Current Approaches for Diagnosis of Influenza Virus Infections in Humans

Inactivated influenza virus vaccines expressing COBRA hemagglutinin elicited broadly reactive, long-lived protective antibodies

The influenza viruses cause seasonal respiratory illness that affect millions of people globally every year. Prophylactic vaccines are the recommended method to prevent the breakout of influenza epidemics. One of the current commercial influenza vaccines consists of inactivated viruses that are selected months prior to the start of a new influenza season. In many seasons, the vaccine effectiveness (VE) of these vaccines can be relatively low. Therefore, there is an urgent need to develop an improved, more universal influenza vaccine (UIV) that can provide broad protection against various drifted strains in all age groups. To meet this need, the computationally optimized broadly reactive antigen (COBRA) methodology was developed to design a hemagglutinin (HA) molecule as a new influenza vaccine. In this study, COBRA HA-based inactivated influenza viruses (IIV) expressing the COBRA HA from H1 or H3 influenza viruses were developed and characterized for the elicitation of immediate and long-term protective immunity in both immunologically naïve or influenza pre-immune animal models. These results were compared to animals vaccinated with IIV vaccines expressing wild-type H1 or H3 HA proteins (WT-IIV). The COBRA-IIV elicited long-lasting broadly reactive antibodies that had hemagglutination-inhibition (HAI) activity against drifted influenza variants.

Loop-mediated isothermal amplification linked a nanoparticles-based biosensor for detecting Epstein-Barr virus

Epstein-Barr virus (EBV) is a ubiquitous gamma herpesvirus that maintains a lifelong latent association with B lymphocytes. Here, a rapid and reliable diagnosis platform for detecting EBV infection, employing loop-mediated isothermal amplification (LAMP) combined with a gold nanoparticles-based lateral flow biosensors (AuNPs-LFB) (termed LAMP Amplification Mediated AuNPs-LFB Detection, LAMAD), was developed in the current study. A set of specific LAMP primers targeting the Epstein-Barr nuclear antigen (EBNA) leader protein (EBNA-LP) gene was designed and synthesized. Subsequently, these templates extracted from various pathogens and whole blood samples were used to optimize and evaluate the EBV-LAMAD assay. As a result, the limit of detection (LoD) of the EBV-LAMAD assay was 45 copies/reaction. The EBV-LAMAD assay can detect all representative EBV pathogens used in the study, and of note, no cross-reactions were observed with other non-EBV organisms. Moreover, the whole workflow of the EBV-LAMAD assay can be completed within 70 min, including rapid EBV template preparation, EBV-LAMP amplification, and AuNPs-LFB-mediated detection. Taken together, the EBV-LAMAD assay targeting the EBNA-LP gene is a rapid, simplified, sensitive, reliable, and easy-to-use detection protocol that can be used as a competitive potential diagnostic/screening tool for EBV infection in clinical settings, especially in basic laboratories in resource-limited regions. KEY POINTS: • A novel, simplified, and easy-to-use AuNPs-LFB biosensor was designed and prepared. • LAMP combined with an AuNPs-LFB targeting the novel EBNA-LP gene was established. • EBV-LAMAD is a rapid, sensitive, and reliable detection protocol for EBV infection.

Establishment and performance analysis of a new multiplex detection method for influenza an and B virus antigen

BACKGROUND

Influenza A and B virus detection is pivotal in epidemiological surveillance and disease management. Rapid and accurate diagnostic techniques are crucial for timely clinical intervention and outbreak prevention. Quantum dot-encoded microspheres have been widely used in immunodetection. The integration of quantum dot-encoded microspheres with flow cytometry is a well-established technique that enables rapid analysis. Thus, establishing a multiplex detection method for influenza A and B virus antigens based on flow cytometry quantum dot microspheres will help in disease diagnosis.

AIM

To establish a codetection method of influenza A and B virus antigens based on flow cytometry quantum dot-encoded microsphere technology, which forms the foundation for the assays of multiple respiratory virus biomarkers.

METHODS

Different quantum dot-encoded microspheres were used to couple the monoclonal antibodies against influenza A and B. The known influenza A and B antigens were detected both separately and simultaneously on a flow cytometer, and the detection conditions were optimized to establish the influenza A and B antigen codetection method, which was utilized for their detection in clinical samples. The results were compared with the fluorescence quantitative polymerase chain reaction (PCR) method to validate the clinical performance of this method.

RESULTS

The limits of detection of this method were 26.1 and 10.7 pg/mL for influenza A and B antigens, respectively, which both ranged from 15.6 to 250000 pg/mL. In the clinical sample evaluation, the proposed method well correlated with the fluorescent quantitative PCR method, with positive, negative, and overall compliance rates of 57.4%, 100%, and 71.6%, respectively.

CONCLUSION

A multiplex assay for quantitative detection of influenza A and B virus antigens has been established, which is characterized by high sensitivity, good specificity, and a wide detection range and is promising for clinical applications.

Advancing Microfluidic Immunity Testing Systems: New Trends for Microbial Pathogen Detection

Pathogenic microorganisms play a crucial role in the global disease burden due to their ability to cause various diseases and spread through multiple transmission routes. Immunity tests identify antigens related to these pathogens, thereby confirming past infections and monitoring the host's immune response. Traditional pathogen detection methods, including enzyme-linked immunosorbent assays (ELISAs) and chemiluminescent immunoassays (CLIAs), are often labor-intensive, slow, and reliant on sophisticated equipment and skilled personnel, which can be limiting in resource-poor settings. In contrast, the development of microfluidic technologies presents a promising alternative, offering automation, miniaturization, and cost efficiency. These advanced methods are poised to replace traditional assays by streamlining processes and enabling rapid, high-throughput immunity testing for pathogens. This review highlights the latest advancements in microfluidic systems designed for rapid and high-throughput immunity testing, incorporating immunosensors, single molecule arrays (Simoas), a lateral flow assay (LFA), and smartphone integration. It focuses on key pathogenic microorganisms such as SARS-CoV-2, influenza, and the ZIKA virus (ZIKV). Additionally, the review discusses the challenges, commercialization prospects, and future directions to advance microfluidic systems for infectious disease detection.

CRISPR-Based Assays for Point-of-Need Detection and Subtyping of Influenza

The high disease burden of influenza virus poses a significant threat to human health. Optimized diagnostic technologies that combine speed, sensitivity, and specificity with minimal equipment requirements are urgently needed to detect the many circulating species, subtypes, and variants of influenza at the point of need. Here, we introduce such a method using Streamlined Highlighting of Infections to Navigate Epidemics (SHINE), a clustered regularly interspaced short palindromic repeats (CRISPR)-based RNA detection platform. Four SHINE assays were designed and validated for the detection and differentiation of clinically relevant influenza species (A and B) and subtypes (H1N1 and H3N2). When tested on clinical samples, these optimized assays achieved 100% concordance with quantitative RT-PCR. Duplex Cas12a/Cas13a SHINE assays were also developed to detect two targets simultaneously. This study demonstrates the utility of this duplex assay in discriminating two alleles of an oseltamivir resistance (H275Y) mutation as well as in simultaneously detecting influenza A and human RNAse P in patient samples. These assays have the potential to expand influenza detection outside of clinical laboratories for enhanced influenza diagnosis and surveillance.

An oleanic acid decorated gold nanorod for highly efficient inhibition of hemagglutinin and visible rapid detection of the influenza virus

Accurate diagnosis and effective antiviral treatments are urgently needed for the prevention and control of flu caused by influenza viruses. In this study, a novel oleanic acid (OA) functionalized gold nanorod OA-AuNP was prepared through a convenient ligand-exchange reaction. As hemagglutinin (HA) on the viral surface binds strongly to the multiple OA molecules on the surface of the nanoparticle, the prepared OA-AuNP was found to exhibit potent antiviral activity against a wide range of influenza A virus strains. Furthermore, the change in color resulting from the specific binding between HA and OA and the resultant aggregation of the OA-AuNP can be visually observed or measured by UV-vis spectra with a detection limit of 2 and 0.18 hemagglutination units (HAU), respectively, which is comparable to the commercially available influenza colloid gold rapid diagnostic kits. These findings demonstrate the potential of the OA-AuNP for the development of novel multivalent antiviral conjugates and the diagnosis of influenza virus.

