Effect of heat inactivation for the detection of severe acute respiratory syndrome-corona virus-2 (SARS-CoV-2) with reverse transcription real time polymerase chain reaction (rRT-PCR): evidence from Ethiopian study

The Biosafety Research Road Map: The Search for Evidence to Support Practices in the Laboratory-SARS-CoV-2

Introduction

The SARS-CoV-2 virus emerged as a novel virus and is the causative agent of the COVID-19 pandemic. It spreads readily human-to-human through droplets and aerosols. The Biosafety Research Roadmap aims to support the application of laboratory biological risk management by providing an evidence base for biosafety measures. This involves assessing the current biorisk management evidence base, identifying research and capability gaps, and providing recommendations on how an evidence-based approach can support biosafety and biosecurity, including in low-resource settings.

Methods

A literature search was conducted to identify potential gaps in biosafety and focused on five main sections, including the route of inoculation/modes of transmission, infectious dose, laboratory-acquired infections, containment releases, and disinfection and decontamination strategies.

Results

There are many knowledge gaps related to biosafety and biosecurity due to the SARS-CoV-2 virus's novelty, including infectious dose between variants, personal protective equipment for personnel handling samples while performing rapid diagnostic tests, and laboratory-acquired infections. Detecting vulnerabilities in the biorisk assessment for each agent is essential to contribute to the improvement and development of laboratory biosafety in local and national systems.

Short-term prognostic analysis of patients with systemic lupus erythematosus co-infection and comparison of mNGS and conventional microbiological test results

Objectives

Infection is one of the major causes of morbidity and mortality in patients with systemic lupus erythematosus (SLE), and as a new diagnostic technique, metagenomic next-generation sequencing (mNGS) is increasingly used for the pathogenetic detection of co-infected SLE patients. However, conventional microbiological testing (CMT) is still the gold standard for pathogenic diagnosis, and the specific diagnostic efficacy of mNGS versus CMT in such patients is not known. In addition, there are few studies on the short-term prognosis of co-infected SLE patients.

Methods

This study retrospectively included 58 SLE patients with co-infection admitted to the First Affiliated Hospital of Zhengzhou University from October 2020 to August 2022. Patients were divided into a survivors (n=27) and a non-survivors (n=31) according to their discharge status. Baseline characteristics and etiological data were collected and statistically analyzed for all patients during their hospitalization. The sequential organ failure assessment (SOFA) score, acute physiology and chronic health evaluation (APACHE) II and systemic lupus erythematosus disease activity index (SLEDAI) were calculated for each patient to assess the predictive ability of the 3 scores on the short-term prognosis of SLE patients. The mNGS and CMT culture results were also compared to clarify the flora characteristics of patients with SLE infection.

Results

More patients in the non-survivors had renal impairment, neurological manifestations, multiplasmatic cavity effusion and gastrointestinal manifestations compared to the survivors (p < 0.05). The SOFA score, APACHE II and SLEDAI were significantly higher in the non-survivors than in the survivors (p < 0.01). There were also significant differences between the two groups in several tests such as hemoglobin, platelets, albumin, total bilirubin, C-reactive protein (CRP), procalcitonin (PCT), and complement C3 (p < 0.05). In addition, the absolute values of T lymphocytes, CD4+ T cells and CD8+ T cells were smaller in the non-survivors than in the survivors (p < 0.05). The most common type of infection in this study was pulmonary infection, followed by bloodstream infection. mNGS and CMT positivity rates were not significantly different among patients in the non-survivors, but were significantly different among patients in the survivors (p=0.029). In-hospital survival of patients with SLE infection could be predicted based on the SOFA score in relation to 6. For patients with SOFA <6, we recommend earlier mNGS testing to identify the pathogen and improve patient prognosis.

Conclusions

For SLE patients with co-infection, in-hospital survival can be predicted based on SOFA score. For patients with SOFA <6, advising them to complete mNGS testing as early as possible may improve the prognosis to some extent.

