Skip to content
cookies to track usage and preferences." data-cookieaccepttext="I Understand" data-cookiedeclinetext="Disable Cookies" data-cookiepolicytext="Privacy Policy">
1887

Coronaviruses

/content/coronaviruses
Coronaviruses
OK
Cancel

Coronaviruses are a large family of viruses that can infect a range of hosts. They are known to cause diseases including the common cold, Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS) in humans.

In January 2020, China saw an outbreak of a new coronavirus strain now named SARS-CoV-2. Although the animal reservoir for the SARS and MERS viruses are known, this has yet to have been confirmed for SARS-CoV-2. All three strains are transmissible between humans.

To allow the widest possible distribution of relevant research, the Microbiology Society has brought together articles from across our portfolio and made this content freely available.

Image credit: "MERS-CoV" by NIAID is licensed under CC BY 2.0, this image has been modified.

Collection Contents

21 - 40 of 298 results

    • Effect of RNA quality to SARS-CoV-2 RT-qPCR detection from saliva

      Saliva is an alternative sample material to nasopharyngeal swab in SARS-CoV-2 diagnostics. We investigated possible aspects to improve the reliability of SARS-CoV-2 detection from saliva. Saliva was collected from asymptomatic healthy subjects (=133) and COVID-19 patients (=9). SARS-CoV-2 detection was performed with quantitative reverse-transcriptase PCR (RT-qPCR) with two viral and one host target serving as an internal control. The use of internal control revealed that in the first RT-qPCR run 25–30 % of assays failed. The failure is associated with poor RNA quality. When the amount of RNA was cut down to half from the original amount, the performance of RT-qPCR was greatly enhanced (95 % of the assays succeeded). The quality of RNA was not affected by the use of different nucleic acid stabilizing buffers. Our study showed that saliva is suitable material for RT-qPCR based SARS-CoV-2 diagnostics, but the use of internal control is essential to distinguish the true negative samples from failed assays.

    • Incidence of COVID-19 infection and its variation with demographic and clinical profile: lessons learned at a COVID-19 RT-PCR laboratory in Nagpur, India

      The coronavirus disease 2019 (COVID-19) pandemic emerged as a global health crisis in 2020. The first case in India was reported on 30 January 2020 and the disease spread throughout the country within months. Old persons, immunocompromised patients and persons with co-morbidities, especially of the respiratory system, have a more severe and often fatal outcome to the disease. In this study we have analysed the socio-demographic trend of the COVID-19 outbreak in Nagpur and adjoining districts.

      The study was conducted from April to December 2020. Nasopharyngeal and oropharyngeal swabs collected from suspected cases of COVID-19 were tested using reverse-transcription polymerase chain reaction (RT-PCR) at a diagnostic molecular laboratory at a tertiary care hospital in central India. Patient-related data on demographic profile and indication for testing were obtained from laboratory requisition forms. The results of the inconclusive repeat samples were also noted. The data were analysed using SPSS v24.0.

      A total of 46 898 samples were received from April to December 2020, of which 41 410 were included in the study; 90.6 % of samples belonged to adults and 9.4 % belonged to children. The overall positivity rate in the samples was 19.3 %, although it varied over the period. The yield was significantly high in the elderly age group (25.5 %) and symptomatic patients (22.6 %). On repeat testing of patients whose first test was inconclusive, 17.1% were positive. There was a steady increase of both the number of tests and the rate of positivity in the initial period of the study, followed by a sharp decline.

      We can conclude that rigorous contact tracing and COVID-appropriate behaviour (wearing a mask, social distancing and hand hygiene) are required to break the chain of transmission. Elderly people are more susceptible to infection and should follow stringent precautions. It is also important to perform repeat testing of those individuals whose tests are inconclusive with fresh samples so that no positive cases are missed. Understanding of demographics is crucial for better management of this crisis and proper allocation of resources.

    • Selection and T-cell antigenicity of synthetic long peptides derived from SARS-CoV-2

      The pandemic caused by SARS-CoV-2 has led to the successful development of effective vaccines however the prospect of variants of SARS-CoV-2 and future coronavirus outbreaks necessitates the investigation of other vaccine strategies capable of broadening vaccine mediated T-cell responses and potentially providing cross-immunity. In this study the SARS-CoV-2 proteome was assessed for clusters of immunogenic epitopes restricted to diverse human leucocyte antigen. These regions were then assessed for their conservation amongst other coronaviruses representative of different alpha and beta coronavirus genera. Sixteen highly conserved peptides containing numerous HLA class I and II restricted epitopes were synthesized from these regions and assessed for their antigenicity against T-cells from individuals with previous SARS-CoV-2 infection. Monocyte derived dendritic cells were generated from these peripheral blood mononuclear cells (PBMC), loaded with SARS-CoV-2 peptides, and used to induce autologous CD4+ and CD8+ T cell activation. The SARS-CoV-2 peptides demonstrated antigenicity against the T-cells from individuals with previous SARS-CoV-2 infection indicating that this approach holds promise as a method to activate anti-SAR-CoV-2 T-cell responses from conserved regions of the virus which are not included in vaccines utilising the Spike protein.