Loop-Mediated Isothermal Amplification and Lateral Flow Immunochromatography Technology for Rapid Diagnosis of Influenza A/B

Influenza viruses cause highly contagious respiratory diseases that cause millions of deaths worldwide. Rapid detection of influenza viruses is essential for accurate diagnosis and the initiation of appropriate treatment. We developed a loop-mediated isothermal amplification and lateral flow assay (LAMP-LFA) capable of simultaneously detecting influenza A and influenza B. Primer sets for influenza A and influenza B were designed to target conserved regions of segment 7 and the nucleoprotein gene, respectively. Optimized through various primer set ratios, the assay operated at 62 °C for 30 min. For a total of 243 (85 influenza A positive, 58 influenza B positive and 100 negative) nasopharyngeal swab samples, the performance of the influenza A/B multiplex LAMP-LFA was compared with that of the commercial AllplexTM Respiratory Panel 1 assay (Seegene, Seoul, Korea). The influenza A/B multiplex LAMP-LFA demonstrated a specificity of 98% for the non-infected clinical samples, along with sensitivities of 94.1% for the influenza A clinical samples and 96.6% for the influenza B clinical samples, respectively. The influenza A/B multiplex LAMP-LFA showed high sensitivity and specificity, indicating that it is reliable for use in a low-resource environment.

ADLM Guidance Document on Laboratory Diagnosis of Respiratory Viruses

Respiratory viral infections are among the most frequent infections experienced worldwide. The COVID-19 pandemic has highlighted the need for testing and currently several tests are available for the detection of a wide range of viruses. These tests vary widely in terms of the number of viral pathogens included, viral markers targeted, regulatory status, and turnaround time to results, as well as their analytical and clinical performance. Given these many variables, selection and interpretation of testing requires thoughtful consideration. The current guidance document is the authors' expert opinion based on the preponderance of available evidence to address key questions related to best practices for laboratory diagnosis of respiratory viral infections including who to test, when to test, and what tests to use. An algorithm is proposed to help laboratories decide on the most appropriate tests to use for the diagnosis of respiratory viral infections.

A novel data augmentation approach for influenza A subtype prediction based on HA proteins

Influenza, a pervasive viral respiratory illness, remains a significant global health concern. The influenza A virus, capable of causing pandemics, necessitates timely identification of specific subtypes for effective prevention and control, as highlighted by the World Health Organization. The genetic diversity of influenza A virus, especially in the hemagglutinin protein, presents challenges for accurate subtype prediction. This study introduces PreIS as a novel pipeline utilizing advanced protein language models and supervised data augmentation to discern subtle differences in hemagglutinin protein sequences. PreIS demonstrates two key contributions: leveraging pre-trained protein language models for influenza subtype classification and utilizing supervised data augmentation to generate additional training data without extensive annotations. The effectiveness of the pipeline has been rigorously assessed through extensive experiments, demonstrating a superior performance with an impressive accuracy of 94.54% compared to the current state-of-the-art model, the MC-NN model, which achieves an accuracy of 89.6%. PreIS also exhibits proficiency in handling unknown subtypes, emphasizing the importance of early detection. Pioneering the classification of HxNy subtypes solely based on the hemagglutinin protein chain, this research sets a benchmark for future studies. These findings promise more precise and timely influenza subtype prediction, enhancing public health preparedness against influenza outbreaks and pandemics. The data and code underlying this article are available in https://github.com/CBRC-lab/PreIS.

Sialic acids in infection and their potential use in detection and protection against pathogens

In structural terms, the sialic acids are a large family of nine carbon sugars based around an alpha-keto acid core. They are widely spread in nature, where they are often found to be involved in molecular recognition processes, including in development, immunology, health and disease. The prominence of sialic acids in infection is a result of their exposure at the non-reducing terminus of glycans in diverse glycolipids and glycoproteins. Herein, we survey representative aspects of sialic acid structure, recognition and exploitation in relation to infectious diseases, their diagnosis and prevention or treatment. Examples covered span influenza virus and Covid-19, Leishmania and Trypanosoma, algal viruses, Campylobacter, Streptococci and Helicobacter, and commensal Ruminococci.

Tackling Influenza A virus by M2 ion channel blockers: Latest progress and limitations

Influenza outbreaks cause pandemics in millions of people. The treatment of influenza remains a challenge due to significant genetic polymorphism in the influenza virus. Also, developing vaccines to protect against seasonal and pandemic influenza infections is constantly impeded. Thus, antibiotics are the only first line of defense against antigenically distinct strains or new subtypes of influenza viruses. Among several anti-influenza targets, the M2 protein of the influenza virus performs several activities. M2 protein is an ion channel that permits proton conductance through the virion envelope and the deacidification of the Golgi apparatus. Both these functions are critical for viral replication. Thus, targeting the M2 protein of the influenza virus is an essential target. Rimantadine and amantadine are two well-known drugs that act on the M2 protein. However, these drugs acquired resistance to influenza and thus are not recommended to treat influenza infections. This review discusses an overview of anti-influenza therapy, M2 ion channel functions, and its working principle. It also discusses the M2 structure and its role, and the change in the structure leads to mutant variants of influenza A virus. We also shed light on the recently identified compounds acting against wild-type and mutated M2 proteins of influenza virus A. These scaffolds could be an alternative to M2 inhibitors and be developed as antibiotics for treating influenza infections.

Plasmonic Fluorescence Sensors in Diagnosis of Infectious Diseases

The increasing demand for rapid, cost-effective, and reliable diagnostic tools in personalized and point-of-care medicine is driving scientists to enhance existing technology platforms and develop new methods for detecting and measuring clinically significant biomarkers. Humanity is confronted with growing risks from emerging and recurring infectious diseases, including the influenza virus, dengue virus (DENV), human immunodeficiency virus (HIV), Ebola virus, tuberculosis, cholera, and, most notably, SARS coronavirus-2 (SARS-CoV-2; COVID-19), among others. Timely diagnosis of infections and effective disease control have always been of paramount importance. Plasmonic-based biosensing holds the potential to address the threat posed by infectious diseases by enabling prompt disease monitoring. In recent years, numerous plasmonic platforms have risen to the challenge of offering on-site strategies to complement traditional diagnostic methods like polymerase chain reaction (PCR) and enzyme-linked immunosorbent assays (ELISA). Disease detection can be accomplished through the utilization of diverse plasmonic phenomena, such as propagating surface plasmon resonance (SPR), localized SPR (LSPR), surface-enhanced Raman scattering (SERS), surface-enhanced fluorescence (SEF), surface-enhanced infrared absorption spectroscopy, and plasmonic fluorescence sensors. This review focuses on diagnostic methods employing plasmonic fluorescence sensors, highlighting their pivotal role in swift disease detection with remarkable sensitivity. It underscores the necessity for continued research to expand the scope and capabilities of plasmonic fluorescence sensors in the field of diagnostics.

Clinical Presentation, Risk Factors, and Comparison of Laboratory Diagnostics for Seasonal Influenza Virus Among Cambodians From 2007 to 2020

Background

Despite its global significance, challenges associated with understanding the epidemiology and accurately detecting, measuring, and characterizing the true burden of seasonal influenza remain in many resource-poor settings.

Methods

A prospective observational study was conducted in Cambodia at 28 health facilities between 2007 and 2020 utilizing passive surveillance data of patients presenting with acute undifferentiated febrile illness (AUFI) to describe the prevalence of influenza A and B and characterize associated risk factors and symptoms using a questionnaire. A comparison of rapid influenza diagnostic tests (RIDTs) and real-time reverse transcription polymerase chain reaction (rRT-PCR) results was also conducted.

