The Main Molecular and Serological Methods for Diagnosing COVID-19: An Overview Based on the Literature

Molecular Interactions Leading to Advancements in the Techniques for COVID-19 Detection: A Review

Since 2019 the world has been in a combat with the highly contagious disease COVID-19 which is caused by the rapid transmission of the SARS-CoV-2 virus (severe acute respiratory syndrome coronavirus 2). Detection of this disease in an early stage helps to control its spread and management. To combat this epidemic with one-time effective medication, improved quick analytical procedures must be developed and validated. The requirement for accurate and precise analytical methods for the diagnosis of the virus and antibodies in infected patients has been a matter of concern. The global impact of this virus has motivated scientists and researchers to investigate and develop various analytical diagnostic techniques. This review includes the study of standard methods which are reliable and accredited for the analytical recognition of the said virus. For early detection of SARS-CoV-2 RNA, RT-PCR (Real-time reverse transcriptase-polymerase chain reaction) is an accurate method among other methods and, thus, considered as the "gold standard" technique. Here, we outline the most extensively used analytical methods for diagnosing COVID-19, along with a brief description of each technique and its analytical aspects/perspective.

Association between SARS-CoV-2 gene specific Ct values and COVID-19 associated in-hospital mortality

Background

Since there are currently no specific SARS-CoV-2 prognostic viral biomarkers for predicting disease severity, there has been interest in using SARS-CoV-2 polymerase chain reaction (PCR) cycle-threshold (Ct) values to predict disease progression.

Objective

This study assessed the association between in-hospital mortality of hospitalized COVID-19 cases and Ct-values of gene targets specific to SARS-CoV-2.

Methods

Clinical data of hospitalized COVID-19 cases from Gauteng Province from April 2020-July 2022 were obtained from a national surveillance system and linked to laboratory data. The study period was divided into pandemic waves: Asp614Gly/wave1 (7 June-22 Aug 2020); beta/wave2 (15 Nov 2020-6 Feb 2021); delta/wave3 (9 May-18 Sept 2021) and omicron/wave4 (21 Nov 2021-22 Jan 2022). Ct-value data of genes specific to SARS-CoV-2 according to testing platforms (Roche-ORF gene; GeneXpert-N2 gene; Abbott-RdRp gene) were categorized as low (Ct < 20), mid (Ct20-30) or high (Ct > 30).

Results

There were 1205 recorded cases: 836(69.4%; wave1), 122(10.1%;wave2) 21(1.7%; wave3) and 11(0.9%;in wave4). The cases' mean age(±SD) was 49 years(±18), and 662(54.9%) were female. There were 296(24.6%) deaths recorded: 241(81.4%;wave1), 27 (9.1%;wave2), 6 (2%;wave3), and 2 (0.7%;wave4) (p < 0.001). Sample distribution by testing platforms was: Roche 1,033 (85.7%), GeneXpert 169 (14%) and Abbott 3 (0.3%). The median (IQR) Ct-values according to testing platform were: Roche 26 (22-30), GeneXpert 38 (36-40) and Abbott 21 (16-24). After adjusting for sex, age and presence of a comorbidity, the odds of COVID-19 associated death were high amongst patients with Ct values 20-30[adjusted Odds Ratio (aOR) 2.25; 95% CI: 1.60-3.18] and highest amongst cases with Ct-values <20 (aOR 3.18; 95% CI: 1.92-5.27), compared to cases with Ct-values >30.

Conclusion

Although odds of COVID19-related death were high amongst cases with Ct-values <30, Ct values were not comparable across different testing platforms, thus precluding the comparison of SARS-CoV-2 Ct-value results.

Long-term monitoring of COVID-19 prevalence in raw and treated wastewater in Salvador, the largest capital of the Brazilian Northeast

Wastewater-based epidemiology (WBE) becomes an interesting epidemiological approach to monitoring the prevalence of SARS-CoV-2 broadly and non-invasively. Herein, we employ for the first time WBE, associated or not with the PEG 8000 precipitation method, for the detection of SARS-CoV-2 in samples of raw or treated wastewater from 22 municipal wastewater treatment stations (WWTPs) located in Salvador, the fourth most populous city in Brazil. Our results demonstrate the success of the application of WBE for detecting SARS-CoV-2 in both types of evaluated samples, regardless of the usage of PEG 8000 concentration procedure. Further, an increase in SARS-CoV-2 positivity rate was observed in samples collected in months that presented the highest number of confirmed COVID-19 cases (May/2021, June/2021 and January/2022). While PEG 8000 concentration step was found to significantly increase the positivity rate in treated wastewater samples (p < 0.005), a strong positive correlation (r: 0.84; p < 0.002) between non-concentrated raw wastewater samples with the number of new cases of COVID-19 (April/2021-February/2022) was observed. In general, the present results reinforce the efficiency of WBE approach to monitoring the presence of SARS-CoV-2 in either low- or high-capacity WWTPs. The successful usage of WBE even in raw wastewater samples makes it an interesting low-cost tool for epidemiological surveillance.

Sample Treatment with Trypsin for RT-LAMP COVID-19 Diagnosis

The SARS-CoV-2 coronavirus is responsible for the COVID-19 pandemic resulting in a global health emergency. Given its rapid spread and high number of infected individuals, a diagnostic tool for a rapid, simple, and cost-effective detection was essential. In this work, we developed a COVID-19 diagnostic test, that incorporates a human internal control, based on the Reverse Transcription Loop-Mediated Isothermal Amplification (RT-LAMP). When working with synthetic SARS-CoV-2 RNA, the optimized RT-LAMP assay has a sensitivity of 10 viral copies and can be detected by fluorescence in less than 15 min or by the naked eye in 25 min using colorimetric RT-LAMP. To avoid the RNA extraction step, a pre-treatment of the sample was optimized. Subsequently, a validation was performed on 268 trypsin treated samples (including nasopharyngeal, buccal, and nasal exudates) and amplified with colorimetric RT-LAMP to evaluate its sensitivity and specificity in comparison with RT-qPCR of extracted samples. The validation results showed a sensitivity and specificity of 100% for samples with Ct ≤ 30. The rapid, simple, and inexpensive RT-LAMP SARS-CoV-2 extraction-free procedure developed may be an alternative test that could be applied for the detection of SARS-CoV-2 or adapted to detect other viruses present in saliva or nasopharyngeal samples with higher sensitivity and specificity of the antibody test.

Simple, Fast and Convenient Magnetic Bead-Based Sample Preparation for Detecting Viruses via Raman-Spectroscopy

We introduce a magnetic bead-based sample preparation scheme for enabling the Raman spectroscopic differentiation of severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2)-positive and -negative samples. The beads were functionalized with the angiotensin-converting enzyme 2 (ACE2) receptor protein, which is used as a recognition element to selectively enrich SARS-CoV-2 on the surface of the magnetic beads. The subsequent Raman measurements directly enable discriminating SARS-CoV-2-positive and -negative samples. The proposed approach is also applicable for other virus species when the specific recognition element is exchanged. A series of Raman spectra were measured on three types of samples, namely SARS-CoV-2, Influenza A H1N1 virus and a negative control. For each sample type, eight independent replicates were considered. All of the spectra are dominated by the magnetic bead substrate and no obvious differences between the sample types are apparent. In order to address the subtle differences in the spectra, we calculated different correlation coefficients, namely the Pearson coefficient and the Normalized cross correlation coefficient. By comparing the correlation with the negative control, differentiating between SARS-CoV-2 and Influenza A virus is possible. This study provides a first step towards the detection and potential classification of different viruses with the use of conventional Raman spectroscopy.

