COVID 19 Special Collection
COVID-19 (SARS-CoV-2) Special Collection
Latest COVID-19 Articles
-
Research Article
Assessment of sample pooling for clinical SARS-CoV-2 testing
Accommodating large increases in sample workloads has presented a major challenge to clinical laboratories during the COVID-19 pandemic. Despite the implementation of automated detection systems, and previous efficiencies including barcoding, electronic data transfer and extensive robotics, capacities have struggled to meet the demand. Sample pooling has been suggested as an additional strategy to address this need. The greatest concern with this approach in clinical settings is the potential for reduced sensitivity, particularly detection failures with weak positive samples. To investigate this possibility, detection rates in pooled samples were evaluated, with a focus on pools containing weak positive specimens. Additionally, the frequency of occurrence of weak positive samples during the pandemic were reviewed. Weak positive specimens, with Ct values of 33 or greater, were detected in 95% of 60 five-sample pools but only 87% of 39 nine-sample pools. The proportion of positive samples with very low viral loads rose markedly during the first few months of the pandemic, peaking in June, decreasing thereafter and remaining level since August. At all times, weak positive specimens comprised a significant component of the sample population, ranging from 29% to greater than 80% for Ct values above 31. In assessing the benefits of pooling strategies however, other aspects of the testing process must be considered. Accessioning, result data management, electronic data transfer, reporting and billing are not streamlined and may be complicated by pooling procedures. Therefore, the impact on the entire laboratory process needs to be carefully assessed prior to implementing such a strategy.
Accepted Manuscript Posted 19 January 2021, JCM; Final Article Posted 19 March 2021
-
Research Article
Comparison of Antibody Class Specific SARS-CoV-2 Serology for the Diagnosis of Acute COVID-19
Accurate diagnosis of acute severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) infection is critical for appropriate management of patients with this disease. We examined the possible complementary role of lab developed class-specific clinical serology in assessing SARS-CoV-2 infection in hospitalized patients. Serological tests for IgG, IgA, and IgM antibodies against the receptor binding domain (RBD) of SARS-CoV-2 were evaluated using samples from real time RT PCR (qRT-PCR)-confirmed in-patient COVID-19 cases. We analyzed the influence of timing and clinical severity on the diagnostic value of class-specific coronavirus disease 2019 (COVID-19) serology testing. Cross-sectional analysis revealed a higher sensitivity and specificity at lower optical density cutoffs for IgA in hospitalized patients when compared to IgG and IgM serology (IgG area under the curve (AUC): 0.91; 95%CI 0.89 to 0.93 vs. IgA AUC: 0.97; 95% CI 0.96 to 0.98 vs. IgM AUC: 0.95; 95% CI 0.92 to 0.97). The enhanced performance of IgA serology was apparent in the first two weeks after symptom onset and the first week after PCR testing. In patients requiring intubation, all three tests exhibit enhanced sensitivity. Among PCR-negative patients under investigation for SARS-CoV-2 infection 2 out of 61 showed clear evidence of seroconversion IgG, IgA and IgM. Suspected false-positive results in the latter population were most frequently observed in IgG and IgM serology tests. Our findings suggest the potential utility of IgA serology in the acute setting and explore the benefits and limitations of class-specific serology as a complementary diagnostic tool to PCR for COVID-19 in the acute setting.
Accepted Manuscript Posted 19 January 2021, JCM; Final Article Posted 19 March 2021
-
Minireview
A systematic review and meta-analysis of upper airways swab collection for detection of viral and bacterial pathogens by individuals or caregivers compared to healthcare workers
Self- or caregiver-collection of upper airway swabs reduces infectious exposures of healthcare workers (HCW) and the need to redeploy clinical staff to testing roles. We aimed to determine whether self- or caregiver-collection has adequate diagnostic performance for detection of viral and bacterial upper airways pathogens. We did a systematic review and meta-analysis of studies comparing diagnostic accuracy of self- or caregiver-collected upper airway swabs collected by patients or caregivers compared to HCW. All study types except case reports and series were included if sufficient data were presented to calculate sensitivity, specificity and Cohen’s kappa. Studies published from 1946 to 17th August 2020 were included in the search. We did a meta-analysis to assess pooled sensitivity and specificity. Twenty studies were included in the systematic review and 15 in the meta-analysis. Overall sensitivity of swabs collected by patients or caregivers compared to HCW was 91% (95% CI: 87-94) and specificity was 98% (95% CI: 96-99). Sensitivity ranged from 65% to 100% and specificity from 73% to 100% across the studies. All but one study concluded that self- or caregiver-collected swabs were acceptable for detection of upper airway pathogens. Self- and caregiver-collection of upper airway swabs had reassuring diagnostic performance for multiple pathogens. There are numerous potential benefits of self- and caregiver-collected swabs for patients, families, researchers, and health systems. Further research to optimize implementation of sample collection by patients and caregivers is warranted.