Results

Of 30 586 total participants, 5634 (18.4%) tested positive for either influenza A or B, with 3557 (11.6%) positive for influenza A and 2288 (7.5%) positive for influenza B during the study. Influenza A and B were strongly associated with the rainy season (odds ratio [OR], 2.30; P < .001) and being from an urban area (OR, 1.45; P < .001). Analysis of individual symptoms identified cough (OR, 2.8; P < .001), chills (OR, 1.4; P < .001), and sore throat (OR, 1.4; P < .001) as having the strongest positive associations with influenza among patients with AUFI. Analysis comparing RIDTs and rRT-PCR calculated the overall sensitivity of rapid tests to be 0.492 (95% CI, 0.479-0.505) and specificity to be 0.993 (95% CI, 0.992-0.994) for both influenza type A and B.

Conclusions

Findings from this 14-year study include describing the epidemiology of seasonal influenza over a prolonged time period and identifying key risk factors and clinical symptoms associated with infection; we also demonstrate the poor sensitivity of RIDTs in Cambodia.

Outlining recent updates on influenza therapeutics and vaccines: A comprehensive review

Influenza virus has presented a considerable healthcare challenge during the past years, particularly in vulnerable groups with compromised immune systems. Therapeutics and vaccination have always been in research annals since the spread of influenza. Efforts have been going on to develop an antiviral therapeutic approach that could assist in better disease management and reduce the overall disease complexity, resistance development, and fatality rates. On the other hand, vaccination presents a chance for effective, long-term, cost-benefit, and preventive response against the morbidity and mortality associated with the influenza. However, the issues of resistance development, strain mutation, antigenic variability, and inability to cure wide-spectrum and large-scale strains of the virus by available vaccines remain there. The article gathers the updated data for the therapeutics and available influenza vaccines, their mechanism of action, shortcomings, and trials under clinical experimentation. A methodological approach has been adopted to identify the prospective therapeutics and available vaccines approved and within the clinical trials against the influenza virus. Review contains influenza therapeutics, including traditional and novel antiviral drugs and inhibitor therapies against influenza virus as well as research trials based on newer drug combinations and latest technologies such as nanotechnology and organic and plant-based natural products. Most recent development of influenza vaccine has been discussed including some updates on traditional vaccination protocols and discussion on next-generation and upgraded novel technologies. This review will help the readers to understand the righteous approach for dealing with influenza virus infection and for deducing futuristic approaches for novel therapeutic and vaccine trials against Influenza.

Unlocking the Power of Influenza Vaccines for Pediatric Population: A Narrative Review

The flu, often known as influenza, is a dangerous public health hazard for the pediatric population. Immunization is essential for decreasing the burden of the disease and avoiding complications related to influenza. However, the immunogenicity, efficacy, and safety of different influenza vaccines in children warrant careful evaluation. The purpose of this narrative review is to give a summary of the existing literature on the immunogenicity, efficacy, and safety of several vaccinations against influenza viruses in children. The review incorporates evidence from a range of studies focusing on the outcomes of interest. Immunogenicity studies have shown that influenza vaccines induce a robust immune response in children, primarily through neutralizing antibodies' formation. However, variations in vaccine composition influence the duration and magnitude of immune responses. Safety is a crucial consideration in pediatric vaccination. In children, influenza vaccinations have generally shown a high safety profile, with mild and temporary side effects being the most common. Vaccinations against influenza have shown a modest level of efficacy in avoiding hospitalizations linked to influenza, laboratory-confirmed influenza infections, and serious consequences in children. Live attenuated vaccines have shown higher effectiveness against matched strains compared to inactivated vaccines. In conclusion, this narrative review highlights that receiving influenza vaccination in children aged six to 47 months is very important. While different vaccines exhibit varying immunogenicity, safety profiles, and effectiveness, they all contribute to reducing the burden of influenza among children. Future research should focus on optimizing vaccine strategies, improving vaccine coverage, and evaluating long-term protection.

Saliva Analysis Based on Microfluidics: Focusing the Wide Spectrum of Target Analyte

Saliva is one of the most critical human body fluids that can reflect the state of the human body. The detection of saliva is of great significance for disease diagnosis and health monitoring. Microfluidics, characterized by microscale size and high integration, is an ideal platform for the development of rapid and low-cost disease diagnostic techniques and devices. Microfluidic-based saliva testing methods have aroused considerable interest due to the increasing need for noninvasive testing and frequent or long-term testing. This review briefly described the significance of saliva analysis and generally classified the targets in saliva detection into pathogenic microorganisms, inorganic substances, and organic substances. By using this classification as a benchmark, the state-of-the-art research results on microfluidic detection of various substances in saliva were summarized. This work also put forward the challenges and future development directions of microfluidic detection methods for saliva.

Safety and immunogenicity of influenza A(H3N2) component vaccine in juvenile systemic lupus erythematosus

INTRODUCTION

Seasonal influenza A (H3N2) virus is an important cause of morbidity and mortality in the last 50 years in population that is greater than the impact of H1N1. Data assessing immunogenicity and safety of this virus component in juvenile systemic lupus erythematosus (JSLE) is lacking in the literature.

OBJECTIVE

To evaluate short-term immunogenicity and safety of influenza A/Singapore (H3N2) vaccine in JSLE.

METHODS

24 consecutive JSLE patients and 29 healthy controls (HC) were vaccinated with influenza A/Singapore/INFIMH-16-0019/2016(H3N2)-like virus. Influenza A (H3N2) seroprotection (SP), seroconversion (SC), geometric mean titers (GMT), factor increase in GMT (FI-GMT) titers were assessed before and 4 weeks post-vaccination. Disease activity, therapies and adverse events (AE) were also evaluated.

RESULTS

JSLE patients and controls were comparable in current age [14.5 (10.1-18.3) vs. 14 (9-18.4) years, p = 0.448] and female sex [21 (87.5%) vs. 19 (65.5%), p = 0.108]. Before vaccination, JSLE and HC had comparable SP rates [22 (91.7%) vs. 25 (86.2%), p = 0.678] and GMT titers [102.3 (95% CI 75.0-139.4) vs. 109.6 (95% CI 68.2-176.2), p = 0.231]. At D30, JSLE and HC had similar immune response, since no differences were observed in SP [24 (100%) vs. 28 (96.6%), p = 1.000)], SC [4 (16.7%) vs. 9 (31.0%), p = 0.338), GMT [162.3 (132.9-198.3) vs. 208.1 (150.5-287.8), p = 0.143] and factor increase in GMT [1.6 (1.2-2.1) vs. 1.9 (1.4-2.5), p = 0.574]. SLEDAI-2K scores [2 (0-17) vs. 2 (0-17), p = 0.765] and therapies remained stable throughout the study. Further analysis of possible factors influencing vaccine immune response among JSLE patients demonstrated similar GMT between patients with SLEDAI < 4 compared to SLEDAI ≥ 4 (p = 0.713), as well as between patients with and without current use of prednisone (p = 0.420), azathioprine (p = 1.0), mycophenolate mofetil (p = 0.185), and methotrexate (p = 0.095). No serious AE were reported in both groups and most of them were asymptomatic (58.3% vs. 44.8%, p = 0.958). Local and systemic AE were alike in both groups (p > 0.05).

CONCLUSION

This is the first study that identified adequate immune protection against H3N2-influenza strain with additional vaccine-induced increment of immune response and an adequate safety profile in JSLE. ( www.

CLINICALTRIALS

gov , NCT03540823).

The convergent evolution of influenza A virus: Implications, therapeutic strategies and what we need to know

Influenza virus infection, more commonly known as the 'cold flu', is an etiological agent that gives rise to recurrent annual flu and many pandemics. Dated back to the 1918- Spanish Flu, the influenza infection has caused the loss of many human lives and significantly impacted the economy and daily lives. Influenza virus can be classified into four different genera: influenza A-D, with the former two, influenza A and B, relevant to humans. The capacity of antigenic drift and shift in Influenza A has given rise to many novel variants, rendering vaccines and antiviral therapies useless. In light of the emergence of a novel betacoronavirus, the SARS-CoV-2, unravelling the underpinning mechanisms that support the recurrent influenza epidemics and pandemics is essential. Given the symptom similarities between influenza and covid infection, it is crucial to reiterate what we know about the influenza infection. This review aims to describe the origin and evolution of influenza infection. Apart from that, the risk factors entail the implication of co-infections, especially regarding the COVID-19 pandemic is further discussed. In addition, antiviral strategies, including the potential of drug repositioning, are discussed in this context. The diagnostic approach is also critically discussed in an effort to understand better and prepare for upcoming variants and potential influenza pandemics in the future. Lastly, this review encapsulates the challenges in curbing the influenza spread and provides insights for future directions in influenza management.

