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Genetic variation of SARS coronavirus in Beijing Hospital.

ABSTRACT: To characterize genetic variation of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) transmitted in the Beijing area during the epidemic outbreak of 2003, we sequenced 29 full-length S genes of SARS-CoV from 20 hospitalized SARS patients on our unit, the Beijing 302 Hospital. Viral RNA templates for the S-gene amplification were directly extracted from raw clinical samples, including plasma, throat swab, sputum, and stool, during the course of the epidemic in the Beijing area. We used a TA-cloning assay with direct analysis of nested reverse transcription-polymerase chain reaction products in sequence. One hundred thirteen sequence variations with nine recurrent variant sites were identified in analyzed S-gene sequences compared with the BJ01 strain of SARS-CoV. Among them, eight variant sites were, we think, the first documented. Our findings demonstrate the coexistence of S-gene sequences with and without substitutions (compared to BJ01) in samples analyzed from some patients.

SUBMITTER: Xu D

PROVIDER: S-EPMC3323231 | biostudies-literature | 2004 May

REPOSITORIES: biostudies-literature

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Genetic variation of SARS coronavirus in Beijing Hospital.

Xu Dongping D Zhang Zheng Z Chu Fuliang F Li Yonggang Y Jin Lei L Zhang Lingxia L Gao George F GF Wang Fu-Sheng FS

Emerging infectious diseases 20040501 5

To characterize genetic variation of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) transmitted in the Beijing area during the epidemic outbreak of 2003, we sequenced 29 full-length S genes of SARS-CoV from 20 hospitalized SARS patients on our unit, the Beijing 302 Hospital. Viral RNA templates for the S-gene amplification were directly extracted from raw clinical samples, including plasma, throat swab, sputum, and stool, during the course of the epidemic in the Beijing area ...[more]

PMID: 15200810

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Project description:The emergence of 2019 novel coronavirus (2019-nCoV) is of global concern and might have emerged from RNA recombination among existing coronaviruses. CoV spike (S) protein which is crucial for receptor binding, membrane fusion via conformational changes, internalization of the virus, host tissue tropism and comprises crucial targets for vaccine development, remain largely uncharacterized. Therefore, the present study has been planned to determine the sequence variation, structural and antigenic divergence of S glycoprotein which may be helpful for the management of 2019-nCoV infection. The sequences of spike glycoprotein of 2019-nCoV and SARS coronavirus (SARS-CoV) were used for the comparison. The sequence variations were determined using EMBOSS Needle pairwise sequence alignment tools. The variation in glycosylation sites was predicted by NetNGlyc 1.0 and validated by N-GlyDE server. Antigenicity was predicted by NetCTL 1.2 and validated by IEDB Analysis Resource server. The structural divergence was determined by using SuperPose Version 1.0 based on cryo-EM structure of the SARS coronavirus spike glycoprotein. Our data suggests that 2019-nCoV is newly spilled coronavirus into humans in China is closely related to SARS-CoV, which has only 12.8% of difference with SARS-CoV in S protein and has 83.9% similarity in minimal receptor-binding domain with SARS-CoV. Addition of a novel glycosylation sites were observed in 2019-nCoV. In addition, antigenic analysis proposes that great antigenic differences exist between both the viral strains, but some of the epitopes were found to be similar between both the S proteins. In spite of the variation in S protein amino acid composition, we found no significant difference in their structures. Collectively, for the first time our results exhibit the emergence of human 2019-nCoV is closely related to predecessor SARS-CoV and provide the evidence that 2019-nCoV uses various novel glycosylation sites as SARS-CoV and may have a potential to become pandemic owing its antigenic discrepancy. Further, demonstration of novel Cytotoxic T lymphocyte epitopes may impart opportunities for the development of peptide based vaccine for the prevention of 2019-nCoV.

Project description:ObjectivesThe coronavirus disease 2019 pandemic has strained many healthcare systems. In response, U.S. hospitals altered their care delivery systems, but there are few data regarding specific structural changes. Understanding these changes is important to guide interpretation of outcomes and inform pandemic preparedness. We sought to characterize emergency responses across hospitals in the United States over time and in the context of local case rates early in the coronavirus disease 2019 pandemic.DesignWe surveyed hospitals from a national acute care trials group regarding operational and structural changes made in response to the coronavirus disease 2019 pandemic from January to August 2020. We collected prepandemic characteristics and changes to hospital system, space, staffing, and equipment during the pandemic. We compared the timing of these changes with county-level coronavirus disease 2019 case rates.Setting and participantsU.S. hospitals participating in the Prevention and Early Treatment of Acute Lung Injury Network Coronavirus Disease 2019 Observational study. Site investigators at each hospital collected local data.InterventionsNone.Measurements and main resultsForty-five sites participated (94% response rate). System-level changes (incident command activation and elective procedure cancellation) occurred at nearly all sites, preceding rises in local case rates. The peak inpatient census during the pandemic was greater than the prior hospital bed capacity in 57% of sites with notable regional variation. Nearly half (49%) expanded ward capacity, and 63% expanded ICU capacity, with nearly all bed expansion achieved through repurposing of clinical spaces. Two-thirds of sites adapted staffing to care for patients with coronavirus disease 2019, with 48% implementing tiered staffing models, 49% adding temporary physicians, nurses, or respiratory therapists, and 30% changing the ratios of physicians or nurses to patients.ConclusionsThe coronavirus disease 2019 pandemic prompted widespread system-level changes, but front-line clinical care varied widely according to specific hospital needs and infrastructure. Linking operational changes to care delivery processes is a necessary step to understand the impact of the coronavirus disease 2019 pandemic on patient outcomes.

Dataset Information

Genetic variation of SARS coronavirus in Beijing Hospital.

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Genetic variation of SARS coronavirus in Beijing Hospital.

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