scholarly journals Epidemiology of SARS-CoV-2 Emergence Amidst Community-Acquired Respiratory Viruses

2020 ◽  
Author(s):  
Karoline Leuzinger ◽  
Tim Roloff ◽  
Rainer Gosert ◽  
Kirstine Soegaard ◽  
Klaudia Naegele ◽  
...  
Keyword(s):  
Differential Diagnosis ◽  
Infection Control ◽  
Respiratory Infections ◽  
Respiratory Viruses ◽  
N Gene ◽  
E Gene ◽  
S Gene ◽  
Gene Assay ◽  
Adults And Children

Background. SARS-CoV-2 emerged in China in December 2019 as new cause of severe viral pneumonia (CoVID-19) reaching Europe by late January 2020. We validated the WHO-recommended assay and describe the epidemiology of SARS-CoV-2 and community-acquired respiratory viruses (CARVs). Methods. Naso-oropharyngeal swabs (NOPS) from 7663 individuals were prospectively tested by the Basel-S-gene and the WHO-based E-gene-assay (Roche) using Basel-N-gene-assay for confirmation. CARVs were tested in 2394 NOPS by multiplex-NAT, including 1816 together with SARS-CoV-2. Results. Basel-S-gene and Roche-E-gene-assays were concordant in 7475 cases (97.5%) including 825 (11%) positive samples. In 188 (2.5%) discordant cases, SARS-CoV-2 loads were significantly lower than in concordant positive ones and confirmed in 105 NOPS. Adults were more likely to test positive for SARS-CoV-2, while children were more likely to test CARV-positive. CARV co-infections with SARS-CoV-2 occurred in 1.8%. SARS-CoV-2 replaced other CARVs within 3 weeks reaching 48% of all detected respiratory viruses followed by rhino/enterovirus (13%), influenzavirus (12%), coronavirus (9%), respiratory syncytial (6%) and metapneumovirus (6%). Conclusions. The differential diagnosis for respiratory infections was broad during the early pandemic, affecting infection control and treatment decisions. We discuss the role of pre-existing immunity and competitive CARV replication for the epidemiology of SARS-CoV-2 infection among adults and children.

scholarly journals Epidemiology of Severe Acute Respiratory Syndrome Coronavirus 2 Emergence Amidst Community-Acquired Respiratory Viruses

2020 ◽  
Vol 222 (8) ◽  
pp. 1270-1279 ◽  
Author(s):  
Karoline Leuzinger ◽  
Tim Roloff ◽  
Rainer Gosert ◽  
Kirstin Sogaard ◽  
Klaudia Naegele ◽  
...  
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Respiratory Viruses ◽  
World Health ◽  
Immune Memory ◽  
N Gene ◽  
E Gene ◽  
S Gene ◽  
Annual Peak ◽  
Gene Assay ◽  
Syncytial Virus

Abstract Background Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in China as the cause of coronavirus disease 2019 in December 2019 and reached Europe by late January 2020, when community-acquired respiratory viruses (CARVs) are at their annual peak. We validated the World Health Organization (WHO)–recommended SARS-CoV-2 assay and analyzed the epidemiology of SARS-CoV-2 and CARVs. Methods Nasopharyngeal/oropharyngeal swabs (NOPS) from 7663 patients were prospectively tested by the Basel S-gene and WHO-based E-gene (Roche) assays in parallel using the Basel N-gene assay for confirmation. CARVs were prospectively tested in 2394 NOPS by multiplex nucleic acid testing, including 1816 (75%) simultaneously for SARS-CoV-2. Results The Basel S-gene and Roche E-gene assays were concordant in 7475 cases (97.5%) including 825 (11%) SARS-CoV-2 positives. In 188 (2.5%) discordant cases, SARS-CoV-2 loads were significantly lower than in concordant positive ones and confirmed in 105 (1.4%). Adults were more frequently SARS-CoV-2 positive, whereas children tested more frequently CARV positive. CARV coinfections with SARS-CoV-2 occurred in 1.8%. SARS-CoV-2 replaced CARVs within 3 weeks, reaching 48% of all detected respiratory viruses followed by rhinovirus/enterovirus (13%), influenza virus (12%), coronavirus (9%), respiratory syncytial virus (6%), and metapneumovirus (6%). Conclusions Winter CARVs were dominant during the early SARS-CoV-2 pandemic, impacting infection control and treatment decisions, but were rapidly replaced, suggesting competitive infection. We hypothesize that preexisting immune memory and innate immune interference contribute to the different SARS-CoV-2 epidemiology among adults and children.