Designing new drug candidates as inhibitors against wild and mutant type neuraminidases: molecular docking, molecular dynamics and binding free energy calculations

Influenza virus is the cause of the death of millions of people with about 3-4 pandemics every hundred years in history. It also turns into a seasonal disease, bringing about approximately 5-15% of the population to be infected and 290,000-650,000 people to die every year. These numbers reveal that it is necessary to be on the alert to work towards influenza in order to protect public health. There are FDA-approved antiviral drugs such as oseltamivir and zanamivir recommended by the World Center for Disease Prevention. However, after the recent outbreaks such as bird flu and swine flu, increasing studies have shown that the flu virus has gained resistance to these drugs. So, there is an urgent need to find new drugs effective against this virus. This study aims to investigate new drug candidates targeting neuraminidase (NA) for the treatment of influenza by using computer aided drug design approaches. They involve virtual scanning, de novo design, rational design, docking, MD, MMGB/PBSA. The investigation includes H1N1, H5N1, H2N2 and H3N2 neuraminidase proteins and their mutant variants possessing resistance to FDA-approved drugs. Virtual screening consists of approximately 30 thousand molecules while de novo and rational designs produced over a hundred molecules. These approaches produced three lead molecules with binding energies for both non-mutant (-34.84, -59.99 and -60.66 kcal/mol) and mutant (-40.40, -58.93, -76.19 kcal/mol) H2N2 NA calculated by MM-PBSA compared with those of oseltamivir -25.64 and -18.40 respectively. The results offer new drug candidates against influenza infection.Communicated by Ramaswamy H. Sarma.

Highly Sensitive and Specific Detection of Influenza A Viruses Using Bimolecular Fluorescence Complementation (BiFC) Reporter System

In this study, we developed a highly sensitive and specific bimolecular fluorescence complementation (BiFC)-based influenza A virus (IAV)-sensing system by combining a galactose/glucose-binding protein (GGBP) with an N-terminal large domain (YN1-172) and a C-terminal small domain (YC173-239) made up of enhanced yellow fluorescence protein (eYFP). The GGBP-based BiFC reporter exhibits the fluorescence reconstitution as a result of conformational changes in GGBP when lactose, which was derived from 6'-silalyllactose and used as a substrate for neuraminidase (NA), binds to GGBP in the presence of IAV. The system showed a linear dynamic range extending from 1 × 100 to 1 × 107 TCID50/mL, and it had a detection limit of 1.1 × 100 TCID50/mL for IAV (H1N1), demonstrating ultra-high sensitivity. Our system exhibited fluorescence intensity enhancements in the presence of IAV, while it displayed weak fluorescence signals when exposed to NA-deficient viruses, such as RSV A, RSV B, adenovirus and rhinovirus, thereby indicating selective responses for IAV detection. Overall, our system provides a simple, highly sensitive and specific IAV detection platform based on BiFC that is capable of detecting ligand-induced protein conformational changes, obviating the need for virus culture or RNA extraction processes.

Influenza A Virus in Pigs in Senegal and Risk Assessment of Avian Influenza Virus (AIV) Emergence and Transmission to Human

We conducted an active influenza surveillance in the single pig slaughterhouse in Dakar to investigate the epidemiology and genetic characteristics of influenza A viruses (IAVs) and to provide serologic evidence of avian influenza virus (AIV) infection in pigs at interfaces with human populations in Senegal. Nasal swab and blood samples were collected on a weekly basis from the same animal immediately after slaughter. Influenza A viruses were diagnosed using RT-qPCR and a subset of positive samples for H3 and H1 subtypes were selected for full genome amplification and NGS sequencing. Serum samples were tested by HI assay for the detection of antibodies recognizing four AIVs, including H9N2, H5N1, H7N7 and H5N2. Between September 2018 and December 2019, 1691 swine nasal swabs were collected and tested. Influenza A virus was detected in 30.7% (520/1691), and A/H1N1pdm09 virus was the most commonly identified subtype with 38.07% (198/520), followed by A/H1N2 (16.3%) and A/H3N2 (5.2%). Year-round influenza activity was noted in pigs, with the highest incidence between June and September. Phylogenetic analyses revealed that the IAVs were closely related to human IAV strains belonging to A/H1N1pdm09 and seasonal H3N2 lineages. Genetic analysis revealed that Senegalese strains possessed several key amino acid changes, including D204 and N241D in the receptor binding site, S31N in the M2 gene and P560S in the PA protein. Serological analyses revealed that 83.5% (95%CI = 81.6-85.3) of the 1636 sera tested were positive for the presence of antibodies against either H9N2, H5N1, H7N7 or H5N2. Influenza H7N7 (54.3%) and H9N2 (53.6%) were the dominant avian subtypes detected in Senegalese pigs. Given the co-circulation of multiple subtypes of influenza viruses among Senegalese pigs, the potential exists for the emergence of new hybrid viruses of unpredictable zoonotic and pandemic potential in the future.

Trends of respiratory virus detection in point-of-care testing: A review

In resource-limited conditions such as the COVID-19 pandemic, on-site detection of diseases using the Point-of-care testing (POCT) technique is becoming a key factor in overcoming crises and saving lives. For practical POCT in the field, affordable, sensitive, and rapid medical testing should be performed on simple and portable platforms, instead of laboratory facilities. In this review, we introduce recent approaches to the detection of respiratory virus targets, analysis trends, and prospects. Respiratory viruses occur everywhere and are one of the most common and widely spreading infectious diseases in the human global society. Seasonal influenza, avian influenza, coronavirus, and COVID-19 are examples of such diseases. On-site detection and POCT for respiratory viruses are state-of-the-art technologies in this field and are commercially valuable global healthcare topics. Cutting-edge POCT techniques have focused on the detection of respiratory viruses for early diagnosis, prevention, and monitoring to protect against the spread of COVID-19. In particular, we highlight the application of sensing techniques to each platform to reveal the challenges of the development stage. Recent POCT approaches have been summarized in terms of principle, sensitivity, analysis time, and convenience for field applications. Based on the analysis of current states, we also suggest the remaining challenges and prospects for the use of the POCT technique for respiratory virus detection to improve our protection ability and prevent the next pandemic.

Point-of-Care Testing for Infectious Diseases Based on Class 2 CRISPR/Cas Technology

The early detection of infectious diseases and microorganisms is critical for effective disease treatment, control, and prevention. Currently, nucleic acid testing and antigen-antibody serum reaction are the two methods most commonly used for the detection of infectious diseases. The former is highly accurate, specific, and sensitive, but it is time-consuming, expensive, and has special technician and instrument requirements. The latter is rapid and economical, but it may not be accurate and sensitive enough. Therefore, it is necessary to develop a quick and on-site diagnostic test for point-of-care testing (POCT) to enable the clinical detection of infectious diseases that is accurate, sensitive, convenient, cheap, and portable. Here, CRISPR/Cas-based detection methods are detailed and discussed in depth. The powerful capacity of these methods will facilitate the development of diagnostic tools for POCT, though they still have some limitations. This review explores and highlights POCT based on the class 2 CRISPR/Cas assay, such as Cas12 and Cas13 proteins, for the detection of infectious diseases. We also provide an outlook on perspectives, multi-application scenarios, clinical applications, and limitations for POCT based on class 2 CRISPR/Cas technology.

A colloidal gold test strip based on catalytic hairpin assembly for the clinical detection of influenza a virus nucleic acid

Influenza A epidemics, which occur annually in varying degrees worldwide, is a global challenge to healthcare facilities owing to several limitations of the current detection methods. Therefore, the development of a rapid, convenient, and economical method for the early diagnosis of influenza A will aid clinical treatment and epidemic control. Currently, most of the commonly used clinical rapid tests utilize colloidal gold test strips that detect specific influenza virus antigens but are limited by low sensitivity. Therefore, this study combined catalytic hairpin assembly (CHA) with colloidal gold immunochromatographic assay (GICA) to develop a highly sensitive and visual CHA-GICA test strip. Clinical sample analysis revealed that the sensitivity of the assay was 81.8% and 74% under optimal (35 °C) and room temperature (25 °C) conditions, respectively. In conclusion, this study developed a rapid nucleic acid assay for detecting influenza A virus with high sensitivity and specificity, which can improve the clinical detection of influenza A.

