False negative RT-PCR or false positive serological testing in SARS-CoV-2 diagnostics? Navigating between Scylla and Charybdis to prevent misclassification bias in COVID-19 clinical investigations

Application of a Machine Learning-Based Classification Approach for Developing Host Protein Diagnostic Models for Infectious Disease

In recent years, infectious disease diagnosis has increasingly turned to host-centered approaches as a complement to pathogen-directed ones. The former, however, typically requires the interpretation of complex multiple biomarker datasets to arrive at an informative diagnostic outcome. This report describes a machine learning (ML)-based classification workflow that is intended as a template for researchers seeking to apply ML approaches for developing host-based infectious disease biomarker classifiers. As an example, we built a classification model that could accurately distinguish between three disease etiology classes: bacterial, viral, and normal in human sera using host protein biomarkers of known diagnostic utility. After collecting protein data from known disease samples, we trained a series of increasingly complex Auto-ML models until arriving at an optimized classifier that could differentiate viral, bacterial, and non-disease samples. Even when limited to a relatively small training set size, the model had robust diagnostic characteristics and performed well when faced with a blinded sample set. We present here a flexible approach for applying an Auto-ML-based workflow for the identification of host biomarker classifiers with diagnostic utility for infectious disease, and which can readily be adapted for multiple biomarker classes and disease states.

Photo-sensitive peptide inducing targeted cross-linking in a one-step and reagent-, enzyme- and antibody-free detection of SARS-Cov-2 marker protein

Modern biosensing technology plays a crucial role in combating the spread of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). However, the associated assays remain costly, considering their extensive daily use. In response, we developed a simplified one-step SARS-CoV-2 protease assay that reduces both time and financial expenses. This approach eliminates the need for extra reagents, enzymes, or antibodies. The simplification involves a photo-sensitive Bengal red-tagged substrate peptide, allowing specific cross-linking upon protease-substrate recognition. This process forms a di-tyrosine product with a distinctive fluorescence signal readout, enabling the detection of SARS-CoV-2 in patient serum samples. This method anticipates a major reduction in assay costs in the near future.

Impact of the Presence Anti-SARS-CoV-2 IgA in the Colostrum of Women Infected by COVID-19 During the Pregnancy in Neonatal Clinical Outcomes: A Cross-Sectional Study

OBJECTIVES

To describe the presence of anti-SARS-CoV-2 IgA and IgG in the blood and colostrum of women with COVID-19 infection during pregnancy and associate the presence of anti-SARS-CoV-2 IgA in colostrum with clinical symptoms of their newborns.

METHODS

A cross-sectional study was developed with 165 participants with COVID-19 infection during pregnancy and their newborns.

DATA COLLECTED

characteristics COVID-19 infection in pregnant women, gestational age, and clinical symptoms in their newborns (fever, hypothermia, respiratory distress, hypotonia, hypoactivity, hypoglycemia, cyanosis, vomiting/regurgitation, abdominal distention, and jaundice). Maternal blood and colostrum samples were collected postpartum to to detect the presence of IgA and IgG anti-SARS-CoV-2.

RESULTS

The median interval between COVID-19 diagnosis and delivery was 37.5 days (IQ = 12.0, 73.0 days). Clinical symptoms during hospitalization were observed in 55 newborns (33.3%), and two (1.6%) tested RT-PCR positive for COVID-19. Positive colostrum for anti-SARS-CoV-2 IgA was found in 117 (70.9%) women. The presence of anti-SARS-CoV-2 IgA in colostrum was associated independently with lower clinical symptoms in their newborns (OR = 0.42; 95% CI 0.202 to 0.84; p = 0.015).

CONCLUSIONS FOR PRACTICE

The presence of anti-SARS-CoV-2 IgA in colostrum was detected in more than two-thirds of the women evaluated and was associated with a lower frequency of clinical symptoms in their newborns.

SARS-CoV-2: The Self-Nonself Issue and Diagnostic Tests

Objective At present, false negatives/positives have been reported in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnostics. Searching for the molecular basis of such tests' unreliability, this study aimed at defining how specific are the sequences used in serological and polymerase chain reaction (PCR) tests to detect SARS-CoV-2.

Materials and Methods Analyses were performed on the leading SARS-CoV-2 biomarker spike glycoprotein (gp). Sharing of peptide sequences between the spike antigen and the human host was analyzed using the Peptide Search program from Uniprot database. Sharing of oligonucleotide sequences was investigated using the nucleotide Basic Local Alignment Search Tool (BLASTn) from National Center for Biotechnology Information (NCBI).

Results Two main points stand out: (1) a massive pentapeptide sharing exists between the spike gp and the human proteome, and only a limited number of pentapeptides (namely 107) identify SARS-CoV-2 spike gp as nonself when compared with the human proteome, and (2) the small phenetic difference practically disappears at the genetic level. Indeed, almost all of the 107 pentadecameric nucleotide sequences coding for the pentapeptides unique to SARS-CoV-2 spike gp are present in human nucleic acids too.

Conclusions The data are of immunological significance for defining the issue of the viral versus human specificity and likely explain the fact that false positives can occur in serological and PCR tests for SARS-CoV-2 detection.

Nucleotide Sequence Sharing between the Human Genome and Primers for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Detection

This study shows that oligonucleotide sequences are shared between the human genome and primers that have been proposed/used for SARS-CoV-2 detection by polymerase chain reaction (PCR). The high level of sharing (namely, up to 19mer with a maximum number of gaps equal to 2) might bear implications for the diagnostic validity of SARS-CoV-2 detection by PCR.