COVID-19 in early 2023: Structure, replication mechanism, variants of SARS-CoV-2, diagnostic tests, and vaccine & drug development studies

Coronavirus Disease-19 (COVID-19) is an infectious disease caused by severe acute respiratory syndrome-coronaviruses-2 (SARS-CoV-2), a highly pathogenic and transmissible coronavirus. Most cases of COVID-19 have mild to moderate symptoms, including cough, fever, myalgias, and headache. On the other hand, this coronavirus can lead to severe complications and death in some cases. Therefore, vaccination is the most effective tool to prevent and eradicate COVID-19 disease. Also, rapid and effective diagnostic tests are critical in identifying cases of COVID-19. The COVID-19 pandemic has a dynamic structure on the agenda and contains up-to-date developments. This article has comprehensively discussed the most up-to-date pandemic situation since it first appeared. For the first time, not only the structure, replication mechanism, and variants of SARS-CoV-2 (Alpha, Beta, Gamma, Omicron, Delta, Epsilon, Kappa, Mu, Eta, Zeta, Theta, lota, Lambda) but also all the details of the pandemic, such as how it came out, how it spread, current cases, what precautions should be taken, prevention strategies, the vaccines produced, the tests developed, and the drugs used are reviewed in every aspect. Herein, the comparison of diagnostic tests for SARS-CoV-2 in terms of procedure, accuracy, cost, and time has been presented. The mechanism, safety, efficacy, and effectiveness of COVID-19 vaccines against SARS-CoV-2 variants have been evaluated. Drug studies, therapeutic targets, various immunomodulators, and antiviral molecules applied to patients with COVID-19 have been reviewed.

Discovery of DNA aptamers targeting SARS-CoV-2 nucleocapsid protein and protein-binding epitopes for label-free COVID-19 diagnostics

The spread of COVID-19 has affected billions of people across the globe, and the diagnosis of viral infection still needs improvement. Because of high immunogenicity and abundant expression during viral infection, SARS-CoV-2 nucleocapsid (N) protein could be an important diagnostic marker. This study aimed to develop a label-free optical aptasensor fabricated with a novel single-stranded DNA aptamer to detect the N protein. The N-binding aptamers selected using asymmetric-emulsion PCR-SELEX and their binding affinity and cross-reactivity were characterized by biolayer interferometry. The tNSP3 aptamer (44 nt) was identified to bind the N protein of wild type and Delta and Omicron variants with high affinity (K_D in the range of 0.6-3.5 nM). Utilizing tNSP3 to detect the N protein spiked in human saliva evinced the potential of this aptamer with a limit of detection of 4.5 nM. Mass spectrometry analysis was performed along with molecular dynamics simulation to obtain an insight into how tNSP3 binds to the N protein. The identified epitope peptides are localized within the RNA-binding domain and C terminus of the N protein. Hence, we confirmed the performance of this aptamer as an analytical tool for COVID-19 diagnosis.

Smartphone-based corona virus detection using saliva: A mini-review

During the ongoing worldwide epidemic, SARS-CoV-2 has infected millions of individuals and taken the lives of numerous victims. It is clear that early detection of infected individuals, especially asymptomatic carriers, is possible with the development of innovative analytical tools for rapid identification of COVID-19 present in nasopharyngeal swabs, serum, and saliva. The saliva, as a diagnostic sample, can be easily collected by the patient with almost no discomfort and needs specialized healthcare personnel to manage, which reduces the risks for the operator. Moreover, smartphone-based sensing systems are one of the most attractive techniques that can speed up the detection time of COVID-19 agents without the need for professional staff and clinical centers. In this review, recent advances in precise salivary-based SARS-CoV-2 diagnosis using smartphones via viral RNA detection, antibody identification, and viral antigen identification were summarized. Finally, the conclusion and future perspective of this field are described in brief.

Malachite Green-Based Detection of SARS-CoV-2 by One-Step Reverse Transcription Loop-Mediated Isothermal Amplification

The pandemic of severe acute respiratory syndrome 2 (SARS-CoV-2) revealed the necessity of diagnosis of the infected people to prevent the prevalence infection cycle. Many commercial pathogen diagnosis methods are based on the detection of genomic materials. Isothermal amplification methods such as loop-mediated-isothermal amplification (LAMP) are the method of choice in these cases. Reverse transcription steps are efficiently coupled to LAMP for the detection of pathogens with genomic RNAs such as SARS-CoV-2. Many detection systems for LAMP include fluorescent readout systems. Although such systems result in desirable limits of detection, the need for special instrumentation is the main dispute of such systems to become real point of care assays. In contrast, colorimetric detection methods would reduce costs and improve the applicability of the system. In this study one-step reverse transcription-LAMP reaction was established that enables visual detection of the SARS-CoV-2 genome. Nasopharyngeal RNA samples were first validated by reverse transcription quantitative polymerase chain reaction and then subjected to RT-LAMP. To lower the cost associated with the readout system equipment, malachite green (MG) was used. The color change of MG to blue allowed visual detection of the virus. Firstly, experiments were set up as two-step RT-LAMP reaction to identify the best primer sets. In addition, MG concentration was optimized with the significant colorimetric signal for the positive samples. Next, a one-step colorimetric method was developed for the detection of SARS-CoV-2 based on MG color shift in 2 h.

Humoral immunogenicity of COVID-19 vaccines in patients with coeliac disease and other noncoeliac enteropathies compared to healthy controls

OBJECTIVES

Data are lacking on the immunogenicity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines in patients affected by coeliac disease, Whipple's disease and other noncoeliac enteropathies (NCE), characterised by primary or drug-related immunosuppression. We aimed to assess humoral response to SARS-CoV-2 vaccination in these patients compared to controls.

METHODS

Between December 2021 and January 2022, IgG anti-SARS-CoV-2 spike protein antibodies were measured in serum samples of coeliac disease, Whipple's disease and NCE patients attending our gastroenterology outpatient clinic for follow-up, who had received their first SARS-CoV-2 vaccination dose 3-6-9 (±1) months prior. Humoral response was compared with healthy controls (vaccinated healthcare workers undergoing serological screening), matched for gender, age, and time from first vaccine dose at sample collection.

RESULTS

A total of 120 patients [107 coeliac disease; 10 Whipple's disease; 2 common-variable immunodeficiency (CVID); 1 idiopathic villous atrophy; 77 F, 42 ± 16 years] and 240 matched controls (154 F, 43 ± 14 years) were enrolled. At 3, 6 and 9 months, humoral response in coeliac patients was not impaired compared to controls. Inadequate humoral response to vaccination was significantly more common among Whipple's disease patients than controls ( P  < 0.001). Patients on immunosuppressive therapy had markedly lower IgG anti-SARS-CoV-2 antibody titres (median 14 vs. 520 BAU/mL, P  < 0.001). As expected, patients with CVID showed no humoral response to vaccination.

CONCLUSIONS

Humoral immunogenicity of SARS-CoV-2 vaccines was not reduced in coeliac disease patients compared to controls, although it was in Whipple's disease and CVID patients. Post-vaccination humoral response should be monitored in patients with Whipple's disease and chronic enteropathies on immunosuppressive therapy in order to schedule vaccine booster doses.