Development of an AlphaLISA assay for sensitive and accurate detection of influenza B virus

Objective

Influenza B virus (IBV) is highly contagious, spreads rapidly, and causes seasonal epidemic respiratory disease in the human population, especially in immunocompromised people and young children. Clinical manifestations in this high-risk population are often more severe than in immunocompetent hosts and sometimes atypical. Therefore, rapid, and accurate detection of IBV is important.

Methods

An amplified luminescent proximity homogeneous assay linked immunosorbent assay (AlphaLISA) was developed for detection of IBV by optimizing the ratio of IBV antibody-labeled receptor beads, streptavidin-conjugated donor beads and biotinylated IBV antibody, as well as the optimal temperature and time conditions for incubation. Assay sensitivity, specificity and reproducibility were evaluated. A total of 228 throat swab samples and inactivated influenza B virus were tested by AlphaLISA and lateral flow colloidal gold-based immunoassay (LFIA).

Results

AlphaLISA produced the best results for detection of inactivated influenza B virus when IBV antibody-labeled acceptor beads were 50 μg/ mL, streptavidin-conjugated donor beads were 40 μg/mL, and biotinylated IBV antibody was 0.5 μg/mL at 37°C for 15-10 min. Under these conditions, AlphaLISA had a limit of detection of 0.24 ng/mL for the detection of influenza B nucleoprotein, did not cross react with other common respiratory viruses, and showed good reproducibility with inter-assay coefficient of variation (CV) and intra-assay CV < 5%. The results of 228 clinical throat swab samples showed good agreement between AlphaLISA and LFIA (Kappa = 0.982), and AlphaLISA showed better sensitivity than LFIA for detecting inactivated influenza B virus.

Conclusion

AlphaLISA showed higher sensitivity and throughput in the detection of IBV and can be used for IBV diagnosis and epidemic control.

Factors associated with viral RNA shedding and evaluation of potential viral infectivity at returning to school in influenza outpatients after treatment with baloxavir marboxil and neuraminidase inhibitors during 2013/2014-2019/2020 seasons in Japan: an observational study

BACKGROUND

This study assessed the differences in daily virus reduction and the residual infectivity after the recommended home stay period in Japan in patients infected with influenza and treated with baloxavir (BA), laninamivir (LA), oseltamivir (OS), and zanamivir (ZA).

METHODS

We conducted an observational study on children and adults at 13 outpatient clinics in 11 prefectures in Japan during seven influenza seasons from 2013/2014 to 2019/2020. Virus samples were collected twice from influenza rapid test-positive patients at the first and second visit 4-5 days after the start of treatment. The viral RNA shedding was quantified using quantitative RT-PCR. Neuraminidase (NA) and polymerase acidic (PA) variant viruses that reduce susceptibility to NA inhibitors and BA, respectively, were screened using RT-PCR and genetic sequencing. Daily estimated viral reduction was evaluated using univariate and multivariate analyses for the factors such as age, treatment, vaccination status, or the emergence of PA or NA variants. The potential infectivity of the viral RNA shedding at the second visit samples was determined using the Receiver Operator Curve based on the positivity of virus isolation.

RESULTS

Among 518 patients, 465 (80.0%) and 116 (20.0%) were infected with influenza A (189 with BA, 58 with LA, 181 with OS, 37 with ZA) and influenza B (39 with BA, 10 with LA, 52 with OS, 15 with ZA). The emergence of 21 PA variants in influenza A was detected after BA treatment, but NA variants were not detected after NAIs treatment. Multiple linear regression analysis showed that the daily viral RNA shedding reduction in patients was slower in the two NAIs (OS and LA) than in BA, influenza B infection, aged 0-5 years, or the emergence of PA variants. The residual viral RNA shedding potentially infectious was detected in approximately 10-30% of the patients aged 6-18 years after five days of onset.

CONCLUSIONS

Viral clearance differed by age, type of influenza, choice of treatment, and susceptibility to BA. Additionally, the recommended homestay period in Japan seemed insufficient, but reduced viral spread to some extent since most school-age patients became non-infectious after 5 days of onset.

Agnostic Sequencing for Detection of Viral Pathogens

The advent of next-generation sequencing (NGS) technologies has expanded our ability to detect and analyze microbial genomes and has yielded novel molecular approaches for infectious disease diagnostics. While several targeted multiplex PCR and NGS-based assays have been widely used in public health settings in recent years, these targeted approaches are limited in that they still rely on a priori knowledge of a pathogen's genome, and an untargeted or unknown pathogen will not be detected. Recent public health crises have emphasized the need to prepare for a wide and rapid deployment of an agnostic diagnostic assay at the start of an outbreak to ensure an effective response to emerging viral pathogens. Metagenomic techniques can nonspecifically sequence all detectable nucleic acids in a sample and therefore do not rely on prior knowledge of a pathogen's genome. While this technology has been reviewed for bacterial diagnostics and adopted in research settings for the detection and characterization of viruses, viral metagenomics has yet to be widely deployed as a diagnostic tool in clinical laboratories. In this review, we highlight recent improvements to the performance of metagenomic viral sequencing, the current applications of metagenomic sequencing in clinical laboratories, as well as the challenges that impede the widespread adoption of this technology.

Estimating sensitivity and specificity of diagnostic tests using latent class models that account for conditional dependence between tests: a simulation study

BACKGROUND

Latent class models are increasingly used to estimate the sensitivity and specificity of diagnostic tests in the absence of a gold standard, and are commonly fitted using Bayesian methods. These models allow us to account for 'conditional dependence' between two or more diagnostic tests, meaning that the results from tests are correlated even after conditioning on the person's true disease status. The challenge is that it is not always clear to researchers whether conditional dependence exists between tests and whether it exists in all or just some latent classes. Despite the increasingly widespread use of latent class models to estimate diagnostic test accuracy, the impact of the conditional dependence structure chosen on the estimates of sensitivity and specificity remains poorly investigated.

METHODS

A simulation study and a reanalysis of a published case study are used to highlight the impact of the conditional dependence structure chosen on estimates of sensitivity and specificity. We describe and implement three latent class random-effect models with differing conditional dependence structures, as well as a conditional independence model and a model that assumes perfect test accuracy. We assess the bias and coverage of each model in estimating sensitivity and specificity across different data generating mechanisms.

RESULTS

The findings highlight that assuming conditional independence between tests within a latent class, where conditional dependence exists, results in biased estimates of sensitivity and specificity and poor coverage. The simulations also reiterate the substantial bias in estimates of sensitivity and specificity when incorrectly assuming a reference test is perfect. The motivating example of tests for Melioidosis highlights these biases in practice with important differences found in estimated test accuracy under different model choices.

CONCLUSIONS

We have illustrated that misspecification of the conditional dependence structure leads to biased estimates of sensitivity and specificity when there is a correlation between tests. Due to the minimal loss in precision seen by using a more general model, we recommend accounting for conditional dependence even if researchers are unsure of its presence or it is only expected at minimal levels.

SARS-CoV-2 detecting rapid metasurface-based sensor

We have proposed a novel approach to detect COVID-19 by detecting the ethyl butanoate which high volume ratio is present in the exhaled breath of a COVID-19 infected person. We have employed a refractive index sensor (RIS) with the help of a metasurface-based slotted T-shape perfect absorber that can detect ethyl butanoate present in exhaled breath of COVID-19 infected person with high sensitivity and in-process SARS-CoV-2. The optimized structure of the sensor is obtained by varying several structure parameters including structure length and thickness, slotted T-shape resonator length, width, and thickness. Sensor's performance is evaluated based on numerous factors comprising of sensitivity, Q factor, detection limit, a figure of merit (FOM), detection accuracy, and other performance defining parameters. The proposed slotted T-shape RIS achieved the largest sensitivity of 2500 nm/RIU, Q factor of 131.06, a FOM of 131.58 RIU^-1, detection limit of 0.0224 RIU.

