The Seasonality of Respiratory Viruses in a Hong Kong Hospital, 2014–2023

Chan, Wai-Sing; Yau, Siu-Kei; To, Man-Yan; Leung, Sau-Man; Wong, Kan-Pui; Lai, Ka-Chun; Wong, Ching-Yan; Leung, Chin-Pang; Au, Chun-Hang; Wan, Thomas Shek-Kong; Ma, Edmond Shiu-Kwan; Tang, Bone Siu-Fai

doi:10.3390/v15091820

Cited by 8 publications

(5 citation statements)

References 13 publications

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“…RSV A/B, SARS-CoV-2, and InfA were other frequently detected viruses. Consistent with this study, many studies have also reported that rhinovirus is the most common respiratory pathogen [ 6 , 7 , 8 , 9 , 10 ]. Unlike most pathogens that cause respiratory infections, RV/EV is non-enveloped and is, therefore, resistant to environmental conditions and disinfectants, and can remain on surfaces for a long time.…”

Section: Discussionsupporting

confidence: 90%

The Epidemiological Features and Pathogen Spectrum of Respiratory Tract Infections, Istanbul, Türkiye, from 2021 to 2023

Karabulut,

Alaçam,

Şen

et al. 2024

Diagnostics

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Respiratory tract infections (RTIs) can lead to both recurrent seasonal epidemic outbreaks and devastating pandemics. The aim of this study was to evaluate the epidemiologic characteristics and pathogen spectrum of RTIs using a multiplex RT-PCR panel. A total of 9354 cases with suspected RTIs between February 2021 and July 2023 were included in this study. A total of 11,048 nasopharyngeal and oropharyngeal samples from these patients were analyzed for 23 respiratory tract pathogens using multiplex RT-PCR. H. influenzae and S. pneumoniae were considered as colonizing bacteria. At least one pathogen was detected in 70.66% of the samples; viral pathogens were detected in 48.41% of the samples, bacterial pathogens were detected in 16.06% of the samples, and viral + bacterial pathogens were detected in 35.53% of the samples. The most frequently detected viral pathogen was rhinovirus/enterovirus (RV/EV) (19.99%). Interestingly, in 2021, respiratory syncytial virus A/B showed atypical activity and replaced RV/EV as the most prevalent pathogen. Human bocavirus, H. influenzae, and S. pneumoniae were detected at higher rates in males (p: 0.038, p: 0.042, and p: 0.035, respectively), while SARS-CoV-2 and B. pertussis were detected at higher rates in females (p < 0.001 and p: 0.033). RTIs were found at higher rates in children (p < 0.001). SARS-CoV-2 and human coronaviruses 229E were detected at higher rates in adults (p < 0.001 and p: 0.001). This comprehensive study with a large sample size investigating RTI pathogens was the first in Türkiye. Understanding the current viral circulation using multiplex RT-PCR panels enables clinicians to predict the most likely pathogens affecting patients and contributes to patient management, in addition to anticipating potential threats.

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Section: Discussionsupporting

confidence: 90%

The Epidemiological Features and Pathogen Spectrum of Respiratory Tract Infections, Istanbul, Türkiye, from 2021 to 2023

Karabulut,

Alaçam,

Şen

et al. 2024

Diagnostics

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“…Children comprised the majority (89/146, 60.96%), followed by adults (25/146, 17.12%) and older adults (19/146, 13.01%). The pattern was similar to the patient population tested with the RP2.1plus in 2022 and the first quarter of 2023 [19]. Male patients (82/146, 56.16%) or inpatients (76/146, 52.05%) were slightly more in number than female (64/146, 43.84%) or outpatients (70/146, 47.95%), respectively.…”

Section: Patient Demographicssupporting

confidence: 69%

“…From the late COVID-19 pandemic, a rebound in the activities of non-SARS-CoV-2 respiratory pathogens has been observed worldwide [ 19 , 20 , 21 , 22 , 23 , 24 ]. In clinical laboratories, the attention and resources have been shifting from SARS-CoV-2 detection to multiplex detection of SARS-CoV-2 plus other respiratory pathogens.…”