Comparative Performance of Serological (IgM/IgG) and Molecular Testing (RT-PCR) of COVID-19 in Three Private Universities in Cameroon during the Pandemic

BACKGROUND

COVID-19 remains a rapidly evolving and deadly pandemic worldwide. This necessitates the continuous assessment of existing diagnostic tools for a robust, up-to-date, and cost-effective pandemic response strategy. We sought to determine the infection rate (PCR-positivity) and degree of spread (IgM/IgG) of SARS-CoV-2 in three university settings in Cameroon Method: Study volunteers were recruited from November 2020 to July 2021 among COVID-19 non-vaccinated students in three Universities from two regions of Cameroon (West and Centre). Molecular testing was performed by RT-qPCR on nasopharyngeal swabs, and IgM/IgG antibodies in plasma were detected using the Abbott Panbio IgM/IgG rapid diagnostic test (RDT) at the Virology Laboratory of CREMER/IMPM/MINRESI. The molecular and serological profiles were compared, and p < 0.05 was considered statistically significant.

RESULTS

Amongst the 291 participants enrolled (mean age 22.59 ± 10.43 years), 19.59% (57/291) were symptomatic and 80.41% (234/291) were asymptomatic. The overall COVID-19 PCR-positivity rate was 21.31% (62/291), distributed as follows: 25.25% from UdM-Bangangte, 27.27% from ISSBA-Yaounde, and 5% from IUEs/INSAM-Yaounde. Women were more affected than men (28.76% [44/153] vs. 13.04% [18/138], p < 0.0007), and had higher seropositivity rates to IgM+/IgG+ (15.69% [24/153] vs. 7.25% [10/138], p < 0.01). Participants from Bangangté, the nomadic, and the "non-contact cases" primarily presented an active infection compared to those from Yaoundé (p= 0.05, p = 0.05, and p = 0.01, respectively). Overall IgG seropositivity (IgM-/IgG+ and IgM+/IgG+) was 24.4% (71/291). A proportion of 26.92% (7/26) presenting COVID-19 IgM+/IgG- had negative PCR vs. 73.08% (19/26) with positive PCR, p < 0.0001. Furthermore, 17.65% (6/34) with COVID-19 IgM+/IgG+ had a negative PCR as compared to 82.35% with a positive PCR (28/34), p < 0.0001. Lastly, 7.22% (14/194) with IgM-/IgG- had a positive PCR.

CONCLUSION

This study calls for a rapid preparedness and response strategy in higher institutes in the case of any future pathogen with pandemic or epidemic potential. The observed disparity between IgG/IgM and the viral profile supports prioritizing assays targeting the virus (nucleic acid or antigen) for diagnosis and antibody screening for sero-surveys.

COVID-19 diagnostic approaches with an extensive focus on computed tomography in accurate diagnosis, prognosis, staging, and follow-up

Although a long time has passed since its outbreak, there is currently no specific treatment for COVID-19, and it seems that the most appropriate strategy to combat this pandemic is to identify and isolate infected individuals. Various clinical diagnosis methods such as molecular techniques, serologic assays, and imaging techniques have been developed to identify suspected patients. Although reverse transcription-quantitative PCR (RT-qPCR) has emerged as a reference standard method for diagnosis of SARS-CoV-2, the high rate of false-negative results and limited supplies to meet current demand are the main shortcoming of this technique. Based on a comprehensive literature review, imaging techniques, particularly computed tomography (CT), show an acceptable level of sensitivity in the diagnosis and follow-up of COVID-19. Indeed, because lung infection or pneumonia is a common complication of COVID-19, the chest CT scan can be an alternative testing method in the early diagnosis and treatment assessment of the disease. In this review, we summarize all the currently available frontline diagnostic tools for the detection of SARS-CoV-2-infected individuals and highlight the value of chest CT scan in the diagnosis, prognosis, staging, management, and follow-up of infected patients.

Avaliação do desenvolvimento tecnológico em saúde a partir da ocorrência das epidemias de zika e chikungunya no Brasil

Buscando compreender como as epidemias de zika e chikungunya incitaram o desenvolvimento tecnológico, este estudo realizou levantamento de dados epidemiológicos e prospecção tecnológica, utilizando dados do Instituto Nacional da Propriedade Industrial (INPI) e do Orbit Intelligence. Ainda, analisou produtos desenvolvidos e em desenvolvimento a nível mundial e aqueles registrados no Brasil por meio da Agência Nacional de Vigilância Sanitária (Anvisa). No ano de 2016, observou-se o maior número de casos totais para ambas as doenças. A prospecção tecnológica nacional revelou que há interesse global em desenvolver tecnologias para essas doenças e depositar suas patentes no Brasil, tendo as empresas como principais depositantes. Por sua vez, a prospecção tecnológica global mostrou que o ano de 2016 configura-se como importante marco na evolução do número de patentes para zika e chikungunya, sugerindo que as epidemias brasileiras estimularam o mundo no desenvolvimento de novos insumos para a saúde. Os Estados Unidos e a China são as principais jurisdições, tendo as universidades como maiores depositantes. A análise de produtos a nível global revelou que apenas dois chegaram ao mercado para zika e um para chikungunya, e as vacinas estão na categoria principal. A busca na Anvisa revelou que há mais produtos registrados para zika do que em comparação à chikungunya. Os principais fabricantes legais são empresas brasileiras, com pedidos de registro realizados principalmente pelas empresas DiaSorin S.p.A., ECO Diagnóstica Ltda. e Chembio Diagnostics Brazil Ltda. Apesar do visível estímulo à pesquisa, desenvolvimento e patenteamento gerado pelas epidemias de zika e chikungunya no Brasil, isso não garantiu a chegada de novos produtos ao mercado nem acesso da população a eles.

Label-free impedimetric immunosensor for point-of-care detection of COVID-19 antibodies

The COVID-19 pandemic has posed enormous challenges for existing diagnostic tools to detect and monitor pathogens. Therefore, there is a need to develop point-of-care (POC) devices to perform fast, accurate, and accessible diagnostic methods to detect infections and monitor immune responses. Devices most amenable to miniaturization and suitable for POC applications are biosensors based on electrochemical detection. We have developed an impedimetric immunosensor based on an interdigitated microelectrode array (IMA) to detect and monitor SARS-CoV-2 antibodies in human serum. Conjugation chemistry was applied to functionalize and covalently immobilize the spike protein (S-protein) of SARS-CoV-2 on the surface of the IMA to serve as the recognition layer and specifically bind anti-spike antibodies. Antibodies bound to the S-proteins in the recognition layer result in an increase in capacitance and a consequent change in the impedance of the system. The impedimetric immunosensor is label-free and uses non-Faradaic impedance with low nonperturbing AC voltage for detection. The sensitivity of a capacitive immunosensor can be enhanced by simply tuning the ionic strength of the sample solution. The device exhibits an LOD of 0.4 BAU/ml, as determined from the standard curve using WHO IS for anti-SARS-CoV-2 immunoglobulins; this LOD is similar to the corresponding LODs reported for all validated and established commercial assays, which range from 0.41 to 4.81 BAU/ml. The proof-of-concept biosensor has been demonstrated to detect anti-spike antibodies in sera from patients infected with COVID-19 within 1 h. Photolithographically microfabricated interdigitated microelectrode array sensor chips & label-free impedimetric detection of COVID-19 antibody.