A Preliminary Study on the Frequency of Influenza Infections during the Early 2022 Amid COVID-19 Epidemic in Libya

Background At the time of conducting this study, we were at the peak of the influenza season, and influenza vaccinations were not readily accessible throughout the country. Thus, predisposing many high-risk individuals to influenza infections in a time when coronavirus disease 2019 (COVID-19) was also highly circulating, and the emerging Omicron variant of concern was peaking in many countries worldwide.

Methods We conducted a brief survey to prospectively estimate the frequency of influenza A and B and severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) in samples received at our laboratories at Libyan Biotechnology Research Center, Tripoli, Libya, between December 1, 2021, and January 31, 2022, for patients complaining of respiratory symptoms using a multiplex reverse transcription-polymerase chain reaction test for SARS-COV-2, influenza A and B, and RSV.

Results We analyzed nasopharyngeal swabs in viral transport media from 2,186 samples. About 27% (589/2186) of study patients tested positive for SARS-COV-2, 2.8% (61/2186) were positive for influenza A virus, 0.18% (4/2186) for influenza B virus, and 1.4% (31/2186) tested positive for RSV.

Conclusions These results revealed that along with COVID-19, influenza infections were also rising. As the COVID-19 pandemic continues, the most significant concern is the development of an influenza outbreak in the upcoming months. Therefore, continuing annual influenza vaccination is critical to increasing population immunity. National influenza surveillance and testing should also be conducted. Furthermore, sequencing and antigenic characterization should be performed regularly. There is a need for continuous monitoring in national laboratories to detect any zoonotic cases and substantial viral evolution.

Recent Advances in Biosensors for Detection of COVID-19 and Other Viruses

This century has introduced very deadly, dangerous, and infectious diseases to humankind such as the influenza virus, Ebola virus, Zika virus, and the most infectious SARS-CoV-2 commonly known as COVID-19 and have caused epidemics and pandemics across the globe. For some of these diseases, proper medications, and vaccinations are missing and the early detection of these viruses will be critical to saving the patients. And even the vaccines are available for COVID-19, the new variants of COVID-19 such as Delta, and Omicron are spreading at large. The available virus detection techniques take a long time, are costly, and complex and some of them generates false negative or false positive that might cost patients their lives. The biosensor technique is one of the best qualified to address this difficult challenge. In this systematic review, we have summarized recent advancements in biosensor-based detection of these pandemic viruses including COVID-19. Biosensors are emerging as efficient and economical analytical diagnostic instruments for early-stage illness detection. They are highly suitable for applications related to healthcare, wearable electronics, safety, environment, military, and agriculture. We strongly believe that these insights will aid in the study and development of a new generation of adaptable virus biosensors for fellow researchers.

Single-chirality of single-walled carbon nanotubes (SWCNTs) through chromatography and its potential biological applications

Gel chromatography is used to separate single-chirality and selective-diameter SWCNTs. We also explore the use of photothermal therapy and biosensor applications based on single-chirality, selected-diameter, and unique geometric shape.

Numerical simulation and optimization of AC electrothermal microfluidic biosensor for COVID-19 detection through Taguchi method and artificial network

Microfluidic biosensors have played an important and challenging role for the rapid detection of the new severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Previous studies have shown that the kinetic binding reaction of the target antigen is strongly affected by process parameters. The purpose of this research was to optimize the performance of a microfluidic biosensor using two different approaches: Taguchi optimization and artificial neural network (ANN) optimization. Taguchi L8(2⁵) orthogonal array involving eight groups of experiments for five key parameters, which are microchannel shape, biosensor position, applied alternating current voltage, adsorption constant, and average inlet flow velocity, at two levels each, are performed to minimize the detection time of a biosensor excited by an alternating current electrothermal force. Signal to noise ratio ( S / N ) and analysis of variance were used to reach the optimal levels of process parameters and to demonstrate their percentage contributions, in terms of improved device response time. The principal results of this study showed that the Taguchi method was able to identify that the kinetic adsorption rate is the most influential parameter at 93% contribution, and the reaction surface position is the least influential parameter at 0.07% contribution. Also, the ANN model was able to accurately predict the optimal input values with a very low prediction error. Overall, the major conclusion of this study is both the Taguchi and ANN approaches can be effectively utilized to optimize the performance of a microfluidic biosensor. These advances have the potential to revolutionize the field of biosensing.

Development of reverse-transcription loop-mediated isothermal amplification assays for point-of-care testing of human influenza virus subtypes H1N1 and H3N2

Influenza A virus (IAV) is the most widespread pathogen causing human respiratory infections. Although polymerase chain reaction (PCR)-based methods are currently the mostcommonly used tools for IAV detection, PCR is not ideal for point-of-care testing. In thisstudy, we aimed to develop a more rapid and sensitive method than PCR-based tools todetect IAV using loop-mediated isothermal amplification (LAMP) technology. We designedreverse-transcriptional (RT)-LAMP primers targeting the hemagglutinin gene. RNAs fromreference H1N1 and H3N2 showed specific RT-LAMP signals with the designed primers.We optimized the reaction conditions and developed universal reaction conditions for bothLAMP assays. Under these conditions, the detection limit was 50 copies for both RT-LAMPassays. There was no non-specific signal to 19 non-IAV respiratory viruses, such as influenza B virus, coronaviruses, and respiratory syncytial viruses. Regarding the reaction time, apositive signal was detected within 25 min after starting the reaction. In conclusion, ourRT-LAMP assay has high sensitivity and specificity for the detection of the H1 and H3 subtypes, making it suitable for point-of-care IAV testing.

Metagenomic next-generation sequencing shotgun for the diagnosis of infection in connective tissue diseases: A retrospective study

Objective

Patients with connective tissue diseases (CTDs) are at high risk of infection due to various reasons. The purpose of the study was to investigate the infection diagnosis value of metagenomic next-generation sequencing (mNGS) shotgun in CTDs to guide the use of anti-infective therapy more quickly and accurately.

Methods

In this retrospective study, a total of 103 patients with CTDs admitted with suspected infection between December 2018 and September 2021 were assessed using mNGS as well as conventional microbiological tests (CMT).

Results

Among these 103 patients, 65 were confirmed to have an infection (Group I) and 38 had no infection (Group II). mNGS reached a sensitivity of 92.31% in diagnosing pathogens in Group I. Moreover, mNGS showed good performance in identifying mixed infection. In all infection types, lung infection was the most common. mNGS also played an important role in detecting Pneumocystis jirovecii, which was associated with low CD4+ T-cell counts inextricably.

Conclusion

mNGS is a useful tool with outstanding diagnostic potential in identifying pathogens in patients with CTDs and conduce to provide guidance in clinical practice.

Loop-Mediated Isothermal Amplification-Based Microfluidic Platforms for the Detection of Viral Infections

Purpose of Review

Easy-to-use, fast, and accurate virus detection method is essential for patient management and epidemic surveillance, especially during severe pandemics. Loop-mediated isothermal amplification (LAMP) on a microfluidic platform is suitable for detecting infectious viruses, regardless of the availability of medical resources. The purpose of this review is to introduce LAMP-based microfluidic devices for virus detection, including their detection principles, methods, and application.

Recent Findings

Facing the uncontrolled spread of viruses, the large-scale deployment of LAMP-based microfluidic platforms at the grassroots level can help expand the coverage of nucleic acid testing and shorten the time to obtain test reports. Microfluidic chip technology is highly integrated and miniaturized, enabling precise fluid control for effective virus detection. Performing LAMP on miniaturized systems can reduce analysis time, reagent consumption and risk of sample contamination, and improve analytical performance.

Summary

Compared to traditional benchtop protocols, LAMP-based microfluidic devices reduce the testing time, reagent consumption, and the risk of sample contamination. In addition to simultaneous detection of multiple target genes by special channel design, microfluidic chips can also integrate digital LAMP to achieve absolute quantification of target genes.

