Background: Pandemic type A (H1N1) influenza arose in early 2009, probably in Mexico and the United States, and reappeared in North America in September for seven more months. An amino acid substitution in the hemagglutinin (HA), D222G, has been reported in a significant proportion of patients with a severe and fatal outcome. We studied the prevalence of HA222 substitutions in patients in Mexico during the second wave and its association with clinical outcome and pathogenicity in a mouse model. Methods: The nucleotide sequences of hemagglutinin (HA) from viruses collected from 77 patients were determined including 50 severe and fatal cases and 27 ambulatory cases. Deep sequencing was done on 5 samples from severe or fatal cases in order to determine the quasispecies proportion. Weight loss and mortality due to infection with cultured influenza viruses were analyzed in a mouse model. Results: Viruses from 14 out of 50 hospitalized patients (28%) had a non aspartic acid residue at the HA 222 position (nD222), while all 27 ambulatory patients had D222 (p = 0.0014). G222 was detected as sole species or in coexistence with N222 and D222 in 12 patients with severe disease including 8 who died. N222 in coexistence with D222 was detected in 1 patient who died and co-occurrence of A222 and V222, together with D222, was detected in another patient who died. The patients with a nD222 residue had higher mortality (71.4%), compared to the group with only D222 (22.2%, p = 0.0008). Four of the 14 viruses from hospitalized patients were cultured and intranasally infected into mice. Two viruses with G222 were lethal while a third virus, with G222, caused only mild illness in mice similar to the fourth virus that contained D222. Conclusions: We confirm the elevated incidence of HA222 (H1N1)pdm09 variants in severe disease and mortality. Both clinical and mouse infection data support the idea that nD222 mutations contribute to increased severity of disease but additional determinants in disease outcome may be present.

Whole genome sequencing (WGS) has emerged as a powerful tool to facilitate the study of existing and emerging infectious diseases. WGS-based genomic surveillance provides information on the genetic diversity and tracks the evolution of important viral pathogens, including respiratory syncytial virus (RSV). Multiplex tiling polymerase chain reaction (PCR) assays have been used to facilitate sequencing of a variety of pathogens in support of genomics-based surveillance initiatives. We developed, optimized, and implemented multiplex tiling PCR assays for RSVA and RSVB capable of generating near-complete genomes in the majority of contemporaneous specimens tested. A pilot data set comprising 52 RSVA and 37 RSVB genomes derived from Canadian clinical specimens during the 2022–2023 respiratory virus season was used to perform phylogenetic analyses using both near-complete genome and glycoprotein (G) sequences. Overall, the RSV phylogenetic tree built with whole genomes showed identical lineage clusters as compared to the G gene but was more discriminatory. Moreover, the availability of complete genomes enables the identification of a broader range of mutations. For instance, mutations identified in the fusion protein among Canadian isolates tested here, including S377N, K272M, S276N, S211N, S206I, and S209Q, could affect the efficacy of current vaccines or antiviral-based therapeutics. In conclusion, our work reinforces other recent studies demonstrating the utility of multiplex tiling PCR assays to facilitate high-throughput WGS of RSV, which is capable of supporting enhanced genomic surveillance initiatives, as well as the more comprehensive genomic analyses required to inform public health strategies for the development and usage of vaccines and antiviral drugs. IMPORTANCE: We present assays to efficiently sequence genomes of RSVA and RSVB. This enables researchers and public health agencies to acquire high-quality genomic data using rapid and cost-effective approaches. Genomic data-based comparative analysis can be used to conduct surveillance and monitor circulating isolates for efficacy of vaccines and antiviral therapeutics.

Since 2020, the Gs/Gd H5N1 influenza virus (clade 2.3.4.4b) has established itself within wild bird populations across Asia, Europe, and the Americas, causing outbreaks in wild mammals, commercial poultry, and dairy farms. The impacts on the bird populations and the agricultural industry has been significant, requiring a One Health approach to enhanced surveillance in both humans and animals. To support pandemic preparedness efforts, we evaluated the Cepheid Xpert Xpress CoV-2/Flu/RSV plus kit and the BioFire Respiratory 2.1 Panel for their ability to detect the presence of non-seasonal, zoonotic influenza A viruses, including circulating H5N1 viruses from clade 2.3.4.4b. Both assays effectively detected the presence of influenza virus in clinically-contrived nasal swab and saliva specimens at low concentrations. The results generated using the Cepheid Xpert Xpress CoV-2/Flu/RSV plus kit and the BioFire Respiratory 2.1 Panel, in conjunction with clinical and epidemiological findings provide valuable diagnostic findings that can strengthen pandemic preparedness and surveillance initiatives.

