMC8632187 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Bat sarbecovirus BANAL-236 is highly related to SARS-CoV-2 and infects human cells, albeit lacking the furin cleavage site in its spike protein. BANAL-236 replicates efficiently and pauci-symptomatically in humanized mice and in macaques, where its tropism is enteric, strongly differing from that of SARS-CoV-2. BANAL-236 infection leads to protection against superinfection by a virulent strain. We find no evidence of antibodies recognizing bat sarbecoviruses in populations in close contact with bats in which the virus was identified, indicating that such spillover infections, if they occur, are rare. Six passages in humanized mice or in human intestinal cells, mimicking putative early spillover events, select adaptive mutations without appearance of a furin cleavage site and no change in virulence. Therefore, acquisition of a furin site in the spike protein is likely a pre-spillover event that did not occur upon replication of a SARS-CoV-2-like bat virus in humans or other animals. Other hypotheses regarding the origin of the SARS-CoV-2 should therefore be evaluated, including the presence of sarbecoviruses carrying a spike with a furin cleavage site in bats.
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Project description:SARS-CoV-2 induces widespread transcriptomic changes in host cells upon infection, in part through activation and modulation of innate immunity pathways and downstream gene regulation. However, the mechanisms by which SARS-CoV-2 and its evolutionary variants differentially affect host cell transcriptomic states remain largely unclear. Through chromatin proteomic (iDAPT-MS) analysis, we found that although SARS-CoV-2 and other pathogenic coronaviruses exhibit similar proteomic shifts on chromatin, SARS-CoV-2 uniquely promotes TP53 nuclear accumulation and activation. Parallel assessment of SARS-CoV-2 viral protein expression on host chromatin states (ATAC-seq) identifies intracellular spike protein as a key determinant of virus-mediated chromatin accessibility changes. Multilevel chromatin profiling reveals increased TP53 nuclear accumulation, TP53-associated chromatin accessibility changes, and TP53 target gene activation upon expression of SARS-CoV-2 alpha (B.1.1.7) and delta (B.1.617.2) spike variants relative to the ancestral spike sequence. TP53, ACE2, and furin cleavage are required for these changes, driving decreased cellular proliferation, increased cellular senescence, and increased cytokine release. Finally, BA.1 but not BA.2, BA.2.12.1, nor BA.4/BA.5 spike expression leads to attenuated TP53 activity and fusogenicity relative to ancestral spike. Our findings implicate spike-mediated host TP53 activation as a “rheostat” of COVID-19 pathogenicity.
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2021-06-19 | E-MTAB-10442 | biostudies-arrayexpress
Project description:Background and Purpose:We aimed to investigate the acute stroke presentations during the coronavirus disease 2019 (COVID-19) pandemic.Methods:The data were obtained from a health system with 19 emergency departments in northeast Ohio in the United States. Baseline period from January 1 to March 8, 2020, was compared with the COVID period from March 9, to April 2, 2020. The variables included were total daily stroke alerts across the hospital emergency departments, thrombolysis, time to presentation, stroke severity, time from door-to-imaging, time from door-to-needle in thrombolysis, and time from door-to-puncture in thrombectomy. The 2 time periods were compared using nonparametric statistics and Poisson regression.Results:Nine hundred two stroke alerts during the period across the emergency departments were analyzed. Total daily stroke alerts decreased from median, 10 (interquartile range, 8–13) during baseline period to median, 8 (interquartile range, 4–10, P=0.001) during COVID period. Time to presentation, stroke severity, and time to treatment were unchanged. COVID period was associated with decrease in stroke alerts with rate ratio of 0.70 (95% CI, 0.60–0.28). Thrombolysis also decreased with rate ratio, 0.52 (95% CI, 0.28–0.97) but thrombectomy remained unchanged rate ratio, 0.93 (95% CI, 0.52–1.62)Conclusions:We observed a significant decrease in acute stroke presentations by ?30% across emergency departments at the time of surge of COVID-19 cases. This observation could be attributed to true decline in stroke incidence or patients not seeking medical attention for emergencies during the pandemic.