Recent advances in acoustofluidic separation technology in biology

Acoustofluidic separation of cells and particles is an emerging technology that integrates acoustics and microfluidics. In the last decade, this technology has attracted significant attention due to its biocompatible, contactless, and label-free nature. It has been widely validated in the separation of cells and submicron bioparticles and shows great potential in different biological and biomedical applications. This review first introduces the theories and mechanisms of acoustofluidic separation. Then, various applications of this technology in the separation of biological particles such as cells, viruses, biomolecules, and exosomes are summarized. Finally, we discuss the challenges and future prospects of this field.

An overview of advancement in aptasensors for influenza detection

INTRODUCTION

The platforms for early identification of infectious diseases such as influenza has seen a surge in recent years as delayed diagnosis of such infections can lead to dreadful effects causing large numbers of deaths. The time taken in detection of an infectious disease may vary from a few days to a few weeks depending upon the choice of the techniques. So, there is an urgent need for advanced methodologies for early diagnosis of the influenza.

AREAS COVERED

The emergence of "Aptasensor" synergistically with biosensors for diagnosis has opened a new era for sensitive, selective and early detection approaches. This review described various conventional as well as advanced methods based on artificial immunogenic nucleotide sequences complementing a part of the virus, i.e., aptamers based aptasensors for influenza diagnosis and the challenges faced in their commercialization.

EXPERT OPINION

Although numerous traditional methods are available for influenza detection but mostly associated with low sensitivity, specificity, high cost, trained personnel, and animals required for virus culture/ antibody raising as the major drawbacks. Aptamers can be manufactured invitro as 'chemical antibodies' at commercial level, no animal required. Following these advantages, aptamers can pave the way for an efficient diagnostic technique as compared to other existing conventional methods..

From Clinical Specimen to Whole Genome Sequencing of A(H3N2) Influenza Viruses: A Fast and Reliable High-Throughput Protocol

(1) Background: Over the last few years, there has been growing interest in the whole genome sequencing (WGS) of rapidly mutating pathogens, such as influenza viruses (IVs), which has led us to carry out in-depth studies on viral evolution in both research and diagnostic settings. We aimed at describing and determining the validity of a WGS protocol that can obtain the complete genome sequence of A(H3N2) IVs directly from clinical specimens. (2) Methods: RNA was extracted from 80 A(H3N2)-positive respiratory specimens. A one-step RT-PCR assay, based on the use of a single set of specific primers, was used to retro-transcribe and amplify the entire IV type A genome in a single reaction, thus avoiding additional enrichment approaches and host genome removal treatments. Purified DNA was quantified; genomic libraries were prepared and sequenced by using Illumina MiSeq platform. The obtained reads were evaluated for sequence quality and read-pair length. (3) Results: All of the study specimens were successfully amplified, and the purified DNA concentration proved to be suitable for NGS (at least 0.2 ng/µL). An acceptable coverage depth for all eight genes of influenza A(H3N2) virus was obtained for 90% (72/80) of the clinical samples with viral loads >105 genome copies/mL. The mean depth of sequencing ranged from 105 to 200 reads per position, with the majority of the mean depth values being above 103 reads per position. The total turnaround time per set of 20 samples was four working days, including sequence analysis. (4) Conclusions: This fast and reliable high-throughput sequencing protocol should be used for influenza surveillance and outbreak investigation.

Second near-infrared fluorescent dye for lateral flow immunoassays rapid detection of influenza A/B virus

Sensitive and rapid diagnostic point of care testing (POCT) system is of great significance to prevent and control human virus infection. Here reported an immunochromatographic strip technology. The second near-infrared (NIR-II) fluorescent dye encapsulated into polystyrene (PS) nanoparticles, was integrated into a lateral flow assay platform to achieve excellent detection of influenza A/B. This surface-functionalized and mono-dispersed PS nanoparticles has been conjugated with influenza nucleoprotein monoclonal antibody as targets for influenza antigen-detection. This assay achieved the detection limit of 0.015 ng/mL for influenza A nucleoprotein and 4.3*10^-5 HAU/mL (10^2.08 TCID₅₀/mL) influenza A virus (influenza B: 0.037 ng/mL, 9.7*10^-7 HAU/mL (10^0.43 TCID₅₀/mL)). Compared with an Au-based lateral flow test strip, the strip's sensitivity is about 16-fold higher than it. Strip detection properties remain stable for 6 months under 4 °C to 30 °C storage. The assay's intra assay variation is 5.14% and the inter assay variation is 7.74%. Other potential endogenous and exogenous interfering substances (whole blood, nasal mucin, saliva, antipyretics, antihistamines and neuraminidase inhibitors) showed negative results, which verified the excellent specificity of this method. This assay was successfully applied to the POCT quantitative detection of influenza A/B virus, the sensitivity to influenza A and B viruses was 70% and 87.5% respectively, and the specificity was 100%. Therefore, these microspheres can be used as an effective material for rapid POCT detection in clinical specimens.

Prevalence and Characteristics of Malaria and Influenza Co-Infection in Febrile Patients: A Systematic Review and Meta-Analysis

Malaria and influenza are co-endemic in several geographical areas, and differentiation of their clinical features is difficult. The present study aimed to qualitatively and quantitatively analyze the prevalence and characteristics of malaria and influenza co-infection in febrile patients. The systematic review was registered at PROSPERO (CRD42021264525). Relevant literature that reported malaria and influenza co-infection in febrile patients were searched in PubMed, Web of Science, and Scopus from 20 June to 27 June 2021 and the risk of bias for each study was assessed. Quantitative analysis included pooled prevalence, and the odds of malaria and influenza virus co-infection among febrile patients were estimated using a random-effects model. Subgroup analyses were performed to summarize the effect estimate for each group. Funnel plot, Egger’s test, and contour-enhanced funnel plot were used to demonstrate any publication bias among outcomes of included studies. Among 4253 studies retrieved, 10 studies that enrolled 22,066 febrile patients with 650 co-infected patients were included for qualitative and quantitative syntheses. The pooled prevalence of malaria and influenza virus co-infection among febrile patients was 31.0% in Nigeria, 1.0% in Tanzania, 1.0% in Uganda, 1.0% in Malawi, 1.0% in Ghana, 0% in Cambodia, 7.0% in the Central African Republic, and 7.0% in Kenya. Meta-analysis also showed co-infection occurrence by chance (p = 0.097, odds ratio 0.54, 95% CI 0.26–1.12, I² 94.9%). The prevalence of malaria and influenza virus co-infection among febrile patients was heterogeneous by country, characteristics of febrile participants, and diagnostic tests for influenza virus. Further studies should investigate severe clinical manifestations or differentiate clinical outcomes between mono-infected or co-infected individuals, whether the co-infection leads to severe disease outcome.

Recent advances in airborne pathogen detection using optical and electrochemical biosensors

The world is currently facing an adverse condition due to the pandemic of airborne pathogen SARS-CoV-2. Prevention is better than cure; thus, the rapid detection of airborne pathogens is necessary because it can reduce outbreaks and save many lives. Considering the immense role of diverse detection techniques for airborne pathogens, proper summarization of these techniques would be beneficial for humans. Hence, this review explores and summarizes emerging techniques, such as optical and electrochemical biosensors used for detecting airborne bacteria (Bacillus anthracis, Mycobacterium tuberculosis, Staphylococcus aureus, and Streptococcus pneumoniae) and viruses (Influenza A, Avian influenza, Norovirus, and SARS-CoV-2). Significantly, the first section briefly focuses on various diagnostic modalities applied toward airborne pathogen detection. Next, the fabricated optical biosensors using various transducer materials involved in colorimetric and fluorescence strategies for infectious pathogen detection are extensively discussed. The third section is well documented based on electrochemical biosensors for airborne pathogen detection by differential pulse voltammetry, cyclic voltammetry, square-wave voltammetry, amperometry, and impedance spectroscopy. The unique pros and cons of these modalities and their future perspectives are addressed in the fourth and fifth sections. Overall, this review inspected 171 research articles published in the last decade and persuaded the importance of optical and electrochemical biosensors for airborne pathogen detection.