Since 2020, the Gs/Gd H5N1 influenza virus (clade 2.3.4.4b) has established itself within wild bird populations across Asia, Europe, and the America’s, causing outbreaks in wild mammals, commercial poultry, and dairy farms. The impacts on the bird populations and the agricultural industry has been significant, requiring an One Health approach to enhanced surveillance in both humans and animals. To support pandemic preparedness efforts, we evaluated the Cepheid Xpert Xpress CoV-2/Flu/RSV plus kit and the BioFire Respiratory 2.1 Panel for their ability to detect the presence of non-seasonal, zoonotic influenza A viruses, including circulating H5N1 viruses from clade 2.3.4.4b. Both assays effectively detected the presence of influenza virus in clinically-contrived nasal swab and saliva specimens at low concentrations. The results generated using the Cepheid Xpert Xpress CoV-2/Flu/RSV plus kit and the BioFire Respiratory 2.1 Panel, in conjunction with clinical and epidemiological findings provide valuable diagnostic findings that can strengthen pandemic preparedness and surveillance initiatives.

Whole genome sequencing is increasingly being deployed to support respiratory virus influenza clinical studies and surveillance. However, PCR amplification inefficiency results in an imbalanced distribution among the eight segments, which makes it challenging to obtain complete genomes. The difficulties of amplifying the longer polymerase genes, particularly when the cycle threshold (Ct) of a specimen is greater than 25, were highlighted by the whole genome sequencing (WGS) data of 109 influenza A virus (IAV) specimens. We addressed the low genome coverage of the PB1 segment by incorporating additional singleplex PB1 primers into the WGS PCR assay, as well as balancing the ratio of forward primer variants targeting a single nucleotide polymorphism - either uracil (U) or cytosine (C) - located at the 4th position of the promoter region at the 3' terminus. Furthermore, we have verified the improved performance of the Invitrogen™ UniPrime™ enzyme when compared to its predecessor, SuperScript IV™, and developed a more efficient thermal cycling condition ("C") to generate eight complete IAV segments. Lastly, we determined that the optimal amplicon-to-bead volume ratio for removal of shorter, unwanted DNA fragments during PCR amplicon purification is 1:0.5. In summary, these optimizations improve the recovery of lower coverage segments and provide strategies aimed at obtaining high quality IAV genomes by means of Oxford Nanopore Technologies-based sequencing, ultimately providing valuable insights for better serving influenza clinical research and surveillance.

Pathogen genomic surveillance is globally recognized as a pillar of public health. This field has expanded rapidly following the onset of the coronavirus disease 2019 (COVID-19) pandemic, and there is an urgent need to ensure the quality, comparability and reliability of the results of genomic analyses across diverse settings and analytical platforms. Currently, no methodology or framework has been universally adopted to mitigate this issue. This study aimed to provide a solution within the Canadian public health landscape by using standardized test datasets for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomic analysis. In this context, a test dataset refers to a curated set of genomic sequences designed to evaluate the accuracy, consistency and performance of sequencing workflows, bioinformatics pipelines and analytical tools. These datasets serve as benchmarks, allowing laboratories to validate their methodologies and ensure comparability across different platforms. The test datasets included in this analysis were selected based on the use of well-characterized experimental protocols from the application of specimen selection criteria, through to sequence generation. Datasets generated using Illumina and Nanopore sequencing of samples from COVID-19 patients in Saskatchewan, Canada, were used and included clean controls, variable lineages and spiked-in lower-quality run data. Illumina libraries were sequenced using ARTIC network PCR amplification, while Nanopore libraries underwent similar protocols with some modifications. Public test dataset access on Zenodo further facilitates reproducibility, providing data summary outputs and pipeline environment files. A customized R script was developed to compare Illumina data, generating multiple tables and figures highlighting comparisons between analyses. The significance of this study lies in its contribution to the implementation of bioinformatic pipeline validation tools and protocols, which are essential for reliable genomic surveillance and outbreak response. By establishing a structured framework for computational validation, this study enhances the accuracy, comparability and efficiency of genomic surveillance in an evolving landscape of viral strains and testing strategies.