Accepted Manuscript Posted 19 January 2021, JCM
-
Commentary
The time for COVID-19 vaccination
The composition and dynamics of viral mutant spectra in infected individuals advice that to avoid selection of SARS-CoV-2 escape mutants, vaccination campaigns for COVID-19 should be launched when disease incidence is low.
Accepted Manuscript Posted 19 January 2021, JVI
-
Research Article
Genome Sequencing of Sewage Detects Regionally Prevalent SARS-CoV-2 Variants
Viral genome sequencing has guided our understanding of the spread and extent of genetic diversity of SARS-CoV-2 during the COVID-19 pandemic. SARS-CoV-2 viral genomes are usually sequenced from nasopharyngeal swabs of individual patients to track viral spread. Recently, RT-qPCR of municipal wastewater has been used to quantify the abundance of SARS-CoV-2 in several regions globally. However, metatranscriptomic sequencing of wastewater can be used to profile the viral genetic diversity across infected communities. Here, we sequenced RNA directly from sewage collected by municipal utility districts in the San Francisco Bay Area to generate complete and nearly complete SARS-CoV-2 genomes. The major consensus SARS-CoV-2 genotypes detected in the sewage were identical to clinical genomes from the region. Using a pipeline for single nucleotide variant calling in a metagenomic context, we characterized minor SARS-CoV-2 alleles in the wastewater and detected viral genotypes which were also found within clinical genomes throughout California. Observed wastewater variants were more similar to local California patient-derived genotypes than they were to those from other regions within the United States or globally. Additional variants detected in wastewater have only been identified in genomes from patients sampled outside California, indicating that wastewater sequencing can provide evidence for recent introductions of viral lineages before they are detected by local clinical sequencing. These results demonstrate that epidemiological surveillance through wastewater sequencing can aid in tracking exact viral strains in an epidemic context.
19 January 2021, mBio
-
Research Article
Engineering a Reliable and Convenient SARS-CoV-2 Replicon System for Analysis of Viral RNA Synthesis and Screening of Antiviral Inhibitors
COVID-19 has caused a severe global pandemic. Until now, there has been no simple and reliable system available in a lower-biosafety-grade laboratory for SARS-CoV-2 virologic research and inhibitor screening. We reported a replicon system which consists of four ordinary plasmids expressing the required segments of SARS-CoV-2. Using the replicon system, we developed three application scenarios: (i) to identify the effects of viral proteins on virus replication, (ii) to identify the effects of mutations on viral replication during viral epidemics, and (iii) to perform high-throughput screening of antiviral drugs. Collectively, this replicon system would be useful for virologists to study SARS-CoV-2 virology, for epidemiologists to monitor virus mutations, and for industry to develop antiviral drugs.
19 January 2021, mBio
-
Research Article
SARS-CoV-2 Infection Severity Is Linked to Superior Humoral Immunity against the Spike
With the ongoing pandemic, it is critical to understand how natural immunity against SARS-CoV-2 and COVID-19 develops. We have identified that subjects with more severe COVID-19 disease mount a more robust and neutralizing antibody response against SARS-CoV-2 spike protein. Subjects who mounted a larger response against the spike also mounted antibody responses against other viral antigens, including the nucleocapsid protein and ORF8. Additionally, this study reveals that subjects with more severe disease mount a larger memory B cell response against the spike. These data suggest that subjects with more severe COVID-19 disease are likely better protected from reinfection with SARS-CoV-2.
19 January 2021, mBio
-
Research Article
Atypical Divergence of SARS-CoV-2 Orf8 from Orf7a within the Coronavirus Lineage Suggests Potential Stealthy Viral Strategies in Immune Evasion
Orf8 is one of the most puzzling genes in the SARS lineage of coronaviruses, including SARS-CoV-2. Using sophisticated sequence comparisons, we confirm its origins from Orf7a, another gene in the lineage that appears as more conserved, compared to Orf8. Orf7a is a potential immune antagonist of known structure, while a deletion of Orf8 was shown to decrease the severity of the infection in a cohort study. The subtle sequence similarities imply that Orf8 has the same immunoglobulin-like fold as Orf7a, confirmed by structure determination. We characterize the subgroups of this superfamily and demonstrate the highly idiosyncratic divergence patterns during the evolution of the virus.