The correlation between IgM and IgG antibodies with blood profile in patients infected with severe acute respiratory syndrome coronavirus

OBJECTIVES

This study aimed to determine the levels of IgM and IgG antibody response to the severe acute respiratory syndrome coronavirus (SARS-CoV)-2 in coronavirus disease 2019 (COVID-19) patients with different disease severity.

METHODS

IgM and IgG antibody levels were evaluated via enzyme-linked immunosorbent assay (ELISA). In total, 100 patients with confirmed SARS-CoV-2 infection were enrolled in this study and viral RNA was detected by using Real-time PCR technique. Clinical and laboratory data were collected and analyzed after hospital admission for COVID-19 and two months post-admission.

RESULTS

The level of anti-SARS-CoV-2 antibody IgG was significantly higher in the severe patients than those in moderate and mild groups, 2 months after admission. Also, level of IgG was positively associated with increased WBC, NUT and LYM counts in sever than mild or moderate groups after admission to hospital.

CONCLUSION

Our findings suggested that patients with severe illness might experience longer virus exposure times and have a stronger antibody response against viral infection. Thus, they have longer time immunity compared with other groups.

SARS-CoV-2: Challenges in Reconverting Diagnostic Laboratories to Combat the Pandemic

Coronavirus disease 2019 (COVID-19) was first detected in Mexico in February 2020. Even though health authorities did not perceive then the value of viral detection tests, we anticipated the demand for them. We set up to develop an expeditious severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) molecular diagnostic service through the implementation of standardized protocols for biospecimen sampling, transportation, biobanking, preanalytical validation, and nucleic acids (NA) testing (NAT). Nasopharyngeal and oropharyngeal swabs collected in a special transportation medium were the biospecimens from which NAs were purified either manually or automatically. Viral RNA genome presence was determined using commercial SARS-CoV-2 detection kits (based on reverse transcription coupled with real-time PCR [RT-PCR]). Improvements in laboratory processing speed and reliability resulted from semi-automatizing laboratory processes and adopting a quality control/quality assurance system (QC/QA), respectively. NAs that were purified, either manually or automatically, were validated by preanalytical spectrophotometric characterization. Automated purification was less prone to contamination and reduced the processing time. The following six RT-PCR kits were evaluated for their convenience, specificity, sensitivity, time consumption, and required materials (in order, starting with the kit with the best results): RIDA gene and Viasure (tied), Vircell, LightMix, 1copy, and Logix Smart. Redesigning the laboratories' working areas, equipment, fluxes of personnel and material, and personnel skills, and overemphasizing biosafety safeguards were major challenges encountered in the middle of the sanitary crisis. Adopting a QC/QA system, utilizing automatization processes, and working closely with health authorities were key factors in our success. IMPORTANCE Rearranging our diagnostic laboratories to improve the fight against a new unexpected, unpredictable, and sudden public health threat demanded that we move quickly to redesign not only the laboratory processes but also the distribution of space, personnel activities, and fluxes of material coming in and out. We also had to work closely with governmental health authorities to gain their trust in our technical competence. Gaining the confidence of the clients, i.e., mainly individuals, the human resource departments of factories and corporations sending employees for testing, and medical institutions, and implementing as much automatization as possible of processes, in which only officially approved reagents (for extraction and analysis of NA) were used to generate opportune trustable testing results, were key factors. Our laboratories have gathered a considerable amount of experience and significant number of solutions, considering our geographic contexts alongside this continuously morphing pandemic, validating many techniques that might help other laboratories find a better and more precise workflow.

Role of Technology in Detection of COVID-19

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus caused coronavirus infection termed as COVID-19, an illness that has spread devastation all over the world. It was developed first in China and had swiftly spread throughout the world. COVID has created imposed burden on health in the lives of all individuals around the globe. This article provides a number of unprecedented detection technologies used in the detection of infection. COVID has created a large number of symptoms in the young, adolescent as well as elderly population. Old age people are susceptible to fatal serious symptoms because of low immunity. With these goals in mind, this article includes substantial condemning descriptions of the majority of initiatives in order to create diagnostic tools for easy diagnosis. It also provides the reader with a multidisciplinary viewpoint on how traditional approaches such as serology and reverse transcriptase polymerase chain reaction (RT-PCR) along with the frontline techniques such as clustered regularly interspaced short palindromic repeats (CRISPR)/Cas and artificial intelligence/machine learning have been utilized to gather information. The story will inspire creative new ways for successful detection therapy and to prevent this pandemic among a wide audience of operating and aspiring biomedical scientists and engineers.

Utility of in silico-identified-peptides in spike-S1 domain and nucleocapsid of SARS-CoV-2 for antibody detection in COVID-19 patients and antibody production

SARS-CoV-2 contains four structural proteins, two of which, the spike and nucleocapsid, are commonly used for the standardization of novel methods for antibody detection; however, some limitations in their use have been observed due to the homology of this virus with other phylogenetically-related viruses. We performed in silico analysis to search for novel immunogenic and antigenic peptides. A total of twenty-five peptides were preliminarily selected, located in the 3D structure of both proteins. Finally, eight peptides were selected: one located in the N protein and seven in the S1 domain of the spike protein. Additionally, the localization of selected peptides in 2D structures and possible changes in the sequences of these peptides in SARS-CoV-2 variants of concern were analyzed. All peptides were synthetized in MAP8 format, and recombinant S (trimer and RBD) and N proteins were used as antigens to search for antibodies in serum samples derived from COVID-19 patients, and for antibody response in New Zealand rabbits. Results showed high recognition of the serum derived from COVID-19 patients to all selected peptides; however, only the RBD3 peptide induced antibody production. In conclusion, this work provides evidence for a new strategy in peptide selection and its use for antibody detection or antibody production in animals.

An improved, simple and field deployable CRISPR-Cas12a assay for detection of SARS-CoV-2

AIMS

The RT-PCR is the most popular confirmatory test for SARS-CoV-2. It is sensitive, but high instrumentation cost makes it difficult for use outside routine clinical setup. This has necessitated development of alternative methods such as CRISPR-based DETECTR method which uses lateral flow technology. Though accurate and sensitive, this method is limited by complex steps and recurrent cost of high quality lateral flow strips. The main goal of this study was to improve the Cas12a-based SARS-CoV-2 DETECTR method and develop a portable and field deployable system to reduce the recurring consumable cost.

METHODS AND RESULTS

Specific regions of N and E genes from SARS-CoV-2 virus and human RNase P (internal control) were reverse transcribed (RT) and amplified by loop-mediated isothermal amplification (LAMP). The amplified products were detected by a Cas12a-based trans-cleavage reaction that generated a fluorescent signal which could be easily visualised by naked eye. Detection of internal control, RNase P gene was improved and optimised by re-designing RT-LAMP primers. Number of steps were reduced by combining the reagents related to detection of Cas12a trans-cleavage reaction into a single ready-to-use mix. A portable, cost-effective battery-operated instrument, CRISPR-CUBE was developed to run the assay and visualise the outcome. The method and instrument were validated using both contrived and patient samples.

CONCLUSIONS

The simplified CRISPR-based SARS-CoV-2 detection and instrument developed in this study, along with improved design for internal control detection allows for easier, more definitive viral detection requiring only reagents, consumables and the battery operable CRISPR-CUBE.

SIGNIFICANCE AND IMPACT OF STUDY

Significant improvement in Cas12 method, coupled with simple visualisation of end-point makes the method and instrument deployable at the point of care for SARS-CoV-2 detection, without any recurrent cost for the lateral flow strips which is used in other POC methods.