scholarly journals Frequency of human bocavirus respiratory infections among at-risk patients in São Paulo, Brazil

2012 ◽  
Vol 54 (6) ◽  
pp. 307-310 ◽  
Author(s):  
Elaine Regina Baptista Caccia ◽  
Aripuana Sakurada Aranha Watanabe ◽  
Emerson Carraro ◽  
Elcio Leal ◽  
Celso Granato ◽  
...  
Keyword(s):  
At Risk ◽  
Respiratory Infections ◽  
Tertiary Hospital ◽  
Marrow Transplant ◽  
Human Bocavirus ◽  
Virus Infections ◽  
Risk Patients ◽  
Adults And Children ◽  
Respiratory Virus Infections

BACKGROUND AND OBJECTIVES: Human Bocavirus (HBoV) has been described since 2005 as an etiological agent of respiratory virus infections. From 2001 to 2008 we investigated the etiology of HBoV among adults and children in different groups at risk of presenting complications arising from acute respiratory infection, the investigation was carried out in a tertiary hospital health care system in Brazil. METHODS: HBoV DNA was assayed in 598 respiratory samples from community and hospitalized patients by PCR. RESULTS: Of the 598 tested samples, 2.44% (8/328) of children, including five children with heart disease, and 0.4% (1/270) of adult bone-marrow-transplant were HBoV positive. CONCLUSIONS: These data suggested lower HBoV frequency among different at-risk patients and highlights the need to better understand the real role of HBoV among acute respiratory symptomatic patients.

scholarly journals Analysis of human coronavirus 229E spike and nucleoprotein genes demonstrates genetic drift between chronologically distinct strains

2006 ◽  
Vol 87 (5) ◽  
pp. 1203-1208 ◽  
Author(s):  
Doris Chibo ◽  
Chris Birch
Keyword(s):  
Phylogenetic Analysis ◽  
Respiratory Infections ◽  
N Gene ◽  
Human Coronavirus ◽  
S Gene ◽  
Limited Variation ◽  
Contrast Analysis ◽  
Human Coronaviruses ◽  
Human Coronavirus 229E ◽  
S Genes

Historically, coronaviruses have been recognized as a cause of minor respiratory infections in humans. However, the recent identification of three novel human coronaviruses, one causing severe acute respiratory syndrome (SARS), has prompted further examination of these viruses. Previous studies of geographically and chronologically distinct Human coronavirus 229E (HCoV-229E) isolates have found only limited variation within S gene nucleotide sequences. In contrast, analysis of the S genes of contemporary Human coronavirus OC43 variants identified in Belgium revealed two distinct viruses circulating during 2003 and 2004. Here, the S and N gene sequences of 25 HCoV-229E variants identified in Victoria, Australia, between 1979 and 2004 in patients with symptomatic infections were determined. Phylogenetic analysis showed clustering of the isolates into four groups, with evidence of increasing divergence with time. Evidence of positive selection in the S gene was also established.

Case 9

2020 ◽  
pp. 55-61
Author(s):  
Nicola Jones
Keyword(s):  
Intensive Care ◽  
Infection Control ◽  
Respiratory Infections ◽  
Rapid Assessment ◽  
Supportive Therapy ◽  
Respiratory Viruses ◽  
Rapid Diagnostics ◽  
Highly Pathogenic ◽  
Returning Travellers ◽  
Exposure History

Severe respiratory infections in returning travellers usually present to Emergency Departments and then require intensive care support. There needs to be early and rapid assessment, including a detailed travel and exposure history to assess the risk of highly pathogenic imported respiratory viruses with potential for transmission to healthcare workers. Such cases need to be managed with appropriate infection control precautions, rapid diagnostics, supportive therapy, and, in most cases, antivirals. A case returning from the Middle East is described

scholarly journals Correlation Of Pcr Ct Values With Symptom Onset Across Diagnostic Platforms For Sars-Cov-2