    • SARS-CoV-2 genetic variations associated with COVID-19 pathogenicity

      In this study, we performed genome-wide association analyses on SARS-CoV-2 genomes to identify genetic mutations associated with pre-symptomatic/asymptomatic COVID-19 cases. Various potential covariates and confounding factors of COVID-19 severity, including patient age, gender and country, as well as virus phylogenetic relatedness were adjusted for. In total, 3021 full-length genomes of SARS-CoV-2 generated from original clinical samples and whose patient status could be determined conclusively as either ‘pre-symptomatic/asymptomatic’ or ‘symptomatic’ were retrieved from the GISAID database. We found that the mutation 11 083G>T, located in the coding region of non-structural protein 6, is significantly associated with asymptomatic COVID-19. Patient age is positively correlated with symptomatic infection, while gender is not significantly correlated with the development of the disease. We also found that the effects of the mutation, patient age and gender do not vary significantly among countries, although each country appears to have varying baseline chances of COVID-19 symptom development.

    • Characteristics of patients with suspected COVID-19 pneumonia and repeatedly negative RT-PCR

      Challenges remain and there are still a sufficient number of cases with epidemiological, clinical features and radiological data suggestive of COVID-19 pneumonia that persist negative in their RT-PCR results. The aim of the study was to define the distinguishing characteristics between patients developing a serological response to SARS-CoV-2 and those who did not.

      RT-PCR tests used were TaqPath 2019-nCoV Assay Kit v1 (ORF-1ab, N and S genes) from Thermo Fisher Diagnostics and SARS-COV-2 Kit (N and E genes) from Vircell. Serological response was tested using the rapid SARS-CoV2 IgG/IgM Test Cassette from T and D Diagnostics Canada and CMC Medical Devices and Drugs, S.L, CE.

      In this cross-sectional study, we included a cohort of 52 patients recruited from 31 March 2020 to 23 April 2020. Patients with positive serology had an older average age (73.29) compared to those who were negative (54.82) (<0.05). Sat0 in 27 of 34 patients with positive serology were below 94% (<0.05). There was a frequency of 1.5% negative SARS-CoV-2 RT-PCRs during the study period concurring with 36.7% of positivity.

      Clinical features and other biomarkers in a context of a positive serology can be considered crucial for diagnosis.

    • Insights on the SARS-CoV-2 genome variability: the lesson learned in Brazil and its impacts on the future of pandemics

      Since the beginning of the SARS-CoV-2 spread in Brazil, few studies have been published analysing the variability of viral genome. Herein, we described the dynamic of SARS-CoV-2 strains circulating in Brazil from May to September 2020, to better understand viral changes that may affect the ongoing pandemic. Our data demonstrate that some of the mutations identified are currently observed in variants of interest and variants of concern, and emphasize the importance of studying previous periods in order to comprehend the emergence of new variants. From 720 SARS-CoV-2 genome sequences, we found few sites under positive selection pressure, such as the D614G (98.5 %) in the spike, that has replaced the old variant; the V1167F in the spike (41 %), identified in the P.2 variant that emerged from Brazil during the period of analysis; and I292T (39 %) in the N protein. There were a few alterations in the UTRs, which was expected, however, our data suggest that the emergence of new variants was not influenced by mutations in UTR regions, since it maintained its conformational structure in most analysed sequences. In phylogenetic analysis, the spread of SARS-CoV-2 from the large urban centres to the countryside during these months could be explained by the flexibilization of social isolation measures and also could be associated with possible new waves of infection. These results allow a better understanding of SARS-CoV-2 strains that have circulated in Brazil, and thus, with relevant infomation, provide the potential viral changes that may have affected and/or contributed to the current and future scenario of the COVID-19 pandemic.