| S-EPMC7309646 | biostudies-literature
Project description:BackgroundAir pollution exposure may make people more vulnerable to COVID-19 infection. However, previous studies in this area mostly focused on infection before May 2020 and long-term exposure.ObjectiveTo assess both long-term and short-term exposure to air pollution and COVID-19 incidence across four case surges from 03/1/2020 to 02/28/2021.MethodsThe cohort included 4.6 million members from a large integrated health care system in southern California with comprehensive electronic medical records (EMR). COVID-19 cases were identified from EMR. Incidence of COVID-19 was computed at the census tract-level among members. Prior 1-month and 1-year averaged air pollutant levels (PM2.5, NO2, and O3) at the census tract-level were estimated based on hourly and daily air quality data. Data analyses were conducted by each wave: 3/1/2020-5/31/2020, 6/1/202-9/30/2020, 10/1/2020-12/31/2020, and 1/1/2021-2/28/2021 and pooled across waves using meta-analysis. Generalized linear mixed effects models with Poisson distribution and spatial autocorrelation were used with adjustment for meteorological factors and census tract-level social and health characteristics. Results were expressed as relative risk (RR) per 1 standard deviation.ResultsThe cohort included 446,440 COVID-19 cases covering 4609 census tracts. The pooled RRs (95% CI) of COVID-19 incidence associated with 1-year exposures to PM2.5, NO2, and O3 were 1.11 (1.04, 1.18) per 2.3 μg/m3,1.09 (1.02, 1.17) per 3.2 ppb, and 1.06 (1.00, 1.12) per 5.5 ppb respectively. The corresponding RRs (95% CI) associated with prior 1-month exposures were 1.11 (1.03, 1.20) per 5.2 μg/m3 for PM2.5, 1.09 (1.01, 1.17) per 6.0 ppb for NO2 and 0.96 (0.85, 1.08) per 12.0 ppb for O3.ConclusionLong-term PM2.5 and NO2 exposures were associated with increased risk of COVID-19 incidence across all case surges before February 2021. Short-term PM2.5 and NO2 exposures were also associated. Our findings suggest that air pollution may play a role in increasing the risk of COVID-19 infection.
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Project description:The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Gamma variant has been hypothesized to cause more severe illness than previous variants, especially in children. Successive SARS-CoV-2 IgG serosurveys in the Brazilian Amazon showed that age-specific attack rates and proportions of symptomatic SARS-CoV-2 infections were similar before and after Gamma variant emergence.
| S-EPMC8888227 | biostudies-literature
Project description:This is the first known case of a Coronavirus disease (COVID-19) positive patient treated entirely with Ayurveda. So far in Modern Western Medicine (MWM), no cure has been found which is specific to COVID-19. The only literature relevant to the treatment of Coronavirus disease has surfaced from Traditional Chinese Medicine (TCM). TCM which was extensively used to control the epidemic in China, also consists of herbal medicines similar to Ayurveda. In this case, the patient, who was familiar with the use of Ayurvedic medicines, fully aware that no proven cure exists in MWM, decided to entirely rely on the limited Ayurvedic medicines that he had in his possession at the time of falling ill. Despite the patient presenting with symptoms, namely high fever, severe body pain and severe cough, along with many of the other associated symptoms of COVID-19, the progress of the disease could be arrested within a short period by being exclusively on Ayurvedic medicines. This illustrates that there is a wide scope to explore the variety of pertinent medicines present in Ayurvedic pharmacopoeia which can be used more rationally to suit every stage of the disease. Being the first-of-its-kind it is a valuable contribution to scientific literature from the world of Ayurveda. This should encourage the healthcare policy makers to quickly use Ayurveda to bring the COVID-19 pandemic under control in India, as they seemed to have demonstrated it in China with TCM.
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