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N6-methyladenosine (m⁶A) RNA methylation is the most abundant epitranscriptomic modification of eukaryotic messenger RNAs (mRNAs). Previous reports have found m⁶A on both cellular and viral transcripts and defined its role in regulating numerous biological processes, including viral infection. Here, we show that m⁶A and its associated machinery regulate the life cycle of hepatitis B virus (HBV). HBV is a DNA virus that completes its life cycle via an RNA intermediate, termed pregenomic RNA (pgRNA). Silencing of enzymes that catalyze the addition of m⁶A to RNA resulted in increased HBV protein expression, but overall reduced reverse transcription of the pgRNA. We mapped the m⁶A site in the HBV RNA and found that a conserved m⁶A consensus motif situated within the epsilon stem loop structure, is the site for m⁶A modification. The epsilon stem loop is located in the 3′ terminus of all HBV mRNAs and at both the 5′ and 3′ termini of the pgRNA. Mutational analysis of the identified m⁶A site in the 5′ epsilon stem loop of pgRNA revealed that m⁶A at this site is required for efficient reverse transcription of pgRNA, while m⁶A methylation of the 3′ epsilon stem loop results in destabilization of all HBV transcripts, suggesting that m⁶A has dual regulatory function for HBV RNA. Overall, this study reveals molecular insights into how m⁶A regulates HBV gene expression and reverse transcription, leading to an increased level of understanding of the HBV life cycle.

The HIV capsid is semipermeable and covered in electropositive pores that are essential for viral DNA synthesis and infection. Here, we show that these pores bind the abundant cellular polyanion IP6, transforming viral stability from minutes to hours and allowing newly synthesised DNA to accumulate inside the capsid. An arginine ring within the pore coordinates IP6, which strengthens capsid hexamers by almost 10°C. Single molecule measurements demonstrate that this renders native HIV capsids highly stable and protected from spontaneous collapse. Moreover, encapsidated reverse transcription assays reveal that, once stabilised by IP6, the accumulation of new viral DNA inside the capsid increases >100 fold. Remarkably, isotopic labelling of inositol in virus-producing cells reveals that HIV selectively packages over 300 IP6 molecules per infectious virion. We propose that HIV recruits IP6 to regulate capsid stability and uncoating, analogous to picornavirus pocket factors. HIV-1/IP6/capsid/co-factor/reverse transcription. Viruses like HIV invade cells and replicate their genome to create new viruses. To hide from components of our immune system that are active inside the cell, HIV uses a protein shell called a capsid, which protects its genome from detection and destruction. However, the capsid faces an engineering challenge beyond those faced by even the most complex man-made structures. This is because the capsid must be strong enough to survive for hours inside the cell but not so strong that it cannot quickly open when the virus needs to release its genome. How this process, called ‘uncoating’, is achieved is one of the great unanswered questions in HIV biology. In 2016, researchers made the unexpected discovery that the HIV capsid is decorated with hundreds of pores: one at the center of every subunit from which it is built. Each pore contains a ring of six positively charged amino acids that should destabilize the capsid and cause it to break apart. Yet similar pores are found on a diverse range of viruses. Mallery et al. – who include several of the researchers involved in the 2016 work – set out to investigate why the HIV capsid contains the positively charged pores. Initial experiments revealed that a molecule called IP6, which is abundant in cells, can bind to the HIV capsid. To do so, six negatively charged phosphate groups in IP6 match up with the six positively charged residues in the pore. In a related study, Márquez et al. developed a new method that allows the fate of individual capsids to be visualized through time. Here, Mallery et al. use the method to show that IP6 increases how long the capsid remains intact from several minutes to over 10 hours. This allows HIV to copy its genome inside the capsid, meaning it remains protected while the virus prepares to produce new viruses. Mallery et al. also show that HIV packages more than 300 IP6 molecules into itself when it replicates. Other viruses called picornaviruses use small molecules called pocket factors to stabilize the capsid and to trigger uncoating. Mallery et al. propose that IP6 is an HIV pocket factor. Just as studies of pocket factors have stimulated the development of anti-picornavirus drugs, understanding the role of IP6 may help to develop new treatments for HIV.