Efficiency of Diagnostic Test for SARS-CoV-2 in a Nursing Home

Background: there is no consensus on how to optimally use diagnostic tests in each stage of COVID-19 pandemic. The objective of this research is to determine the efficiency of sorting positive antibody test quarterly. Methods: this research uses a retrospective, observational study. COVID-19 diagnostic tests performed and avoided refer to a Spanish nursing home. Population: 261 employees and 107 residents. A quarterly antibody test was performed on subjects who had tested positive during the first wave of coronavirus, and a antibody rapid test on the remaining subjects. Results: during the first wave, 24.0% of the employees and 51.4% of the residents had a positive antibody test. Seronegativization was observed in 7.6% of employees and 1.6% of residents. An employee was infected with COVID-19 in September 2020, followed by a nursing home outbreak in October: 118 Polymerase Chain Reactions tests were avoided in residents and 18 in employees, which in turn prevented 15 workers from going on sick leave and the quarantine of 59 residents. This represents savings of about $15,000. Conclusions: our study supports the need to know and apply the strategies for early detection, surveillance and control of COVID-19 for future outbreaks. We conclude that surveillance for positive COVID-19 serology among long-term care staff and residents may be a cost-effective strategy during a pandemic.

COVID-19 diagnostic methods in developing countries

COVID-19 has become one of the few leading causes of death and has evolved into a pandemic that disrupts everyone's routine, and balanced way of life worldwide, and will continue to do so. To bring an end to this pandemic, scientists had put their all effort into discovering the vaccine for SARS-CoV-2 infection. For their dedication, now, we have a handful of COVID-19 vaccines. Worldwide, millions of people are at risk due to the current pandemic of coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2). Despite the lack of clinically authorized antiviral medications and vaccines for COVID-19, clinical trials of many recognized antiviral agents, their combination, and vaccine development in patients with confirmed COVID-19 are still ongoing. This discovery gave us a chance to get immune to this disease worldwide and end the pandemic. However, the unexpected capacity of mutation of the SARS-CoV-2 virus makes it difficult, like the recent SAS-CoV-2 Omicron variant. Therefore, there is a great necessity to spread the vaccination programs and prevent the spread of this dreadful epidemic by identifying and isolating afflicted patients. Furthermore, several COVID-19 tests are thought to be expensive, time-consuming, and require the use of adequately qualified persons to be carried out efficiently. In addition, we also conversed about how the various COVID-19 testing methods can be implemented for the first time in a developing country and their cost-effectiveness, accuracy, human resources requirements, and laboratory facilities.

Serology as a Tool to Assess Infectious Disease Landscapes and Guide Public Health Policy

Understanding the local burden and epidemiology of infectious diseases is crucial to guide public health policy and prioritize interventions. Typically, infectious disease surveillance relies on capturing clinical cases within a healthcare system, classifying cases by etiology and enumerating cases over a period of time. Disease burden is often then extrapolated to the general population. Serology (i.e., examining serum for the presence of pathogen-specific antibodies) has long been used to inform about individuals past exposure and immunity to specific pathogens. However, it has been underutilized as a tool to evaluate the infectious disease burden landscape at the population level and guide public health decisions. In this review, we outline how serology provides a powerful tool to complement case-based surveillance for determining disease burden and epidemiology of infectious diseases, highlighting its benefits and limitations. We describe the current serology-based technologies and illustrate their use with examples from both the pre- and post- COVID-19-pandemic context. In particular, we review the challenges to and opportunities in implementing serological surveillance in low- and middle-income countries (LMICs), which bear the brunt of the global infectious disease burden. Finally, we discuss the relevance of serology data for public health decision-making and describe scenarios in which this data could be used, either independently or in conjunction with case-based surveillance. We conclude that public health systems would greatly benefit from the inclusion of serology to supplement and strengthen existing case-based infectious disease surveillance strategies.

On the caveats of a multiplex test for SARS-CoV-2 to detect seroconversion after infection or vaccination

The Covid-19 pandemic, caused by SARS-CoV-2, has resulted in over 6 million reported deaths worldwide being one of the biggest challenges the world faces today. Here we present optimizations of all steps of an enzyme-linked immunosorbent assay (ELISA)-based test to detect IgG, IgA and IgM against the trimeric spike (S) protein, receptor binding domain (RBD), and N terminal domain of the nucleocapsid (N-NTD) protein of SARS-CoV-2. We discuss how to determine specific thresholds for antibody positivity and its limitations according to the antigen used. We applied the assay to a cohort of 126 individuals from Rio de Janeiro, Brazil, consisting of 23 PCR-positive individuals and 103 individuals without a confirmed diagnosis for SARS-CoV-2 infection. To illustrate the differences in serological responses to vaccinal immunization, we applied the test in 18 individuals from our cohort before and after receiving ChAdOx-1 nCoV-19 or CoronaVac vaccines. Taken together, our results show that the test can be customized at different stages depending on its application, enabling the user to analyze different cohorts, saving time, reagents, or samples. It is also a valuable tool for elucidating the immunological consequences of new viral strains and monitoring vaccination coverage and duration of response to different immunization regimens.

The Importance of Vaccination in the Context of the COVID-19 Pandemic: A Brief Update Regarding the Use of Vaccines

The COVID-19 pandemic has led the world to undertake the largest vaccination campaign in human history. In record time, unprecedented scientific and governmental efforts have resulted in the acquisition of immunizers utilizing different technologies (nucleotide acids, viral vectors, inactivated and protein-based vaccines). Currently, 33 vaccines have already been approved by regulatory agencies in different countries, and more than 10 billion doses have been administered worldwide. Despite the undeniable impact of vaccination on the control of the pandemic, the recurrent emergence of new variants of interest has raised new challenges. The recent viral mutations precede new outbreaks that rapidly spread at global proportions. In addition, reducing protective efficacy rates have been observed among the main authorized vaccines. Besides these issues, several other crucial issues for the appropriate combatting of the pandemic remain uncertain or under investigation. Particularly noteworthy issues include the use of vaccine-boosting strategies to increase protection; concerns related to the long-term safety of vaccines, child immunization reliability and uncommon adverse events; the persistence of the virus in society; and the transition from a pandemic to an endemic state. In this review, we describe the updated scenario regarding SARS-CoV-2 variants and COVID-19 vaccines. In addition, we outline current discussions covering COVID-19 vaccine safety and efficacy, and the future pandemic perspectives.

Detection of SARS-CoV-2 antibodies in febrile patients from an endemic region of dengue and chikungunya in Peru

INTRODUCTION

The rapid expansion of the novel SARS-CoV-2 virus has raised serious public health concerns due to the possibility of misdiagnosis in regions where arboviral diseases are endemic. We performed the first study in northern Peru to describe the detection of SARS-CoV-2 IgM antibodies in febrile patients with a suspected diagnosis of dengue and chikungunya fever.

MATERIALS AND METHODS

A consecutive cross-sectional study was performed in febrile patients attending primary healthcare centers from April 2020 through March 2021. Patients enrolled underwent serum sample collection for the molecular and serological detection of DENV and CHIKV. Also, serological detection of IgM antibodies against SARS-CoV-2 was performed.