    • Not all wavelengths are created equal: disinfection of SARS-CoV-2 using UVC radiation is wavelength-dependent

      SARS-CoV-2 is mostly transmitted through close contact with infected people by infected aerosols and fomites. Ultraviolet subtype C (UVC) lamps and light-emitting diodes can be used to disrupt the transmission chain by disinfecting fomites, thus managing the disease outbreak progression. Here, we assess the ultraviolet wavelengths that are most effective in inactivation of SARS-CoV-2 on fomites. Variations in UVC wavelengths impact the dose required for disinfection of SARS-CoV-2 and alter how rapidly and effectively disruption of the virus transmission chain can be achieved. This study reveals that shorter wavelengths (254–268 nm) take a maximum of 6.25 mJ/cm over 5 s to obtain a target SARS-CoV-2 reduction of 99.9%. Longer wavelengths, like 280 nm, take longer irradiation time and higher dose to inactivate SARS-CoV-2. These observations emphasize that SARS-CoV-2 inactivation is wavelength-dependent.

    • Effect of COVID-19 on vaccination coverage in Brazil

      During the COVID-19 pandemic, recommendations for maintaining physical distance, restricted mobility measures, as well as fear of mass transmission by going to health centers have significantly contributed to the general vaccination coverage, which by and large is decreasing worldwide; thus, favoring the potential re-emergence of vaccine-preventable diseases. In this study, we have used the existing data on vaccination coverage during the pre-pandemic (2019) as well as the pandemic (2020) period to evaluate the impact of coronavirus outbreaks during the vaccination drive in Brazil. Furthermore, we have accumulated data since 2015 among the different regions of the country to acquire more consistent information. The various vaccines analyzed in our study were meningococcal C conjugate, Triple antigen vaccine, 10-valent pneumococcal conjugate, and BCG; subsequently, the data were obtained from the National Disease Notification System. This study revealed that the ongoing immunization drive saw a steep decline of around 10 to 20% during the (2019–2020) pandemic period in Brazil. These results provide strong evidence towards the decreasing trends following the vaccination programs during the COVID-19 pandemic period in Brazil. Furthermore, our results also highlight the importance of adopting widespread multi-component interventions to improve vaccination uptake rates.

    • SARS-CoV-2 IgG antibody responses in rt-PCR-positive cases: first report from India

      Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibody responses remain poorly understood and the clinical utility of serological testing is still unclear.

      To understand the relationship between the antibody response to SARS-CoV-2 infection and the demographics and cycle threshold ( ) values of confirmed RT-PCR patients.

      A total of 384 serum samples were collected from individuals between 4–6 weeks after confirmed SARS-CoV-2 infection and tested for the development of immunoglobulin class G (IgG) against SARS-CoV-2. The values, age, gender and symptoms of the patients were correlated with the development of antibodies.

      IgG positivity was found to be 80.2 % (95 % CI, 76.2–84.2). Positivity increased with a decrease in the value, with the highest (87.6 %) positivity observed in individuals with values <20. The mean (±) values for IgG positives and negatives were 23.34 (±6.09) and 26.72 (±7.031), respectively. No significant difference was found for demographic characteristics such as age and sex and symptoms and antibody response. The current study is the first of its kind wherein we have assessed the correlation of the RT-PCR with the development of IgG against SARS-CoV-2.

      Although values might not have any relation with the development of symptoms, they are associated with the antibody response among SARS-CoV-2-infected individuals.

    • Prevalence and molecular characteristics of feline coronavirus in southwest China from 2017 to 2020

      Feline coronavirus (FCoV) is the causative agent of feline infectious peritonitis and diarrhoea in kittens worldwide. In this study, a total of 173 feline diarrhoeal faecal and ascetic samples were collected from 15 catteries and six veterinary hospitals in southwest China from 2017 to 2020. FCoV was detected in 80.35 % (139/173) of the samples using the RT-nPCR method; these included infections with 122 type I FCoV and 57 type II FCoV. Interestingly, 51 cases had co-infection with types I and II, the first such report in mainland China. To further analyse the genetic diversity of FCoV, we amplified 23 full-length spike (S) genes, including 18 type I and five type II FCoV. The type I FCoV and type II FCoV strains shared 85.5–98.7% and 97.4–98.9% nucleotide (nt) sequence identities between one another, respectively. The N-terminal domain (NTD) of 23 FCoV strains showed a high degree of variation (73.6–80.3 %). There was six type I FCoV strains with two amino acid insertions (159HL160) in the NTD. In addition, 18 strains of type I FCoV belonged to the Ie cluster, and five strains of type II FCoV were in the IIb cluster based on phylogenetic analysis. Notably, it was first time that two type I FCoV strains had recombination in the NTD, and the recombination regions was located 140–857 nt of the S gene. This study constitutes a systematic investigation of the current infection status and molecular characteristics of FCoV in southwest China.