19 January 2021, mBio
-
Research Article
SARS-CoV-2 Genomic Variation in Space and Time in Hospitalized Patients in Philadelphia
Understanding how SARS-CoV-2 spreads globally and within infected individuals is critical to the development of mitigation strategies. We found that most lineages in Philadelphia had resembled sequences from New York, suggesting infection primarily but not exclusively from this location. Many genomes had even nearer neighbors within Philadelphia, indicating local spread. Multiple genome sequences were available for some subjects and in a subset of cases could be shown to differ between time points and body sites within an individual, indicating heterogeneous viral populations within individuals and raising questions on the mechanisms responsible. There was no evidence that different lineages were associated with different outcomes in patients, emphasizing the importance of individual-specific vulnerability.
19 January 2021, mBio
-
Research Article
Stenoparib, an Inhibitor of Cellular Poly(ADP-Ribose) Polymerase, Blocks Replication of the SARS-CoV-2 and HCoV-NL63 Human Coronaviruses In Vitro
New therapeutics are urgently needed in the fight against COVID-19. Repurposing drugs that are either already approved for human use or are in advanced stages of the approval process can facilitate more rapid advances toward this goal. The PARP inhibitor stenoparib may be such a drug, as it is currently in phase II clinical trials for the treatment of ovarian cancer and its safety and dosage in humans have already been established. Our results indicate that stenoparib possesses strong antiviral activity against SARS-CoV-2 and other coronaviruses in vitro. This activity appears to be based on multiple modes of action, where both pre-entry and postentry viral replication processes are impeded. This may provide a therapeutic advantage over many current options that have a narrower target range. Moreover, our results suggest that stenoparib and remdesivir in combination may be especially potent against coronavirus infection.
19 January 2021, mBio
-
Review
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2): a Systemic Infection
To date, seven identified coronaviruses (CoVs) have been found to infect humans; of these, three highly pathogenic variants have emerged in the 21st century. The newest member of this group, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was first detected at the end of 2019 in Hubei province, China. Since then, this novel coronavirus has spread worldwide, causing a pandemic; the respiratory disease caused by the virus is called coronavirus disease 2019 (COVID-19). The clinical presentation ranges from asymptomatic to mild respiratory tract infections and influenza-like illness to severe disease with accompanying lung injury, multiorgan failure, and death. Although the lungs are believed to be the site at which SARS-CoV-2 replicates, infected patients often report other symptoms, suggesting the involvement of the gastrointestinal tract, heart, cardiovascular system, kidneys, and other organs; therefore, the following question arises: is COVID-19 a respiratory or systemic disease? This review aims to summarize existing data on the replication of SARS-CoV-2 in different tissues in both patients and ex vivo models.
13 January 2021, CMR
-
Research Article
Correlation of SARS-CoV-2 nucleocapsid antigen and RNA concentrations in nasopharyngeal samples from children and adults using an ultrasensitive and quantitative antigen assay
Diagnosis of COVID-19 by PCR offers high sensitivity, but the utility of detecting samples with high cycle threshold (Ct) values remains controversial. Currently available rapid diagnostic tests (RDTs) for SARS-CoV-2 nucleocapsid antigens (Ag) have sensitivity well below PCR. The correlation of Ag and RNA quantities in clinical nasopharyngeal (NP) samples is unknown. An ultrasensitive, quantitative electrochemiluminescence immunoassay for SARS-CoV-2 nucleocapsid (the MSD® S-PLEX® CoV-2 N assay) was used to measure Ag in clinical NP samples from adults and children previously tested by PCR. The S-PLEX Ag assay had a limit of detection (LOD) of 0.16 pg/mL and a cutoff of 0.32 pg/mL. Ag concentrations measured in clinical NP samples (collected in 3.0 mL media) ranged from less than 160 fg/mL to 2.7 ug/mL. Log-transformed Ag concentrations correlated tightly with Ct values. In 35 adult and 101 pediatric PCR-positive samples, sensitivity was 91% (95% CI, 77-98%) and 79% (70-87%), respectively. In samples with Ct ≤ 35, sensitivity was 100% (88-100%) and 96% (88-99%), respectively. In 50 adult and 40 pediatric PCR-negative specimens, specificity was 100% (93-100%) and 98% (87-100%), respectively. Nucleocapsid concentrations in clinical NP samples span 8 orders of magnitude and correlate closely with RNA concentrations (Ct values). The S-PLEX Ag assay had 96-100% sensitivity in samples from children and adults with Ct values ≤ 35, and 98-100% specificity. These results clarify Ag concentration distributions in clinical samples, providing insight into the performance of Ag RDTs and offering a new approach to diagnosis of COVID-19.