RESULTS

464 patients were included during the study period, of which (40.51%) were positive for one pathogen, meanwhile (6.90%) presented co-infections between 2 or more pathogens. The majority of patients with monoinfections were positive for SARS-CoV-2 IgM with (73.40%), followed by DENV 18.09% and CHIKV (8.51%). The most frequent co-infection was DENV + SARS-CoV-2 with (65.63%), followed by DENV + CHIKV and DENV + CHIKV + SARS-CoV-2, both with (12.50%). The presence of polyarthralgias in hands (43.75%, p<0.01) and feet (31.25%, p = 0.05) were more frequently reported in patients with CHIKV monoinfection. Also, conjunctivitis was more common in patients positive for SARS-CoV-2 IgM (11.45%, p<0.01). The rest of the symptoms were similar among all the study groups.

CONCLUSION

SARS-CoV-2 IgM antibodies were frequently detected in acute sera from febrile patients with a clinical suspicion of arboviral disease. The presence of polyarthralgias in hands and feet may be suggestive of CHIKV infection. These results reaffirm the need to consider SARS-CoV-2 infection as a main differential diagnosis of acute febrile illness in arboviruses endemic areas, as well as to consider co-infections between these pathogens.

An easy pipeline for one-step purification of SARS-CoV-2 nucleocapsid protein from insect cell suspension culture

The COVID-19 pandemic has demanded a range of biotechnological products for detection of SARS-CoV-2 variants and evaluation of human seroconversion after infection or vaccination. In this work, we describe an easy pipeline for expression of SARS-CoV-2 nucleocapsid (N) protein in insect cells followed by its purification via affinity chromatography. The N gene was cloned into the genome of Autographa californica multiple nucleopolyhedrovirus (AcMNPV) via transposition and the resulting recombinant baculovirus was used for infection of lepidopteran Sf9 cells adapted to high-density suspension. Using Tris-HCl pH 8.0 buffer as mobile phase and eluting bound proteins with 175 mM imidazole as part of a three-step gradient, an average of 1 mg N protein could be purified from each 50 mg of total protein from clarified supernatant. Such protein amount allows the manufacturing of serological tests and the development of basic studies on cellular responses to SARS-CoV-2.

Molecular diagnosis of SARS-CoV-2 in seminal fluid

PURPOSE

Due to relevant repercussions on reproductive medicine, we aimed to evaluate feasibility of RT-PCR as a detection method of SARS-CoV-2 RNA in seminal fluid.

METHODS

A qualitative determination of the RT-PCR assays in semen was performed through different approaches: (1) efficiency of RNA extraction from sperm and seminal plasma was determined using PRM1 and PRM2 mRNA and a heterologous system as control; (2) samples obtained by diluting viral preparation from a SARS-CoV-2 panel (virus cultured in Vero E6 cell lines) were tested; (3) viral presence in different fractions of seminal fluid (whole sample, seminal plasma and post-centrifugation pellet) was evaluated. Semen samples from mild and recovered COVID-19 subjects were collected by patients referring to the Infectious Disease Department of the Policlinico Umberto I Hospital - "Sapienza" University of Rome. Control subjects were recruited at the Laboratory of Seminology-Sperm Bank "Loredana Gandini'' of the same hospital.

RESULTS

The control panel using viral preparations diluted in saline and seminal fluid showed the capability to detect viral RNA presence with C_t values depending on the initial viral concentration. All tested semen samples were negative for SARS-CoV-2, regardless of the nasopharyngeal swab result or seminal fluid fraction.

CONCLUSION

These preliminary data show that RT-PCR for SARS-CoV-2 RNA testing appears to be a feasible method for the molecular diagnosis of SARS-CoV-2 in seminal fluid, supported by results of the control panel. The ability to detect SARS-CoV-2 in semen is extremely important for reproductive medicine, especially in assisted reproductive technology and sperm cryopreservation.

Respiratory Tract Pathogens in the COVID-19 Era: Data from a Pediatric Emergency Department

Objective The frequency of coinfections in pediatric Coronavirus disease 2019 (COVID-19) cases and their impact on the clinical course are not fully understood. We aimed to investigate the viral and bacterial respiratory pathogens in children admitted to the pediatric emergency department (PED), their clinical course, and the presence of coinfections during the early months of the COVID-19 pandemic.

Methods Clinical, laboratory and radiological findings, viral and bacterial pathogens detected by multiplex polymerase chain reaction (PCR) tests in nasopharyngeal swabs, clinical course, and treatments of all children who were tested for severe acute respiratory coronavirus 2 (SARS-CoV-2) at the PED between March 16 and May 15, 2020, were recorded. SARS-CoV-2 PCR-positive and negative groups were compared.

Results Out of 570 patients tested for SARS-CoV-2 during the study period, 43 were found positive (7.5%). Non-SARS-CoV-2 viral pathogens were more common in the SARS-CoV-2 PCR-negative group than the SARS-CoV-2 PCR-positive group (13.2%, n = 68 versus 4.7%, n = 2), but this result was not statistically significant. Leukocyte, neutrophil, lymphocyte, and platelet counts were lower in SARS-CoV-2 PCR-positive group. Bacterial panel positivity was significantly higher in the SARS-CoV-2 PCR-positive group compared with the SARS-CoV-2 PCR-negative group (52%, n = 12 versus 28%, n = 91; p < 0.05). The presence of coinfection did not alter the course of therapy in SARS-CoV-2 PCR-positive cases.

Conclusion While viral coinfections were rare, bacterial panel positivity was common in children with COVID-19, but this had not influenced management decisions. The limitations of the tests should be kept in mind while interpreting the results.

Strategy to Develop and Evaluate a Multiplex RT-ddPCR in Response to SARS-CoV-2 Genomic Evolution

The worldwide emergence and spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) since 2019 has highlighted the importance of rapid and reliable diagnostic testing to prevent and control the viral transmission. However, inaccurate results may occur due to false negatives (FN) caused by polymorphisms or point mutations related to the virus evolution and compromise the accuracy of the diagnostic tests. Therefore, PCR-based SARS-CoV-2 diagnostics should be evaluated and evolve together with the rapidly increasing number of new variants appearing around the world. However, even by using a large collection of samples, laboratories are not able to test a representative collection of samples that deals with the same level of diversity that is continuously evolving worldwide. In the present study, we proposed a methodology based on an in silico and in vitro analysis. First, we used all information offered by available whole-genome sequencing data for SARS-CoV-2 for the selection of the two PCR assays targeting two different regions in the genome, and to monitor the possible impact of virus evolution on the specificity of the primers and probes of the PCR assays during and after the development of the assays. Besides this first essential in silico evaluation, a minimal set of testing was proposed to generate experimental evidence on the method performance, such as specificity, sensitivity and applicability. Therefore, a duplex reverse-transcription droplet digital PCR (RT-ddPCR) method was evaluated in silico by using 154 489 whole-genome sequences of SARS-CoV-2 strains that were representative for the circulating strains around the world. The RT-ddPCR platform was selected as it presented several advantages to detect and quantify SARS-CoV-2 RNA in clinical samples and wastewater. Next, the assays were successfully experimentally evaluated for their sensitivity and specificity. A preliminary evaluation of the applicability of the developed method was performed using both clinical and wastewater samples.

