Human noroviruses and persistent bacterial pathogens remain major food-safety concerns. This screening study compared 40
Viral diseases are among the most serious threats to shrimp aquaculture, causing large-scale mortality and production losses. This review summarizes current knowledge on the major viral diseases affecting cultured penaeid shrimp and freshwater prawns, with particular emphasis on white spot syndrome virus (WSSV), yellow head virus (YHV), Taura syndrome virus (TSV), infectious hypodermal and hematopoietic necrosis virus (IHHNV), infectious myonecrosis virus (IMNV), and Macrobrachium rosenbergii nodavirus (MrNV), the causative agent of white tail disease. We present a comparative overview of their genomic features, transmission routes, host range, and pathogenesis. Particular attention is given to the genome organization of WSSV and TSV, including variable regions and structural genes commonly used in molecular detection and strain differentiation. We also discuss mechanisms that may contribute to viral persistence in host populations, such as vertical transmission, chronic infections, and viral integration into host genomes. Finally, the review outlines current disease management strategies, including biosecurity measures, environmental control, and selective breeding. By compiling and contextualizing virological and epidemiological data, this review serves as a reference for disease surveillance and control in shrimp aquaculture.
Wastewater/sewage represents a highly complex environmental matrix and harbors various viruses including viruses of epidemic and pandemic potential like Influenza A and, SARS-CoV-2. The limitations of available methods for sample concentration are cost, efficiency and time. NGS- metagenomics offer sample to virus genomic characterization for even non-cultivable viruses at highest resolution. In this study, we have collected samples from sewage treatment plants located in Gwalior region of Central India (December 2023 to March 2025). In this study a novel in house nanoweb membrane-based sample enrichment followed by magnetic bead based nucleic acid extraction was optimized in conjunction to shotgun whole genome metagenomics on Nanopore and ion torrent NGS. Both the methods were found comparable with commercially available methods by virus specific TaqMan qPCR. Both the methods were found successful in virus recovery at two log through 102GC/50 ml feline calicivirus, Influenza A virus, Zika virus, SARS-CoV-2 spiked in sewage matrix alone or in mixture), suggesting the optimized protocol found working for virus characterization at strain level. Here, we have standardized a simple field amenable waste water sample enrichment followed by nucleic acid extraction protocol, that can easily be integrated with latest onsite downstream molecular diagnostic platforms. The developed method is very simple, cost effective and field deployable. This will help to develop a suitable strategic plan for sewage surveillance towards early warning/microbial forensics and future decisions for prevention and therapeutic interventions.
Human norovirus (HuNoV) and hepatitis A virus (HAV) are highly prevalent and contagious foodborne pathogens that pose a significant threat to global public health. Current molecular detection methods such as RT-qPCR and RT-ddPCR are highly sensitive and specific but time-consuming, require specialized equipment, and are unsuitable for on-site detection. We developed a multiplex reverse transcription recombinase polymerase amplification (RT-RPA) assay coupled with CRISPR-Cas12a and lateral flow detection for rapid, simultaneous identification of HuNoV GI, GII, and HAV. Through rigorous in silico design and experimental validation, we optimized primer pools and crRNAs to ensure broad genotype coverage and high specificity. Using 2 µL of input per target per 50 µL reaction, the assay achieved limits of detection of 10¹ copies/µL (2 × 10¹ copies/reaction) for HAV, 10³ copies/µL (2 × 10³ copies/reaction) for GI HuNoV, and 10² copies/µL (2 × 10² copies/reaction) for GII HuNoV, with a total assay time of 50 min from purified RNA to final readout. No cross-reactivity occurred with other common foodborne viruses. Validation using total RNA extracted from shellfish digestive glands artificially spiked with RNA standards provided preliminary evidence supporting the feasibility of the method under laboratory conditions. This portable system shows strong potential as a rapid multiplex molecular detection platform.
Hepatitis A (HepA) is a viral hepatitis caused by the hepatitis A virus (HAV), and currently Mexico is considered to have an intermediate-HAV endemicity. Wastewater-based epidemiology (WBE) is a tool for monitoring infectious diseases but has been poorly evaluated in intermediate-HAV-endemicity settings. From June 2024 to June 2025, 24-hour composite wastewater samples were collected twice a week from three wastewater treatment plants in the metropolitan area of San Luis Potosí, Mexico. Wastewater samples were ultracentrifuged, RNA was extracted, and HAV and crAssphage (for normalization) were detected by qPCR and weighted by the wastewater treatment plant’s inflow. We compared these results with HepA hospital admissions from eight public hospitals in the city during the same period. We compared HAV genotype sequences obtained from wastewater and patients. We processed 244 wastewater samples over 46 weeks, of which 35.1