The genetic characterization of hemagglutinin (HA), neuraminidase (NA) and polymerase acidic (PA) genes of H3N2 influenza viruses circulated in Guangdong Province of China during 2019-2020

The evolution of seasonal influenza viruses, which can cause virus antigenic drift to escape human herd immunity, is a significant public health problem. Here, we obtained hemagglutinin (HA), neuraminidase (NA), and polymerase acidic protein (PA) the gene sequences of 84 influenza virus isolates collected in Guangdong Province during the 2019-2020 influenza season. Phylogenetic analyses revealed all these isolates were genetically similar to the viruses of clade 3C2a A1b, specifically those within subclades of A1b 137F (59 cases), A1b 186D (19 cases), and A1b 94 N (6 cases). The influenza virus isolates were distinct from the World Health Organization recommended influenza A vaccine virus for the 2019-2020 Northern Hemisphere season (A/Kansas/14/2017; H3N2). Phylogenies inferred from the individual gene segment sequences revealed that one reassortment event occurred among these clades. The genetic variation involved mutations within viral antigenic epitopes and two N-glycosylation site alterations. The novel mutation sites of G202D and D206N in the HA gene, E344K in the NA gene, and K626R in the PA gene which may affect the spread of the virus were observed. We investigated the evolution of these genes and found that the HA and NA genes were under greater pressure than PA gene. Mutations associated with conferring resistance to NA inhibitors or baloxavir acid were not found. Our results suggest that a rapid evolution of the H3N2 influenza virus occurred, thus continuous monitoring is critical for establishing appropriate vaccine formulations or drug delivery for targeting influenza.

Fast and ultrafast thermal contrast amplification of gold nanoparticle-based immunoassays

For highly sensitive point-of-care (POC) diagnostics, we explored the limit of thermal contrast amplification (TCA) reading of gold nanoparticles (GNPs/mm²) at test regions in immunoassays. More specifically, we built and compared fast (minute scale) and ultrafast (seconds scale) TCA setups using continuous-wave (CW) and ms pulsed lasers, respectively. TCA improved the limit of detection (LoD) for silica-core gold nanoshells (GNSs) preloaded in nitrocellulose (NC) membrane as model lateral flow immunoassays (LFAs) by 10- to 20-fold over visual reading. While the ultrafast TCA led to higher thermal signals, this came with a twofold loss in LoD vs. fast TCA primarily due to noise within the infrared sensor and a necessity to limit power to avoid burning. To allow higher laser power, and therefore amplification fold, we also explored transparent glass coverslip substrate as a model microfluidic immunoassay (MIA). We found the ultrafast TCA reading of GNS-coated coverslips achieved a maximal signal amplification (57-fold) over visual reading of model LFAs. Therefore, ultrafast TCA-MIA is promising for ultrasensitive and ultrafast diagnostics. Further advantages of using TCA in MIA vs. LFA could include lower sample volume, multiplexed tests, higher throughput, and fast reading. In summary, TCA technology is able to enhance the sensitivity and speed of reading GNPs (GNPs/mm²) within both LFAs and MIAs.

Evolution of the PB1 gene of human influenza A (H3N2) viruses circulating between 1968 and 2019

One avian H3N2 influenza virus, providing its PB1 and HA segments, reassorted with one human H2N2 virus and caused a pandemic outbreak in 1968, killing over 1 million people. After its introduction to humanity, the pandemic H3N2 virus continued adapting to humans and has resulted in epidemic outbreaks every influenza season. To understand the functional roles of the originally avian PB1 gene in the circulating strains of human H3N2 influenza viruses, we analyzed the evolution of the PB1 gene in all human H3N2 isolates from 1968 to 2019. We found several specific residues dramatically changed around 2002-2009 and remained stable through to 2019. Then, we verified the functions of these PB1 mutations in the genetic background of the early pandemic virus, A/Hong Kong/1/1968(HK/68), as well as a recent seasonal strain, A/Jiangsu/34/2016 (JS/16). The PB1 V709I or PB1 V113A/K586R/D619N/V709I induced higher polymerase activity of HK/68 in human cells. And the four mutations acted cooperatively that had an increased replication capacity in vitro and in vivo at an early stage of infection. In contrast, the backward mutant, A113V/R586K/N619D/I709V, reduced polymerase activity in human cells. The PB1 I709V decreased viral replication in vitro, but this mutant only showed less effect on mice infection experiment, which suggested influenza A virus evolved in human host was not always consisted with highly replication efficiency and pathogenicity in other mammalian host. Overall, our results demonstrated that the identified PB1 mutations contributed to the viral evolution of human influenza A (H3N2) viruses.

Influenza A, Influenza B, and SARS-CoV-2 Similarities and Differences – A Focus on Diagnosis

In late December 2019, the first cases of viral pneumonia caused by an unidentified pathogen were reported in China. Two years later, SARS-CoV-2 was responsible for almost 450 million cases, claiming more than 6 million lives. The COVID-19 pandemic strained the limits of healthcare systems all across the world. Identifying viral RNA through real-time reverse transcription-polymerase chain reaction remains the gold standard in diagnosing SARS-CoV-2 infection. However, equipment cost, availability, and the need for trained personnel limited testing capacity. Through an unprecedented research effort, new diagnostic techniques such as rapid diagnostic testing, isothermal amplification techniques, and next-generation sequencing were developed, enabling accurate and accessible diagnosis. Influenza viruses are responsible for seasonal outbreaks infecting up to a quarter of the human population worldwide. Influenza and SARS-CoV-2 present with flu-like symptoms, making the differential diagnosis challenging solely on clinical presentation. Healthcare systems are likely to be faced with overlapping SARS-CoV-2 and Influenza outbreaks. This review aims to present the similarities and differences of both infections while focusing on the diagnosis. We discuss the clinical presentation of Influenza and SARS-CoV-2 and techniques available for diagnosis. Furthermore, we summarize available data regarding the multiplex diagnostic assay of both viral infections.

Clinical Evaluation of BD Veritor SARS-CoV-2 and Flu A+B Assay for Point-Of-Care System

Differential diagnosis of COVID-19 and/or influenza (flu) at point of care is critical for efficient patient management and treatment of both these diseases. The study presented here characterizes the BD Veritor System for Rapid Detection of SARS-CoV-2 and Flu A+B (“Veritor SARS-CoV-2/Flu”) triplex assay. The performance for SARS-CoV-2 detection was determined using 298 specimens from patients reporting COVID-19 symptoms within 7 days from symptom onset (DSO) in comparison with the Lyra SARS-CoV-2 RT-PCR (reverse transcriptase PCR) assay (“Lyra SARS-CoV-2”) as the reference. The performance for flu A and flu B detection was determined using 75 influenza-positive and 40 influenza-negative retrospective specimens in comparison with the previously FDA-cleared BD Veritor System for Rapid Detection of Flu A+B assay (“Veritor Flu”) as the reference. The Veritor SARS-CoV-2/Flu assay met the FDA EUA acceptance criteria (86.7%; 95% confidence interval [95% CI]: 75.8 to 93.1) for SARS-CoV-2 testing compared to Lyra SARS-CoV-2. The Veritor SARS-CoV-2/Flu assay also demonstrated 100% agreement with the Veritor Flu for Flu A+B assay. For flu A detection, the lower bound of the 95% CI was 91.2%; for flu B detection, the lower bound was 90.0%. The dual detection capability of Veritor SARS-CoV-2/Flu for the etiologic agents causing COVID-19 and flu will allow efficient differentiation between the two illnesses, inform disease management, and facilitate optimal treatment.

IMPORTANCE COVID-19 and flu are two respiratory illnesses which share similar clinical symptoms. The BD Veritor SARS-CoV-2/Flu assay has high sensitivity and specificity for detecting the SARS-CoV-2 and influenza A/B, the two etiologic agents causing COVID-19 and flu, respectively. This dual detection capability is critical when overlap occurs between the COVID-19 pandemic and the flu season. This triplex assay will allow efficient differentiation between the two respiratory illnesses and support a point-of-care physician diagnosis to facilitate the proper treatment and disease management for patients exhibiting overlapping symptoms.