Impact of Viral Co-Detection on the Within-Host Viral Diversity of Influenza Patients
Abstract
:1. Introduction
2. Methods
2.1. Study Design
2.2. Sample Collection and Virus Identification
2.3. Library Preparation and Whole-Genome Sequencing
2.4. Phylogenetic Analysis
2.5. Identification of Intra-Host Single-Nucleotide Variants (iSNVs)
2.6. Statistical Analysis
3. Results
3.1. Study Cohort and ILI Incidence
3.2. Influenza and Rhinoviruses Were Most Commonly Detected and Were a Frequently Co-Detected Pair of Viruses
3.3. Whole-Genome Sequencing of RT-PCR-Confirmed Influenza A Viruses
3.4. Identification of Clustering by Viral Co-Detection Status on Phylogeny
3.5. Intra-Host Diversity in Influenza-Only Cases Versus Virus Co-Detected Cases
3.6. Factors Associated with the Number of iSNVs Found in A/H3N2 WGS Samples
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Characteristics | N (%) |
---|---|
Number of ILI episodes | 2407 |
Age group | |
<6 | 546 (22.7) |
6–18 | 707 (29.3) |
19–64 | 693 (28.8) |
≥65 | 450 (18.7) |
Total sampled | 2305 |
By pathogen identification | |
Influenza A (IAV) | 538 (23.3) |
Influenza B (IBV) | 22 (0.9) |
Human rhinovirus (hRV) | 264 (11.5) |
Human metapneumovirus (hMPV) | 8 (0.4) |
Parainfluenza virus (I-IV) (PIV I-IV) | 43 (1.9) |
Respiratory syncytial virus (RSV) | 20 (0.9) |
Human coronavirus (OC43, 229E) (hCOV) | 14 (0.6) |
Adenovirus (AdV) | 44 (1.9) |
Bocavirus (BoV) | 26 (1.1) |
By number of viruses detected | |
Single virus infection | 777 (33.7) |
No virus detected | 1427 (61.9) |
Multiple infections | |
2 viruses | 96 (4.2) |
>2 viruses | 5 (0.2) |
Virus Detected | hRV | PIV | hCoV | hMPV | RSV | IBV | AdV | BoV | IAV |
---|---|---|---|---|---|---|---|---|---|
hRV | 264 | 5 | 0 | 1 | 0 | 6 | 8 | 4 | 48 |
PIV | 43 | 0 | 0 | 0 | 0 | 0 | 0 | 4 | |
hCoV | 14 | 0 | 0 | 0 | 0 | 1 | 2 | ||
hMPV | 8 | 0 | 1 | 0 | 0 | 0 | |||
RSV | 20 | 1 | 0 | 0 | 11 | ||||
IBV | 22 | 0 | 0 | 4 | |||||
AdV | 44 | 0 | 7 | ||||||
BoV | 26 | 3 | |||||||
IAV | 538 |
Pair | Observed | Expected | Odd Ratios | p-Value * |
---|---|---|---|---|
hRV & PIV | 5 | 5 | 0.90 (0.28–2.31) | 1.000 |
hRV & hCoV | 0 | 2 | 0.27 (0.00–2.34) | 0.391 |
hRV & hMPV | 1 | 1 | 0.97 (0.02–7.26) | 1.000 |
hRV & RSV | 0 | 2 | 0.19 (0.00–2.34) | 0.156 |
hRV & IBV | 6 | 3 | 2.09 (0.69–5.38) | 0.129 |
hRV & AdV | 8 | 5 | 1.38 (0.64–2.96) | 0.544 |
hRV & BoV | 4 | 3 | 1.18 (0.30–3.43) | 0.772 |
hRV & IAV | 48 | 61 | 0.11 (0.08–0.14) | <0.001 |
PIV & Adeno | 0 | 1 | 0.59 (0.00–4.85) | 1.000 |
PIV & IAV | 4 | 10 | 0.31 (0.11–0.86) | 0.014 |
hCoV & BoV | 1 | 0 | 6.24 (0.14–44.04) | 0.162 |
hCoV & IAV | 2 | 3 | 0.47 (0.05–2.05) | 0.389 |
hMPV & IBV | 1 | 0 | 12.92 (0.28–103.77) | 0.086 |
hMPV & IAV | 0 | 2 | 0.19 (0.00–1.93) | 0.211 |
RSV & IBV | 1 | 0 | 5.16 (0.12–35.31) | 0.190 |
RSV & IAV | 11 | 5 | 1.79 (0.85–3.75) | 0.136 |
IBV & IAV | 4 | 5 | 0.59 (0.20–1.73) | 0.484 |
AdV & IAV | 7 | 10 | 0.51 (0.23–1.14) | 0.131 |
BoV & IAV | 3 | 6 | 0.38 (0.11–1.24) | 0.121 |
Characteristics | Only Influenza (n = 110) | Viral Co-Detection (n = 40) |
---|---|---|