Foot-and-mouth disease (FMD) is a devastating livestock disease caused by foot-and-mouth disease virus (FMDV). Outbreaks of this disease in a country always result in conspicuous economic losses to livestock industry and subsequently lead to serious socioeconomic damages due to the immediate imposition of trade embargo. Rapid and accurate diagnoses are imperative to control this infectious virus. In the current review, enzyme-linked immunosorbent assay (ELISA)-based methods used in FMD diagnosis are extensively reviewed, particularly the sandwich, liquid-phase blocking, and solid-phase competition ELISA. The differentiation of infected animals from vaccinated animals using ELISA-based methods is also highlighted, in which the role of 3ABC polyprotein as a marker is reviewed intensively. Recently, more studies are focusing on the molecular diagnostic methods, which detect the viral nucleic acids based on reverse transcription-polymerase chain reaction (RT-PCR) and RT-loop-mediated isothermal amplification (RT-LAMP). These methods are generally more sensitive because of their ability to amplify a minute amount of the viral nucleic acids. In this digital era, the RT-PCR and RT-LAMP are progressing toward the mobile versions, aiming for on-site FMDV diagnosis. Apart from RT-PCR and RT-LAMP, another diagnostic assay specifically designed for on-site diagnosis is the lateral flow immunochromatographic test strips. These test strips have some distinct advantages over other diagnostic methods, whereby the assay often does not require the aid of an external device, which greatly lowers the cost per test. In addition, the on-site diagnostic test can be easily performed by untrained personnel including farmers, and the results can be obtained in a few minutes. Lastly, the use of FMDV diagnostic assays for progressive control of the disease is also discussed critically.

Cytokines are low molecular weight glycoproteins involved in the regulation of the immune system, and more than 100 cytokines have hitherto been identified in humans. Cytokines similar to those found in humans have also been found in fish. The innate immune response of fish can be examined by using cytokines as markers. We developed a multiplex reverse transcription–polymerase chain reaction assay to analyze the expression of various cytokine genes. Using this assay, we were able to investigate the fish immune response when it had been activated by immunostimulants. The involvement of inflammatory cytokines, such as interleukin-1β, in the immune system of fish was revealed following administration of an immunostimulant.

Background Swine influenza virus (SIV) and porcine reproductive and respiratory syndrome virus (PRRSV) are leading pathogens in pigs, whose co-infections exacerbate disease severity. Current diagnostics like RT-PCR lack suitability for rapid, on-site use, while CRISPR-based systems face challenges in convenient multiplex detection. Results We developed an RT-LAMP-CRISPR-Cas12a/13a-LFD dual-detection platform that integrates reverse transcription loop-mediated isothermal amplification (RT-LAMP) with the orthogonal trans-cleavage activities of CRISPR-Cas12a and Cas13a, followed by lateral flow dipstick (LFD) visualization. This assay achieved detection limits of 5 copies/µL for SIV and 2 copies/µL for PRRSV, and exhibited high specificity against other common swine pathogens. The entire process, including a 20-minute amplification at 40 °C and 5-minute LFD readout, enables rapid and visual diagnosis. A preliminary validation was conducted using respiratory infection samples, demonstrating high concordance with reference methods and specificity against non-target pathogens. Conclusions The RT-LAMP-CRISPR-Cas12a/13a-LFD assay provides a sensitive, specific, and potentially field-adaptable tool for the simultaneous detection of SIV and PRRSV. It is ideally suited for early screening and precise control of these pathogens in resource-limited settings.

The COVID-19 pandemic provides an urgent example where a gap exists between availability of state-of-the-art diagnostics and current needs. As assay protocols and primer sequences become widely known, many laboratories perform diagnostic tests using methods such as RT-PCR or reverse transcription loop mediated isothermal amplification (RT-LAMP). Here, we report an RT-LAMP isothermal assay for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus and demonstrate the assay on clinical samples using a simple and accessible point-of-care (POC) instrument. We characterized the assay by dipping swabs into synthetic nasal fluid spiked with the virus, moving the swab to viral transport medium (VTM), and sampling a volume of the VTM to perform the RT-LAMP assay without an RNA extraction kit. The assay has a limit of detection (LOD) of 50 RNA copies per μL in the VTM solution within 30 min. We further demonstrate our assay by detecting SARS-CoV-2 viruses from 20 clinical samples. Finally, we demonstrate a portable and real-time POC device to detect SARS-CoV-2 from VTM samples using an additively manufactured three-dimensional cartridge and a smartphone-based reader. The POC system was tested using 10 clinical samples, and was able to detect SARS-CoV-2 from these clinical samples by distinguishing positive samples from negative samples after 30 min. The POC tests are in complete agreement with RT-PCR controls. This work demonstrates an alternative pathway for SARS-CoV-2 diagnostics that does not require conventional laboratory infrastructure, in settings where diagnosis is required at the point of sample collection.