    • Sample collection and transport strategies to enhance yield, accessibility, and biosafety of COVID-19 RT-PCR testing

      Non-invasive sample collection and viral sterilizing buffers have independently enabled workflows for more widespread COVID-19 testing by reverse-transcriptase polymerase chain reaction (RT-PCR).

      The combined use of sterilizing buffers across non-invasive sample types to optimize sensitive, accessible, and biosafe sampling methods has not been directly and systematically compared.

      We aimed to evaluate diagnostic yield across different non-invasive samples with standard viral transport media (VTM) versus a sterilizing buffer eNAT- (Copan diagnostics Murrieta, CA) in a point-of-care diagnostic assay system.

      We prospectively collected 84 sets of nasal swabs, oral swabs, and saliva, from 52 COVID-19 RT-PCR-confirmed patients, and nasopharyngeal (NP) swabs from 37 patients. Nasal swabs, oral swabs, and saliva were placed in either VTM or eNAT, prior to testing with the Xpert Xpress SARS-CoV-2 (Xpert). The sensitivity of each sampling strategy was compared using a composite positive standard.

      Swab specimens collected in eNAT showed an overall superior sensitivity compared to swabs in VTM (70 % vs 57 %, =0.0022). Direct saliva 90.5 %, (95 % CI: 82 %, 95 %), followed by NP swabs in VTM and saliva in eNAT, was significantly more sensitive than nasal swabs in VTM (50 %, <0.001) or eNAT (67.8 %, =0.0012) and oral swabs in VTM (50 %, <0.0001) or eNAT (58 %, <0.0001). Saliva and use of eNAT buffer each increased detection of SARS-CoV-2 with the Xpert; however, no single sample matrix identified all positive cases.

      Saliva and eNAT sterilizing buffer can enhance safe and sensitive detection of COVID-19 using point-of-care GeneXpert instruments.

    • Bloodstream infection by in a COVID-19 patient receiving probiotic supplementation in the ICU in Brazil

      Care-related infections (CRIs) have a negative impact on the morbidity and mortality of patients in intensive care. Among them, fungal infections (e.g. spp. and spp.) have high mortality in critically ill patients, particularly those with acute respiratory distress syndrome (ARDS) and immunosuppression. Coronavirus disease 2019 (COVID-19) causes severe respiratory changes and deregulation of the immune system. Here, we describe a case of fungal infection in an intensive care unit (ICU) patient with COVID-19 caused by , a yeast widely used in the baking and wine production industries. It is also used as a probiotic, both for prevention and as adjunctive therapy in patients with diarrhoea. The patient was admitted to the ICU with a diagnosis of COVID-19, respiratory failure, complications of ARDS and renal failure, and was being treated with antibiotics and vasoactive amines. Later, the patient had diarrhoea and, after supplementation with , he developed a bloodstream infection with . The patient died after 61 days of hospitalization due to thrombocytopenia and bleeding. This case report suggests avoiding the use of probiotics in intensive care patients under the administration of antibiotics and amines, and with damage to the intestinal mucosa and immunodeficiency caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), since these factors could favour the translocation of fungi.

    • Effect of multiple freeze–thaw cycles on the detection of anti-SARS-CoV-2 IgG antibodies

      Several studies have investigated the effect of repeated freeze–thaw (F/T) cycles on RNA detection for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). However, no data are available regarding the effect of repeated F/T cycles on SARS-CoV-2 antibody detection in serum. We investigated the effect of multiple F/T cycles on anti-SARS-CoV-2 IgG detection using an ELISA test targeting the nucleocapsid antibodies. Ten positive and 1 negative SARS-CoV-2 IgG sera from 11 participants, in replicates of 5, were subjected to a total of 16 F/T cycles and stored at 4 °C until tested by ELISA. Statistical analysis was performed to test for F/T cycle effect. None of the 10 positive sera became negative after 16 F/T cycles. There was no significant difference in the OD average reading between the first and last F/T cycles, except for one serum with a minimal decline in the OD. The random effect linear regression of log (OD) on the number of cycles showed no significant trend, with a slope consistent with zero (B=−0.0001; 95 % CI −0.0008; 0.0006; -value=0.781). These results suggest that multiple F/T cycles had no effect on the ability of the ELISA assay to detect SARS-CoV-2 IgG antibodies.

◄ 1 2 3 4 5 … 15 ►
20 | 50 | 100 per page
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error