Performances of four Nucleic Acid Amplification Tests for the identification of SARS-CoV-2 in Ethiopia

Since Coronavirus Disease-2019 (COVID-19) outbreak was reported, many commercial Nucleic Acid Amplification Tests (NAAT) have been developed all over the world, and it has been the standard method. Even though several assays were rapidly developed and applied to laboratory diagnostic testing, the performance of these assays was not evaluated in different contexts. Thus, this study aimed to assess the performance of Abbott SARS-CoV-2, Daan Gene, BGI and Sansure Biotech assays by using Composite Reference Standard (CRS). The study was conducted at the Ethiopian Public Health Institute (EPHI) from December 1 to 30/2020. Of the 164 nasopharyngeal samples were extracted by using a QIAamp RNA mini kit and Abbott DNA sample preparation system. Out of 164 samples, 59.1% were positive and 40.9% were negative by CRS. Sansure Biotech positivity was significantly low compared to CRS (p < 0.05). The overall agreement of the four assays compared to CRS was 96.3-100%. The performance of the four assays had almost comparable diagnostic performance, except for a low positive rate of Sansure Biotech assay. Hence, Sansure Biotech assay [Research Use Only (RUO)] needs further verification on its use in Ethiopia. Finally an additional study should be considered for evaluating assays with respective manufacturer claims.

The Comparison of Metagenomic Next-Generation Sequencing with Conventional Microbiological Tests for Identification of Pathogens and Antibiotic Resistance Genes in Infectious Diseases

Background

Metagenomic next-generation sequencing (mNGS) has been widely studied, due to its ability of detecting all the microbial genetic information unbiasedly in a sample at one time and not relying on traditional culture. However, the application of mNGS in the diagnosis of clinical pathogens remains challenging.

Methods

From December 2019 to March 2021, 134 specimens including Broncho alveolar lavage fluid (BAFL), blood, sputum, cerebrospinal fluid (CSF), bile, pleural fluid, pus, were continuously collected in The First Hospital of Qinhuangdao, and their retrospective diagnoses were classified into infectious disease (128, 95.5%) and noninfectious disease (6, 4.5%). The pathogen-detection performance of mNGS was compared with conventional microbiological tests (CMT) and culture method. In addition, the antibiotic resistance genes (ARGs) and evolutionary relationship of common drug-resistant A. baumannii were also analyzed.

Results

Compared with CMT and culture methods, mNGS showed higher sensitivity in pathogen detection (74.2% vs 57.8%; P < 0.001 and 66.3% vs 31.7%; P < 0.001, respectively). Importantly, for cases that mNGS-positive only, 18 (35%) cases result in diagnosis modification, and 7 (23%) cases confirmed the clinical diagnosis. In 17 cases that A. baumannii were both detected in mNGS and culture, ade genes were the most frequently detected ARGs (from 13 cases), followed by sul2 and APH(3”)-Ib (both from 12 cases). High consistency was observed among these ARGs and the related phenotype (100% for ade genes, 91.6% for sul2 and APH(3”)-Ib). A. baumannii strains were classified into three groups, and most were well-clustered. It suggested those strains may be the epidemic strains.

Conclusion

In our study, mNGS had a higher sensitivity than CMT and culture method. And the result of ARGs frequency and cluster analysis of A. baumannii was of great significance to the anti-infective therapy.

CRISPR-Cas-based techniques for pathogen detection: Retrospect, recent advances, and future perspectives

BACKGROUND

Early detection of pathogen-associated diseases are critical for effective treatment. Rapid, specific, sensitive, and cost-effective diagnostic technologies continue to be challenging to develop. The current gold standard for pathogen detection, polymerase chain reaction technology, has limitations such as long operational cycles, high cost, and high technician and instrumentation requirements.

AIM OF REVIEW

This review examines and highlights the technical advancements of CRISPR-Cas in pathogen detection and provides an outlook for future development, multi-application scenarios, and clinical translation.

KEY SCIENTIFIC CONCEPTS OF REVIEW

Approaches enabling clinical detection of pathogen nucleic acids that are highly sensitive, specific, cheap, and portable are necessary. CRISPR-Cas9 specificity in targeting nucleic acids and "collateral cleavage" activity of CRISPR-Cas12/Cas13/Cas14 show significant promise in nucleic acid detection technology. These methods have a high specificity, versatility, and rapid detection cycle. In this paper, CRISPR-Cas-based detection methods are discussed in depth. Although CRISPR-Cas-mediated pathogen diagnostic solutions face challenges, their powerful capabilities will pave the way for ideal diagnostic tools.