2021 ◽  
Vol 156 (Supplement_1) ◽  
pp. S126-S127
Author(s):  
S Q Zia ◽  
H Mehrotra ◽  
R J Tibbetts ◽  
L Samuel
Keyword(s):  
Symptom Onset ◽  
N Gene ◽  
Nsp2 Gene ◽  
Individual Gene ◽  
E Gene ◽  
S Gene ◽  
Asymptomatic Patients ◽  
Orf1 Gene ◽  
The Difference ◽  
Definition Of

Abstract Introduction/Objective Following the definition of SARS-CoV2 outbreak as a pandemic by WHO, FDA gave EUA approval to the CDC real time polymerase chain reaction (PCR) assay and soon to other vendors to increase test availability. Most of testing platforms are PCR based, which test for multiple gene targets. We aimed to compare distribution of crossing threshold (cT) values of Diasorin (DIA), NeuMoDX (NDX) and Cepheid GenXpert (GX) for symptomatic and asymptomatic patients and assess performance of individual gene targets within the assays. We also correlated cT values with time from symptom onset. Methods/Case Report Retrospective review of medical and laboratory records of patients who tested positive for SARS-CoV2 between 08/01/2020 and 10/10/2020 on DIA, NDX, and GX platforms. Results (if a Case Study enter NA) We included 212 patients in our study. Days since symptom onset included 1 to 16 days. For DIA, mean Ct values for 46 symptomatic patients were 21.75 (S gene) and 22.74 (ORF1 gene); whereas 23.49 (S gene) and 25.49 (ORF1 gene) for 12 asymptomatic patients. Similarly, on NDX mean was 22.21 (N gene) and 23.13 (NSP2 gene) for 69 symptomatic, though 28.09 (N gene) and 28.61 (NSP2 gene) for 35 asymptomatic patients. GX manifested mean Ct value of 27.13 (E gene) and 31.22 (N2 gene) for 19 symptomatic; while 33.85 (E gene) and 36.42 (N2 gene) for 31 asymptomatic patients. Correlation coefficient for cT values versus days since symptom onset are DIA (r2 0.19), NDX (r2 0.22), and GX (r2 0.02). Conclusion The difference in cT values was statistically significant for symptomatic versus asymptomatic patients. There was positive correlation between days since symptom onset and cT values for DIA and NDX but not for GX, which may be due to difference in population tested in these platforms. These observations may be used to predict viral load and thus infectivity of patients who test positive for SARS-CoV2.

scholarly journals A role of respiratory infections in exacerbations of asthma

2007 ◽  
pp. 14-18
Author(s):  
A. G. Chuchalin ◽  
T. P. Ospelnikova ◽  
G. L. Osipova ◽  
N. V. Lizogub ◽  
V. B. Gervazieva ◽  
...  
Keyword(s):  
Mycoplasma Pneumoniae ◽  
Viral Infections ◽  
Respiratory Infections ◽  
Direct Detection ◽  
Serum Levels ◽  
Respiratory Viruses ◽  
Chlamydophila Pneumoniae ◽  
Atopic Asthma ◽  
Interferon System

Nineteen patients aged 18–65 years with moderate and severe exacerbations of atopic asthma were examined for respiratory viruses, Mycoplasma pneumoniae, and Chlamydophila pneumoniae. Interferon system, IL-4 and γ-IFN serum levels were also investigated. Viral infections (RS-virus, adenovirus, influenza types A (H1N1, H3N2) and B viruses, parainfluenza types 1 and 3 viruses) were diagnosed serologically or using PCR with direct detection of viral nucleic acids in 73.6 % of the patients. Diagnostic level of Mycoplasma pneumoniae antigen was found in 78.9 % of the patients, anti-Chlamydophila pneumoniae antibodies were detected in 31.6 %. Leukocyte interferon-producing function was decreased in all the patients.

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