An amplicon-based protocol for whole-genome sequencing of human respiratory syncytial virus subgroup A

It is convenient to study complete genome sequences of human respiratory syncytial virus (hRSV) for ongoing genomic characterization and identification of highly transmissible or pathogenic variants. Whole genome sequencing of hRSV has been challenging from respiratory tract specimens with low viral loads. Herein, we describe an amplicon-based protocol for whole genome sequencing of hRSV subgroup A validated with 24 isolates from nasopharyngeal swabs and infected cell cultures, which showed cycle threshold (Ct) values ranging from 10 to 31, as determined by quantitative reverse-transcription polymerase chain reaction. MinION nanopore generated 3200 to 5400 reads per sample to sequence over 93% of the hRSV-A genome. Coverage of each contig ranged from 130× to 200×. Samples with Ct values of 20.9, 25.2, 27.1, 27.7, 28.2, 28.8, and 29.6 led to the sequencing of over 99.0% of the virus genome, indicating high genome coverage even at high Ct values. This protocol enables the identification of hRSV subgroup A genotypes, as primers were designed to target highly conserved regions. Consequently, it holds potential for application in molecular epidemiology and surveillance of this hRSV subgroup.

Evaluating the efficacy of endolysins and membrane permeabilizers against Vibrio parahaemolyticus in marine conditions

Endolysins have garnered significant attention as a potential alternative to antibiotics in aquaculture, mainly for combating Vibrio spp., Gram-negative pathogens responsible for infectious outbreaks. However, endolysin effectiveness against Gram-negative bacteria is limited due to the outer membrane's poor permeability. The combat against marine pathogens poses an additional challenge of finding endolysins that retain their activity in high ionic strength conditions. Thus, this study aimed to demonstrate that certain endolysins retain muralytic activity in seawater and also evaluated outer membrane permeabilizers as endolysin adjuvants. The effectiveness of KZ144 and LysPA26 endolysins, along with EDTA and oregano essential oil, was evaluated against Vibrio parahaemolyticus ATCC-17802 in natural seawater. Results revealed the muralytic activity of both endolysins in seawater. However, the endolysins appeared to counteract the permeabilizers' effect during the initial bactericidal assays. Further investigations revealed that the observed effect was not antagonistic. After the permeabilizer action, V. parahaemolyticus likely used endolysins as a growth substrate. Endolysins may not play an indifferent role if they fail to exert a bactericidal effect. Instead, they can serve as a substrate for fast-growing bacteria, such as V. parahaemolyticus, increasing bacterial density. It should be considered a potential drawback of endolysins' proteinaceous nature as bactericidal agents.

RT-qPCR Assays for Rapid Detection of the N501Y, 69-70del, K417N, and E484K SARS-CoV-2 Mutations: A Screening Strategy to Identify Variants With Clinical Impact

Background

Several variants of the SARS-CoV-2 have been documented globally during the current COVID-19 pandemic. The N501Y, 69-70del, K417N, and E484K SARS-CoV-2 mutations have been documented among the most relevant due to their potential pathogenic biological effects. This study aimed to design, validate, and propose a fast real-time RT-qPCR assay to detect SARS-CoV-2 mutations with possible clinical and epidemiological relevance in the Mexican population.

Methods

Targeting spike (S) gene mutations of SARS-CoV-2 (N501Y, 69-70del, K417N, and E484K), specific primers, and probes for three specific quantitative reverse transcription PCR (RT-qPCR) assays were designed, and validated using Sanger sequencing. These assays were applied in clinical samples of 1060 COVID-19 patients from Jalisco Mexico.

Results

In silico analyzes showed high specificity of the three assays. Amplicons of samples were confirmed through sequencing. The screening of samples of COVID-19 patients allowed the identification of the E484K mutation in nine individuals and the identification of P.2 Brazilian variant in Mexico.

Conclusion

This work provides low-cost RT-qPCR assays for rapid screening and molecular surveillance of mutations with potential clinical impact. This strategy allowed the detection of E484K mutation and P.2 variant for the first time in samples from the Mexican population.

RT-qPCR Assays for Rapid Detection of the N501Y, 69-70del, K417N, and E484K SARS-CoV-2 Mutations: A Screening Strategy to Identify Variants With Clinical Impact

BACKGROUND

Several variants of the SARS-CoV-2 have been documented globally during the current COVID-19 pandemic. The N501Y, 69-70del, K417N, and E484K SARS-CoV-2 mutations have been documented among the most relevant due to their potential pathogenic biological effects. This study aimed to design, validate, and propose a fast real-time RT-qPCR assay to detect SARS-CoV-2 mutations with possible clinical and epidemiological relevance in the Mexican population.

METHODS

Targeting spike (S) gene mutations of SARS-CoV-2 (N501Y, 69-70del, K417N, and E484K), specific primers, and probes for three specific quantitative reverse transcription PCR (RT-qPCR) assays were designed, and validated using Sanger sequencing. These assays were applied in clinical samples of 1060 COVID-19 patients from Jalisco Mexico.

RESULTS

In silico analyzes showed high specificity of the three assays. Amplicons of samples were confirmed through sequencing. The screening of samples of COVID-19 patients allowed the identification of the E484K mutation in nine individuals and the identification of P.2 Brazilian variant in Mexico.

CONCLUSION

This work provides low-cost RT-qPCR assays for rapid screening and molecular surveillance of mutations with potential clinical impact. This strategy allowed the detection of E484K mutation and P.2 variant for the first time in samples from the Mexican population.

Natural genetic transformation of Vibrio parahaemolyticus via pVA1 plasmid acquisition as a potential mechanism causing AHPND

Vibrio parahaemolyticus is the causative bacterium of acute hepatopancreatic necrosis disease (AHPND) in white shrimp Litopenaeus vannamei. This bacterium secretes protein toxins whose genes are encoded in an auto-transmissible plasmid called pVA1. The presence of this plasmid in V. parahaemolyticus is determinant for disease development. Its propagation is not only linked to bacterial colonisation capacity but also to horizontal gene transfer mechanisms. Nevertheless, the active uptake of plasmid, which is known as natural genetic transformation (NGT), has not yet been proposed as a possible acquisition mechanism of the pVA1 plasmid among Vibrio species. Previous studies suggest that some Vibrio species have the ability to undergo NGT in the presence of chitin. Therefore, the objective of this study was to evaluate the induction of NGT mediated by chitin in V. parahaemolyticus (ATCC-17802) through its ability to incorporate and express the pVA1 plasmid. The results showed that a reference strain that does not initially contain the plasmid can incorporate the plasmid under the appropriate transformation conditions, and cause mortality in white shrimp similar to that observed for pathogenic strains isolated from infectious outbreaks. Given the management and conditions of a shrimp farm with large amounts of chitinous exoskeletons, it is feasible that NGT could be a possible acquisition mechanism of plasmid pVA1 among Vibrio species, turning a non-causative strain of V. parahaemolyticus into a causative strain. With this study, we have expanded the knowledge of the pathogenesis process mediated by NGT and the understanding of the possible propagation mechanisms of emerging diseases in the aquaculture sector.