Reliable Diagnostics of SARS-CoV-2 Infections Using One- and Two-Gene Molecular Tests for a Viral RNA Detection-Results Questioning Previous Observations

SARS-CoV-2 is a new virus from the Coronaviridae family and its rapid spread is now the most important medical problem worldwide. Currently used tests vary in the number and selection of SARS-CoV-2 target genes. Meanwhile, the choice of the appropriate target gene may be important in terms of a reliable detection of a viral RNA. As some researchers questioned the sensitivity of the monogenic VIASURE SARS-CoV-2 S gene Real Time PCR Detection Kit (CerTest Biotec, Zaragoza, Spain) in mid-2020, the aim of the study was to evaluate the usefulness of this kit, used along with the BD MAX™ System (Becton Dickinson, East Rutherford, NJ, USA), and compare the results with two-gene Bosphore Novel Coronavirus (2019-nCoV) Detection Kit v1 (Anatolia Diagnostics and Biotechnology Products Inc., Istanbul, Turkey). Both tests were carried out on 306 nasopharyngeal/oropharyngeal swabs. The consistent results (72 positive and 225 negative results found simultaneously in both kits) were obtained for 297 (97.1%) samples altogether, while discrepancies between the results of the evaluated tests were observed for nine (2.9%) specimens. There were no statistically significant differences between the method used and the frequency of positive results. Both tests, targeted at detecting one and two genes, are effective in SARS-CoV-2 RNA detection.

Development and Efficacy of Lateral Flow Point-of-Care Testing Devices for Rapid and Mass COVID-19 Diagnosis by the Detections of SARS-CoV-2 Antigen and Anti-SARS-CoV-2 Antibodies

The COVID-19 pandemic is an ongoing global pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in 2020-2021. COVID-19 is becoming one of the most fatal pandemics in history and brings a huge challenge to the global healthcare system. Opportune detection, confinement, and early treatment of infected cases present the first step in combating COVID-19. Diagnosis via viral nucleic acid amplification tests (NAATs) is frequently employed and considered the standard procedure. However, with an increasing urge for point-of-care tests, rapid and cheaper immunoassays are widely utilized, such as lateral flow immunoassay (LFIA), which can be used for rapid, early, and large-scale detection of SARS-CoV-2 infection. In this narrative review, the principle and technique of LFIA applied in COVID-19 antigen and antibody detection are introduced. The diagnostic sensitivity and specificity of the commercial LFIA tests are outlined and compared. Generally, LFIA antigen tests for SARS-CoV-2 are less sensitive than viral NAATs, the "gold standard" for clinical COVID-19 diagnosis. However, antigen tests can be used for rapid and mass testing in high-risk congregate housing to quickly identify people with COVID-19, implementing infection prevention and control measures, thus preventing transmission. LFIA anti-SARS-CoV-2 antibody tests, IgM and/or IgG, known as serology tests, are used for identification if a person has previously been exposed to the virus or vaccine immunization. Notably, advanced techniques, such as LFT-based CRISPR-Cas9 and surface-enhanced Raman spectroscopy (SERS), have added new dimensions to the COVID-19 diagnosis and are also discussed in this review.

Development and Evaluation of Quantitative Immunoglobulin G Enzyme-Linked Immunosorbent Assay for the Diagnosis of Coronavirus Disease 2019 Using Truncated Recombinant Nucleocapsid Protein as Assay Antigen

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of coronavirus disease 2019 (COVID-19). Real-time RT-PCR is the most commonly used method for COVID-19 diagnosis. However, serological assays are urgently needed as complementary tools to RT-PCR. Hachim et al. 2020 and Burbelo et al. 2020 demonstrated that anti-nucleocapsid(N) SARS-CoV-2 antibodies are higher and appear earlier than the spike antibodies. Additionally, cross-reactive antibodies against N protein are more prevalent than those against spike protein. We developed a less cross-reactive immunoglobulin G (IgG) indirect ELISA by using a truncated recombinant SARS-CoV-2 N protein as assay antigen. A highly conserved region of coronaviruses N protein was deleted and the protein was prepared using an E. coli protein expression system. A total of 177 samples collected from COVID-19 suspected cases and 155 negative control sera collected during the pre-COVID-19 period were applied to evaluate the assay's performance, with the plaque reduction neutralization test and the commercial SARS-CoV-2 spike protein IgG ELISA as gold standards. The SARS-CoV-2 N truncated protein-based ELISA showed similar sensitivity (91.1% vs. 91.9%) and specificity (93.8% vs. 93.8%) between the PRNT and spike IgG ELISA, as well as also higher specificity compared to the full-length N protein (93.8% vs. 89.9%). Our ELISA can be used for the diagnosis and surveillance of COVID-19.

Current state of diagnostic, screening and surveillance testing methods for COVID-19 from an analytical chemistry point of view

Since December 2019, we have been in the battlefield with a new threat to the humanity known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In this review, we describe the four main methods used for diagnosis, screening and/or surveillance of SARS-CoV-2: Real-time reverse transcription polymerase chain reaction (RT-PCR); chest computed tomography (CT); and different complementary alternatives developed in order to obtain rapid results, antigen and antibody detection. All of them compare the highlighting advantages and disadvantages from an analytical point of view. The gold standard method in terms of sensitivity and specificity is the RT-PCR. The different modifications propose to make it more rapid and applicable at point of care (POC) are also presented and discussed. CT images are limited to central hospitals. However, being combined with RT-PCR is the most robust and accurate way to confirm COVID-19 infection. Antibody tests, although unable to provide reliable results on the status of the infection, are suitable for carrying out maximum screening of the population in order to know the immune capacity. More recently, antigen tests, less sensitive than RT-PCR, have been authorized to determine in a quicker way whether the patient is infected at the time of analysis and without the need of specific instruments.

Evaluation and Comparison of Serological Methods for COVID-19 Diagnosis

The worldwide pandemic of COVID-19 has become a global public health crisis. Various clinical diagnosis methods have been developed to distinguish COVID-19-infected patients from healthy people. The nucleic acid test is the golden standard for virus detection as it is suitable for early diagnosis. However, due to the low amount of viral nucleic acid in the respiratory tract, the sensitivity of nucleic acid detection is unsatisfactory. As a result, serological screening began to be widely used with the merits of simple procedures, lower cost, and shorter detection time. Serological tests currently include the enzyme-linked immunosorbent assay (ELISA), lateral flow immunoassay (LFIA), and chemiluminescence immunoassay (CLIA). This review describes various serological methods, discusses the performance and diagnostic effects of different methods, and points out the problems and the direction of optimization, to improve the efficiency of clinical diagnosis. These increasingly sophisticated and diverse serological diagnostic technologies will help human beings to control the spread of COVID-19.

Who should be tested in a pandemic? Ethical considerations

BACKGROUND

In the initial phase of the Covid-19 pandemic, difficult decisions had to be made on the allocation of testing resources. Similar situations can arise in future pandemics. Therefore, careful consideration of who should be tested is an important part of pandemic preparedness. We focus on four ethical aspects of that problem: how to prioritize scarce testing resources, the regulation of commercial direct-to-consumer test services, testing of unauthorized immigrants, and obligatory testing.

MAIN TEXT

The distribution of scarce resources for testing: We emphasize the use of needs-based criteria, but also acknowledge the importance of choosing a testing strategy that contributes efficiently to stopping the overall spread of the disease. Commercial direct-to-consumer test services: Except in cases of acute scarcity, such services will in practice have to be allowed. We propose that they should be subject to regulation that ensures test quality and adequate information to users. Testing of unauthorized immigrants, their children and other people with unclear legal status: Like everyone else, these individuals may be in need of testing, and it is in society's interest to reach them with testing in order to stop the spread of the disease. A society that offers comprehensive medical services to unauthorized immigrants is in a much better position to reach them in a pandemic than a society that previously excluded them from healthcare. Obligatory testing: While there are often strong reasons for universal testing in residential areas or on workplaces, there are in most cases better ways to achieve testing coverage than to make testing mandatory.