Section: Discussionmentioning

confidence: 99%

Clinical Evaluation of the BIOFIRE SPOTFIRE Respiratory Panel

Chan,

Ho,

Chan

et al. 2024

Viruses

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The BIOFIRE SPOTFIRE Respiratory (R) Panel is a novel, in vitro diagnostic PCR assay with 15 pathogen targets. The runtime is about 15 min which is the shortest among similar panels in the market. We evaluated the performance of the SPOTFIRE R Panel with 151 specimens, including 133 collected from the upper respiratory tract (URT), 13 from the lower respiratory tract (LRT) and 5 external quality assessment program (EQAP) samples. The respiratory specimens were enrolled throughout the first two post-COVID-19 influenza seasons in Hong Kong (March to December 2023). For URT specimens, full concordance was observed between the SPOTFIRE R Panel and the standard-of-care FilmArray Respiratory 2.1 plus Panel (RP2.1plus) for 109 specimens (109/133, 81.95%). After discrepant analysis, the SPOTFIRE R Panel identified more pathogens than the RP2.1plus in 15 specimens and vice versa in 3 specimens. The per-target negative and positive percentage agreement (NPA and PPA) were 92.86–100% except the PPA of adenovirus (88.24%). For LRT and EQAP samples, all results were fully concordant. To conclude, the performance of the SPOTFIRE R Panel was comparable to the RP2.1plus.

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“…For this study specifically, we chose individuals within each of the groups who had an HAI titer of <10 against the A/Hawaii/70/2019 (H1N1) vaccine strain prior to vaccination in year 1 (2020-2021); this criterion means that the study focuses on individuals with relatively low initial titers. None of the participants were infected with influenza during the study time frame because there was minimal influenza circulation at the study site in Hong Kong between the initial 2020-2021 blood draw and the 2021-2022 blood draws due to COVID-19 mitigation measures (27,28). We analyzed sera collected immediately before (day 0) and approximately 30 days after the participants were given the 2021-2022 vaccine (Fig.…”

Section: Resultsmentioning

confidence: 99%

High-throughput sequencing-based neutralization assay reveals how repeated vaccinations impact titers to recent human H1N1 influenza strains

Loes,

Tarabi,

Huddleston

et al. 2024

Preprint

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The high genetic diversity of influenza viruses means that traditional serological assays have too low throughput to measure serum antibody neutralization titers against all relevant strains. To overcome this challenge, we have developed a sequencing-based neutralization assay that simultaneously measures titers against many viral strains using small serum volumes via a workflow similar to traditional neutralization assays. The key innovation is to incorporate unique nucleotide barcodes into the hemagglutinin (HA) genomic segment, and then pool viruses with numerous different barcoded HA variants and quantify infectivity of all of them simultaneously using next-generation sequencing. With this approach, a single researcher performed the equivalent of 2,880 traditional neutralization assays (80 serum samples against 36 viral strains) in approximately one month. We applied the sequencing-based assay to quantify the impact of influenza vaccination on neutralization titers against recent human H1N1 strains for individuals who had or had not also received a vaccine in the previous year. We found that the viral strain specificities of the neutralizing antibodies elicited by vaccination vary among individuals, and that vaccination induced a smaller increase in titers for individuals who had also received a vaccine the previous year--although the titers six months after vaccination were similar in individuals with and without the previous-year vaccination. We also identified a subset of individuals with low titers to a subclade of recent H1N1 even after vaccination. This study demonstrates the utility of high-throughput sequencing-based neutralization assays that enable titers to be simultaneously measured against many different viral strains. We provide a detailed experimental protocol (DOI: dx.doi.org/10.17504/protocols.io.kqdg3xdmpg25/v1) and a computational pipeline (https://github.com/jbloomlab/seqneut-pipeline) for the sequencing-based neutralization assays to facilitate the use of this method by others.

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The Seasonality of Respiratory Viruses in a Hong Kong Hospital, 2014–2023

Cited by 8 publications

References 13 publications

The Epidemiological Features and Pathogen Spectrum of Respiratory Tract Infections, Istanbul, Türkiye, from 2021 to 2023

The Epidemiological Features and Pathogen Spectrum of Respiratory Tract Infections, Istanbul, Türkiye, from 2021 to 2023

Clinical Evaluation of the BIOFIRE SPOTFIRE Respiratory Panel

High-throughput sequencing-based neutralization assay reveals how repeated vaccinations impact titers to recent human H1N1 influenza strains

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