Environmental RNA (eRNA) analysis is expected to inclusively provide the physiological information of a population and community without individual sampling, having the potential for the improved monitoring of biodiversity and ecosystem function. Protocol development for maximizing eRNA availability is crucial to interpret its detection and quantification results with high accuracy and reliability, but the methodological validation and improvement of eRNA collection and processing methods are scarce. In this study, the technical steps after eRNA extraction, including genomic DNA (gDNA) removal and reverse transcription, were focused on and their performances were compared by zebrafish ( Danio rerio ) aquarium experiments. Additionally, this study also focused on the eRNA quantification variabilities between replicates and compared them between the PCR and sample levels. Results showed that (i) there was a trade-off between gDNA removal approaches and eRNA yields and an excess gDNA removal could lead to the false-negative eRNA detection, (ii) the use of the gene-specific primers for reverse transcription could increase the eRNA yields for multiple mitochondrial and nuclear genes compared with the random hexamer primers, and (iii) the coefficient of variation (CV) values of eRNA quantifications between PCR replicates were substantially lower for those between samples. Including the study, further knowledge for the sensitive and precise detection of macro-organismal eRNA should be needed for increasing the reliability and robustness of eRNA-based biomonitoring.

The most prevalent viruses currently causing diarrhea are norovirus and rotavirus, and rapid and sensitive detection methods are essential for the early diagnosis of disease. The purpose of this study was to establish a sensitive single‐tube two‐stage nucleic acid amplification method—reverse transcription recombinase‐assisted PCR (RT‐RAP)—for simultaneous detection of norovirus GII and group A Rotavirus, with the first stage consisting of isothermal reverse transcription recombinase‐aided amplification (RT‐RAA) and the second stage consisting of qPCR (quantitative PCR). RT‐RAP is more sensitive than either RT‐RAA or qRT‐PCR (quantitative RT‐PCR) alone. And the addition of a barrier that can be disassembled after heating enabled the detection of samples within 1 h in a single closed tube. Sensitivity was 10 copies/reaction of norovirus (Novs) GII and group A rotavirus (RVA). In parallel, two hundred fecal specimens were used to evaluate the method and compare it with a commercial fluorescent quantitative RT‐PCR. The data showed kappa values of 0.957 and 0.98 (p < 0.05) for detecting Novs GII and RVA by the two methods, indicating the potential of the newly established assay to be applied to clinical and laboratory testing. A sensitive single‐tube two‐stage nucleic acid amplification method—reverse transcription recombinase‐assisted PCR (RT‐RAP)—for simultaneous detection of norovirus GII and group A Rotavirus with the first stage consisting of isothermal reverse transcription recombinase‐aided amplification (RT‐RAA) and the second stage consisting of qPCR (quantitative PCR).

RNA-sequencing (RNA-seq) allows global gene expression analysis at the individual transcript level. Accurate quantification of transcript variants generated by alternative splicing (AS) remains a challenge. We have developed a comprehensive, nonredundant Arabidopsis reference transcript dataset (AtRTD) containing over 74 000 transcripts for use with algorithms to quantify AS transcript isoforms in RNA-seq. The AtRTD was formed by merging transcripts from TAIR10 and novel transcripts identified in an AS discovery project. We have estimated transcript abundance in RNA-seq data using the transcriptome-based alignment-free programmes SAILFISH and SALMON and have validated quantification of splicing ratios from RNA-seq by high resolution reverse transcription polymerase chain reaction (HR RT-PCR). Good correlations between splicing ratios from RNA-seq and HR RT-PCR were obtained demonstrating the accuracy of abundances calculated for individual transcripts in RNA-seq. The AtRTD is a resource that will have immediate utility in analysing Arabidopsis RNA-seq data to quantify differential transcript abundance and expression.

Chikungunya virus (CHIKV) and Dengue virus (DENV) infections present with highly similar clinical symptoms but require distinct management strategies, highlighting an urgent need for rapid and accurate differential diagnostic methods. The current gold standard, reverse transcription quantitative real-time PCR (RT-qPCR), has significant limitations: it relies on expensive thermal cyclers, complex laboratory infrastructure, and specialized personnel, making it difficult to implement in resource-limited settings and for on-site screening. To address this technological bottleneck, this study developed a portable, instrument-independent rapid detection technology based on the CRISPR-Cas12a/Cas13a dual-enzyme cleavage system. By precisely designing specific crRNAs targeting the CHIKV E1 gene and the DENV 3′-UTR region, and integrating them with reverse transcription recombinase-aided amplification (RT-RAA) technology, we established an integrated reaction system that performs nucleic acid amplification and detection under isothermal conditions. The core mechanism of the technology is as follows: upon recognition of the corresponding viral targets, Cas12a (targeting CHIKV) and Cas13a (targeting DENV) become activated and cleave fluorescent reporters or lateral flow strip reporter probes, enabling visual detection. Gradient-diluted viral nucleic acid tests indicated that the lowest detectable concentration that generated a signal reached 10² copies/mL, which is comparable to qPCR. Clinical simulated sample validation showed 100% overall agreement with qPCR, and the system accurately distinguished single infections from co-infections.The CRISPR dual-enzyme cleavage technology established in this study effectively circumvents the reliance of qPCR on sophisticated equipment, providing a rapid, simple, and low-cost solution for CHIKV/DENV differential diagnosis. It holds significant practical value for the early prevention and control of arboviral diseases.