CONCLUSION

In summary, we propose (1) decision-making primarily based on needs-based criteria, (2) strict regulation but not prohibition of direct-to-consumer test services, (3) test services offered to unauthorized immigrants, preferably as part of comprehensive medical services, and (4) broad outreach of testing services whenever possible, but in general not obligatory testing.

Performance characteristics of five SARS-CoV-2 serological assays: Clinical utility in health-care workers

STUDY OBJECTIVE

SARS-CoV-2, which causes coronavirus disease (COVID-19), continues to cause significant morbidity and mortality. The diagnosis of acute infection relies on reverse transcription-polymerase chain reaction (RT-PCR)-based viral detection. The objective of this study was to evaluate the optimal serological testing strategy for anti-SARS-CoV-2 antibodies which provides an important indicator of prior infection and potential short-term immunity.

METHODS

The sensitivity and specificity of four different ELISA assays (Euroimmun IgG, Euroimmun NCP-IgG, Fortress and DIAsource) and one CLIA assay (Roche ELECSYS) were evaluated in 423 samples; 137 patients with confirmed RT-PCR COVID-19 infection (true positives), and 100 pre-pandemic samples collected prior to October 2019 (true negatives). A further 186 samples were collected from health-care staff and analysed by all five assays.

RESULTS

The Fortress ELISA assay demonstrated the highest sensitivity and specificity followed by the Roche ECLIA assay. The highest overall sensitivity came from the assays that measured total antibody (IgM-IgG combined) and the three assays that performed the best (Fortress, Roche, Euroimmun IgG) all have different antigens as their target proteins which suggests that antigen target does not affect assay performance. In mildly symptomatic participants with either a negative RT-PCR or no RT-PCR performed, 16.76% had detectable antibodies suggesting previous infection.

CONCLUSIONS

We recommend a combined testing strategy utilizing assays with different antigenic targets using the fully automated Roche ECLIA assay and confirming discordant samples with the Fortress Total Antibody ELISA assay. This study provides an important indicator of prior infection in symptomatic and asymptomatic individuals.

Population (Antibody) Testing for COVID-19-Technical Challenges, Application and Relevance, an English Perspective

In the UK, population virus or antibody testing using virus swabs, serum samples, blood spots or oral fluids has been performed to a limited extent for several diseases including measles, mumps, rubella and hepatitis and HIV. The collection of population-based infection and immunity data is key to the monitoring of disease prevalence and assessing the effectiveness of interventions such as behavioural modifications and vaccination. In particular, the biological properties of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and its interaction with the human host have presented several challenges towards the development of population-based immunity testing. Measuring SARS-CoV-2 immunity requires the development of antibody assays of acceptable sensitivity and specificity which are capable of accurately detecting seroprevalence and differentiating protection from non-protective responses. Now that anti-COVID-19 vaccines are becoming available there is a pressing need to measure vaccine efficacy and the development of herd immunity. The unprecedented impact of the SARS-CoV-2 pandemic in the UK in terms of morbidity, mortality, and economic and social disruption has mobilized a national scientific effort to learn more about this virus. In this article, the challenges of testing for SARS-CoV-2 infection, particularly in relation to population-based immunity testing, will be considered and examples given of relevant national level studies.

COVID-19 Diagnostic Strategies Part II: Protein-Based Technologies

After the initiation of the current outbreak, humans' lives have been profoundly impacted by COVID-19. During the first months, no rapid and reliable detecting tool was readily available to sufficiently respond to the requirement of massive testing. In this situation, when the development of an effective vaccine requires at least a few months, it is crucial to be prepared by developing and commercializing affordable, accurate, rapid and adaptable biosensors not only to fight Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) but also to be armed to avoid the pandemic in the earliest stages in the future. The COVID-19 diagnostic tools are categorized into two main groups of Nucleic Acid (NA)-based and protein-based tests. To date, nucleic acid-based detection has been announced as the gold-standard strategy for coronavirus detection; however, protein-based tests are promising alternatives for rapid and large-scale screening of susceptible groups. In this review, we discuss the current protein-based biosensing tools, the research advances and the potential protein-detecting strategies for COVID-19 detection. This narrative review aims to highlight the importance of the diagnostic tests, encourage the academic research groups and the companies to eliminate the shortcomings of the current techniques and step forward to mass-producing reliable point-of-care (POC) and point-of-need (PON) adaptable diagnostic tools for large-scale screening in the future outbreaks.

Deepening of In Silico Evaluation of SARS-CoV-2 Detection RT-qPCR Assays in the Context of New Variants

For 1 year now, the world is undergoing a coronavirus disease-2019 (COVID-19) pandemic due to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The most widely used method for COVID-19 diagnosis is the detection of viral RNA by RT-qPCR with a specific set of primers and probe. It is important to frequently evaluate the performance of these tests and this can be done first by an in silico approach. Previously, we reported some mismatches between the oligonucleotides of publicly available RT-qPCR assays and SARS-CoV-2 genomes collected from GISAID and NCBI, potentially impacting proper detection of the virus. In the present study, 11 primers and probe sets investigated during the first study were evaluated again with 84,305 new SARS-CoV-2 unique genomes collected between June 2020 and January 2021. The lower inclusivity of the China CDC assay targeting the gene N has continued to decrease with new mismatches detected, whereas the other evaluated assays kept their inclusivity above 99%. Additionally, some mutations specific to new SARS-CoV-2 variants of concern were found to be located in oligonucleotide annealing sites. This might impact the strategy to be considered for future SARS-CoV-2 testing. Given the potential threat of the new variants, it is crucial to assess if they can still be correctly targeted by the primers and probes of the RT-qPCR assays. Our study highlights that considering the evolution of the virus and the emergence of new variants, an in silico (re-)evaluation should be performed on a regular basis. Ideally, this should be done for all the RT-qPCR assays employed for SARS-CoV-2 detection, including also commercial tests, although the primer and probe sequences used in these kits are rarely disclosed, which impedes independent performance evaluation.

The relationship between IgG and IgM levels and severity of symptoms in COVID-19 patients confirmed by rapid antigen test

This study aims to measure immunoglobulin G (IgG) and immunoglobulin M (IgM) response after detection of Severe Acute Respiratory Syndrome coronavirus (SARS CoV-2) antigens in coronavirus disease 2019 (COVID-19) patients concerning the severity of symptoms. SARS CoV-2 antigen was confirmed by rapid antigen test, and IgG and IgM were confirmed by VIDAS® SARS-COV-2 IgM and VIDAS® SARS-CoV-2 IgG automated qualitative assays used to rapidly detect antibodies 20–30 days after detection. The serological assay for detecting SARS-CoV-2 IgM and IgG antibodies shows a positive correlation for all patients detected with SARS-CoV-2 antigen with sensitivity 100% with differences in antibodies levels between patients regarding age and significantly related clinical symptoms with p-value 0.013 <0.05. The appearance of clinical symptoms was not significantly related to IgG levels at a p-value of 0.4 >0.05. However, the appearance of clinical symptoms was significantly related to IgM levels at a p-value of 0.002 <0.05. Antigen-dependent rapid tests can be used to detect SARS-CoV-2 in an early stage of infection with high sensitivity and specificity. Moreover, this study shows the age groups 21–30 and 31–40 have a better response to SARS-CoV-2 infection.