Age group | ||
<6 | 8 | 5 |
6–18 | 41 | 12 |
19–65 | 52 | 18 |
≥65 | 6 | 4 |
Sex | ||
Male | 52 | 15 |
Female | 58 | 25 |
Vaccination status | ||
Vaccinated | 80 | 26 |
Unvaccinated | 29 | 14 |
Location/Region | ||
Narao | 2 | 2 |
Arikawa | 38 | 13 |
Shinuonome | 23 | 4 |
Kamigoto | 31 | 13 |
Wakamatsu | 14 | 51 |
WGS (passed variant calling criteria) | 99 | 33 |
Segment | Number of Minor iSNVs | Mean (SD) Minor iSNVs Frequency of Occurence (SD) | ||||||||
---|---|---|---|---|---|---|---|---|---|---|
Flu Only (n = 99) | Flu–Other Viruses (n = 33) | Bonferroni-Adjusted p-Value | Flu Only (n = 99) | Flu–Other Viruses (n = 33) | Bonferroni-Adjusted p-Value | |||||
Total Number | Mean (SD)/Subject | Total Number | Mean (SD)/Subject | Max Freq/Site | Mean (SD)/Site | Max Freq | Mean (SD)/Site | |||
PB2 | 45 | 1.80 (0.99) | 17 | 1.59 (0.71) | 0.698 | 8 | 0.27 (0.68) | 3 | 0.20 (0.46) | 0.700 |
PB1 | 38 | 1.40 (0.75) | 11 | 2.00 (1.00) | 0.192 | 3 | 0.18 (0.45) | 2 | 0.16 (0.39) | 0.980 |
PA | 51 | 1.78 (1.56) | 18 | 1.44 (0.92) | 0.219 | 3 | 0.31 (0.55) | 1 | 0.19 (0.40) | 0.328 |
HA | 34 | 1.59 (0.93) | 13 | 1.85 (1.57) | 0.164 | 15 | 0.18 (1.03) | 2 | 0.18 (0.40) | 0.328 |
NP | 41 | 1.95 (1.30) | 9 | 1.44 (1.01) | 0.416 | 19 | 0.27 (1.57) | 3 | 0.10 (0.39) | 0.576 |
NA | 34 | 1.21 (0.41) | 12 | 1.08 (0.29) | 0.545 | 14 | 0.13 (0.94) | 3 | 0.10 (0.37) | 0.663 |
M | 19 | 1.05 (0.23) | 9 | 1.22 (0.44) | 0.244 | 11 | 0.07 (0.66) | 3 | 0.08 (0.37) | 0.531 |
NS | 33 | 1.24 (0.50) | 11 | 1.18 (0.41) | 0.802 | 23 | 0.14 (1.35) | 3 | 0.10 (0.39) | 0.629 |
Characteristics | N = 132 | IRR 1 (95% Confidence Interval) | Bonferroni-Adjusted p-Value |
---|---|---|---|
Age group | |||
19–64 | 63 | 1 | |
<6 | 13 | 0.85 (0.51–1.43) | 1.000 |
6–18 | 46 | 1.38 (1.01–1.90) | 0.280 |
>64 | 10 | 1.80 (1.09–3.06) | 0.173 |
Vaccination status | |||
Non-vaccinated | 37 | 1 | |
Vaccinated | 94 | 0.94 (0.68–1.30) | 1.000 |
Gender | |||
Female | 62 | 1 | |
Male | 70 | 0.98 (0.73–1.30) | 1.000 |
Days post-symptoms | 0.93 (0.83–1.02) | 0.547 | |
Viral co-detection | |||
Only influenza | 99 | 1 | |
Virus co-detected | 33 | 0.90 (0.65–1.26) | 1.000 |
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Han, S.M.; Kubo, Y.; Robert, A.; Baguelin, M.; Ariyoshi, K. Impact of Viral Co-Detection on the Within-Host Viral Diversity of Influenza Patients. Viruses 2025, 17, 152. https://doi.org/10.3390/v17020152
Han SM, Kubo Y, Robert A, Baguelin M, Ariyoshi K. Impact of Viral Co-Detection on the Within-Host Viral Diversity of Influenza Patients. Viruses. 2025; 17(2):152. https://doi.org/10.3390/v17020152
Chicago/Turabian StyleHan, Su Myat, Yoshiano Kubo, Alexis Robert, Marc Baguelin, and Koya Ariyoshi. 2025. "Impact of Viral Co-Detection on the Within-Host Viral Diversity of Influenza Patients" Viruses 17, no. 2: 152. https://doi.org/10.3390/v17020152
APA StyleHan, S. M., Kubo, Y., Robert, A., Baguelin, M., & Ariyoshi, K. (2025). Impact of Viral Co-Detection on the Within-Host Viral Diversity of Influenza Patients. Viruses, 17(2), 152. https://doi.org/10.3390/v17020152