Cytokeratin 18 cell death assays as biomarkers for quantification of apoptosis and necrosis in COVID-19: a prospective, observational study

BACKGROUND

The mechanism by which SARS-CoV-2 triggers cell damage and necrosis are yet to be fully elucidated. We sought to quantify epithelial cell death in patients with COVID-19, with an estimation of relative contributions of apoptosis and necrosis.

METHODS

Blood samples were collected prospectively from adult patients presenting to the emergency department. Circulating levels of caspase-cleaved (apoptosis) and total cytokeratin 18 (CK-18) (total cell death) were determined using M30 and M65 enzyme assays, respectively. Intact CK-18 (necrosis) was estimated by subtracting M30 levels from M65.

RESULTS

A total of 52 COVID-19 patients and 27 matched sick controls (with respiratory symptoms not due to COVID-19) were enrolled. Compared with sick controls, COVID-19 patients had higher levels of M65 (p = 0.046, total cell death) and M30 (p = 0.0079, apoptosis). Hospitalised COVID-19 patients had higher levels of M65 (p= 0.014) and intact CK-18 (p= 0.004, necrosis) than discharged patients. Intensive care unit (ICU)-admitted COVID-19 patients had higher levels of M65 (p= 0.004), M30 (p= 0.004) and intact CK-18 (p= 0.033) than hospitalised non-ICU admitted patients. In multivariable logistic regression, elevated levels of M65, M30 and intact CK-18 were associated with increased odds of ICU admission (OR=22.05, p=0.014, OR=19.71, p=0.012 and OR=14.12, p=0.016, respectively).

CONCLUSION

Necrosis appears to be the main driver of hospitalisation, whereas apoptosis and necrosis appear to drive ICU admission. Elevated levels CK-18 levels are independent predictors of severe disease, and could be useful for risk stratification of COVID-19 patients and in assessment of therapeutic efficacy in early-phase COVID-19 clinical trials.

Serum ACE activity and plasma ACE concentration in patients with SARS-CoV-2 infection

Significant controversy has arisen over the role of the renin-angiotensin-aldosterone system (RAAS) in COVID-19 pathophysiology. In this prospective, observational study, we evaluated plasma angiotensin converting enzyme (ACE) concentration and serum ACE activity in 52 adults with laboratory-confirmed SARS-CoV-2 infection and 27 non-COVID-19 sick controls. No significant differences were observed in ACE activity in COVID-19 patients versus non-COVID-19 sick controls (41.1 [interquartile range (IQR): 23.0–55.2] vs. 42.9 [IQR 13.6–74.2] U/L, p = .649, respectively). Similarly, no differences were observed in ACE concentration in COVID-19 patients versus non-COVID-19 sick controls (108.4 [IQR: 95.8–142.2] vs. 133.8 [IQR: 100.2–173.7] μg/L, p = .059, respectively). Neither ACE activity (p = .751), nor ACE concentration (p = .283) was associated with COVID-19 severity. Moreover, neither ACE activity, nor ACE concentration was correlated with any inflammatory biomarkers.

Early Identification of IgA Anti-SARSCoV-2 in Milk of Mother With COVID-19 Infection

INTRODUCTION

Human milk cannot currently be considered a major source of COVID-19 infection. On the other hand, it can contain specific antibodies that could modulate a possible newborn infection by SARS-CoV-2.

MAIN ISSUE

A 32-year-old pregnant woman, gestational age 37 and 3/7 weeks, was admitted with a flu-like syndrome caused by COVID-19. The female newborn was appropriate for gestational age, with a birth weight of 2,890 g, length 48 cm, and head circumference 34 cm.

MANAGEMENT

The mother-infant dyad remained in the rooming-in unit during hospitalization, exclusively breastfeeding and following World Health Organization recommendations for contact and airway precautions. On the 3rd day after delivery, two mother's milk samples (3 and 5 mL) were collected by hand expression. The samples were centrifuged for 10 min twice consecutively to separate fat, which was removed, and the remaining material was transferred to another tube to determine anti-SARS-CoV-2 Immunoglobulin A and Immunoglobulin G (ELISA, Kit EUROIMMUN AG, Luebeck, Germany). Anti-SARS-CoV-2 Immunoglobulin A was detected in the two samples evaluated, whose values were 2.5 and 1.9, respectively. No anti-SARSCoV-2 immunoglobulin G was detected. The exclusively-breastfed infant remained well through 45 days of age.

CONCLUSION

The presence of SARS-CoV-2 Immunoglobulin A in the milk of mothers infected with COVID-19 may be related to protection against the transmission and severity of the disease in their infants.

Updates on laboratory investigations in coronavirus disease 2019 (COVID-19)

The coronavirus disease 2019 (COVID-19) pandemic is still spreading worldwide, affecting several million people. Unlike the previous two coronavirus outbreaks, COVID-19 has caused several thousand deaths for respiratory and multiple organ failure. As specifically concerns this latest infectious pathology, laboratory medicine can provide a substantial contribution to diagnosing an acute severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection through molecular testing, establishing the presence and extent of an immune response against the virus, mostly through serological testing. However, it can also help to predict the risk of unfavorable disease progression by measuring some conventional laboratory tests and, last but not least, can provide reliable therapeutic guidance. This article is hence aimed at offering recent updates on the important role and value of laboratory investigations in COVID-19, also providing information on some hot topics such as virus RNA detection in different biological samples, causes of recurrent positivity of reverse-transcription polymerase chain reaction (RT-PCR), potential strategies for enhancing the throughput of molecular testing (i.e., pre-test probability assessment, sample pooling, use of rapid tests), as well as pragmatic indications for enhancing the quality and value of serological testing and laboratory-based monitoring.