Accepted Manuscript Posted 13 January 2021, JCM; Final Article Posted 19 March 2021
-
Research Article
Non-steroidal anti-inflammatory drugs dampen the cytokine and antibody response to SARS-CoV-2 infection
Public health officials have raised concerns about the use of nonsteroidal anti-inflammatory drugs (NSAIDs) for treating symptoms of coronavirus disease 2019 (COVID-19). NSAIDs inhibit the enzymes cyclooxygenase-1 (COX-1) and cyclooxygenase-2 (COX-2), which are critical for the generation of prostaglandins – lipid molecules with diverse roles in homeostasis and inflammation. Inhibition of prostaglandin production by NSAIDs could therefore have multiple effects on COVID-19 pathogenesis. Here, we demonstrate that NSAID treatment reduced both the antibody and pro-inflammatory cytokine response to SARS-CoV-2 infection. The ability of NSAIDs to modulate the immune response to SARS-CoV-2 infection has important implications for COVID-19 pathogenesis in patients. Whether this occurs in humans and whether it is beneficial or detrimental to the host remains an important area of future investigation. This also raises the possibility that NSAIDs may alter the immune response to SARS-CoV-2 vaccination.
Accepted Manuscript Posted 13 January 2021, JVI; Final Article Posted 10 March 2021
-
Observation
An Observational Laboratory-Based Assessment of SARS-CoV-2 Molecular Diagnostics in Benin, Western Africa
Months after the start of the COVID-19 pandemic, case numbers from Africa are surprisingly low, potentially because the number of SARS-CoV-2 tests performed in Africa is lower than in other regions. Here, we show an overload of COVID-19-related diagnostics in the central laboratory of Benin, Western Africa, with a stagnating average number of positive samples irrespective of daily sample counts. SARS-CoV-2 genomic surveillance confirmed a high genomic diversity in Benin introduced by travelers returning from Europe and other African countries, including early circulation of the D614G spike mutation associated with potentially higher transmissibility. We validated a widely used RT-PCR kit donated by the Chinese Jack Ma Foundation and confirmed high analytical specificity and clinical sensitivity equivalent to tests used in affluent settings. Our assessment shows that although achievable in an African setting, the burden from COVID-19-related diagnostics on national reference laboratories is very high.
13 January 2021, mSphere
-
Research Article
Evaluation of the Xpert Xpress SARS-CoV-2/Flu/RSV assay for simultaneous detection of SARS-CoV-2, Influenza A/B and Respiratory Syncytial Viruses in nasopharyngeal specimens
Patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza A (flu A), influenza B (flu B), and respiratory syncytial virus (RSV) have overlapping clinical presentations, but the approaches to treatment and management of infections caused by these viruses are different. Therefore, rapid diagnosis in conjunction with infection prevention measures is important to prevent transmission of the diseases. Recently, a new Xpert Xpress SARS-CoV-2/Flu/RSV (Xpert 4-in-1) assay enables the detection and differentiation of SARS-CoV-2, flu A, flu B, and RSV in upper respiratory tract specimens. In this study, we evaluated the performance of the Xpert 4-in-1 assay by comparing it with the Xpert Xpress SARS-CoV-2 and Xpert Xpress Flu/RSV assays for the detection of the four viruses in nasopharyngeal (NP) specimens. A total of 279 NP specimens, including 66, 56, 64 and 53 positive specimens for SARS-CoV-2, flu A, flu B and RSV respectively, were included. The Xpert 4-in-1 assay demonstrated high concordance with the comparator assays, with overall agreement for SARS-CoV-2, flu A, flu B, and RSV at 99.64%, 100%, 99.64%, and 100%, respectively, and a high kappa value ranging from 0.99 to 1.00, indicating an almost perfect correlation between assays. The cycle threshold value association between positive samples also showed a good correlation between assays. In conclusion, the overall performance of the Xpert 4-in-1 assay was highly comparable to that of the Xpert SARS-CoV-2 and Xpert Flu/RSV assays for the detection and differentiation of SARS CoV-2, flu A, flu B, and RSV in NP specimens.
Accepted Manuscript Posted 12 January 2021, JCM; Final Article Posted 19 March 2021