The retrospective study combined descriptive and analytical components using 24 consecutive months of data from the national respiratory pathogen sentinel network. Participating institutions were tertiary general hospitals in Chengdu, Dazhou, Nanchong, Mianyang, Panzhihua, Zigong and Ya’an, representing the Chengdu Plain, northeastern, northern, southern and Panxi areas of Sichuan. The study population combined 14,970 outpatient or emergency cases of influenza-like illness, defined by fever with cough or sore throat within three days of onset, and 7,466 hospitalized patients with severe acute respiratory infection. Respiratory specimens were tested simultaneously for SARS-CoV-2 and influenza virus using a 17-target microfluidic multiplex real-time RT-PCR assay. SARS-CoV-2 was targeted through the ORF1ab and N genes, while conserved M and NP targets detected influenza A and B, with additional targets distinguishing A(H3), A(H1N1)pdm09, B/Victoria and B/Yamagata.

Of 25,624 records initially exported from the surveillance system, 3,188 came from institutions outside the seven designated hospitals and were excluded; after deduplication and completeness verification, 22,436 valid cases remained. Results were reported as positive when the cycle threshold was below 37, while samples with values from 37 to less than 40 were retested using the original specimen. Retested samples with a cycle threshold of at least 40 were classified as negative, and specimens that remained in the borderline range were treated as suspicious and excluded. Positive, negative and blank controls accompanied each batch, and the network laboratory regularly participated in national and provincial external quality assessments with satisfactory results. Wilson score intervals were used to estimate 95% confidence intervals, while multivariable logistic regression examined associations with age, sex, season, case type and region.

Seasonality was the clearest division between the viruses. SARS-CoV-2 positivity ranged from zero to 17.46% by month and followed a summer-centered pattern, with peaks in July and August 2024 and from May through July 2025. Its highest monthly rate occurred in June 2025, when 17.46% of cases tested positive. Influenza followed a winter–spring pattern, with peaks from December 2024 to January 2025 and from November to December 2025; its highest monthly positivity, 40.30%, occurred in December 2025. Multivariable analysis showed that summer carried much higher odds of SARS-CoV-2 positivity than winter, with an odds ratio of 23.88 and a 95% confidence interval of 17.04 to 33.46. The reverse pattern was evident for influenza, for which summer had substantially lower odds than winter, with an odds ratio of 0.16 and a 95% confidence interval of 0.14 to 0.19.

The age profiles also differed. SARS-CoV-2 positivity was highest among people aged 15 to 34 years, at 7.69%, compared with 3.23% in children aged 0 to 5, 4.45% among those aged 6 to 14, 4.84% at ages 35 to 59 and 3.02% among adults aged 60 or older. In the adjusted model, the 15-to-34 group had 2.32 times the odds of SARS-CoV-2 positivity as the youngest group. Influenza positivity was highest among children aged 6 to 14, reaching 15.17%, compared with 6.15% in those aged 0 to 5, 13.37% at ages 15 to 34, 9.76% at ages 35 to 59 and 6.67% among adults aged 60 or older. The adjusted odds ratio for the 6-to-14 group relative to the 0-to-5 group was 2.52, with a 95% confidence interval of 2.21 to 2.88. Sex differences were modest: female patients had a slightly higher SARS-CoV-2 positivity rate than male patients, while influenza detection did not differ significantly by sex.

Influenza A accounted for 87.5% of the 2,205 influenza-positive cases, including 1,045 A(H3) and 875 A(H1N1)pdm09 infections. Influenza B represented 12.5% of positive cases, almost all of them B/Victoria, with no B/Yamagata detections during the study period. Other respiratory targets were also identified by the multiplex panel: Haemophilus influenzae was detected in 15.59% of cases, Streptococcus pneumoniae in 10.98%, rhinovirus in 8.79% and respiratory syncytial virus in 4.15%. These findings concern nucleic-acid detection across the full study population, not the subset testing positive for either influenza virus, and the analysis did not evaluate interactions involving these other detected pathogens.

Regional measurements showed substantial geographic heterogeneity. SARS-CoV-2 positivity ranged from 3.23% in Chengdu to 6.03% in Zigong, while Panzhihua also had a comparatively high rate of 5.38%. Influenza positivity ranged from 6.12% in Ya’an to 13.07% in Dazhou, with Zigong close behind at 12.98%. In the adjusted model, several regions had higher odds of influenza positivity than Nanchong, including Dazhou, with an odds ratio of 2.53, and Zigong, with an odds ratio of 2.37. Regional contrasts describe differences among the sentinel populations during this observation period; because the study included no province-wide pre-pandemic dual-pathogen surveillance baseline, the data cannot establish how the distributions changed relative to earlier years.

The 11 coinfections occurred during months in which both viruses were detected, but they were far below the level predicted by independent circulation. Six occurred in August 2024, the only month in which SARS-CoV-2 positivity exceeded 5% and influenza positivity exceeded 10%. The other five occurred in December 2025, May 2026 and July 2026. Coinfections were more frequent during the concurrent-circulation month: six of 770 cases, or 0.78%, compared with five among 21,666 cases, or 0.02%, in other months, yielding an odds ratio of 34.02 and a 95% confidence interval of 8.62 to 141.16. Even in August 2024, however, the observed number was below the approximately 13 coinfections expected under independence. Seven of the 11 cases came from Dazhou, where the coinfection rate was 0.21%, significantly higher than in the other sentinel cities. The clustering may reflect genuine local overlap, but the small number of events means it cannot exclude clustering related to specimen submission or testing batches.

The findings do not establish that viral interference caused the negative association. Viral interference, in which one virus induces innate immune responses that inhibit another, provides one possible biological mechanism, and the authors cited experimental evidence that influenza A can enhance SARS-CoV-2 infectivity at the cellular level. Those in vitro observations operate at a different scale from population surveillance: staggered epidemic peaks reduce opportunities for people to encounter both viruses at once, potentially explaining the observed O/E ratio without requiring an individual-level interaction. The analysis was ecological and could not distinguish temporal separation in co-exposure opportunities from direct interference. It also did not include vaccination history, underlying disease or clinical outcomes, so the study could not assess whether coinfection affected illness severity. Its urban, hospital-based sampling further limits generalization because the network poorly represented rural residents, community cases and asymptomatic infections.

Overall, the surveillance data indicate that Sichuan’s two major respiratory viruses followed separate seasonal paths during the two-year window: SARS-CoV-2 was concentrated in summer and among people aged 15 to 34, whereas influenza peaked in winter and spring and was most frequent among children aged 6 to 14. Dual infection remained uncommon, with no population-level evidence of synergistic circulation, despite local and temporal clustering. The authors recommend pathogen- and region-specific surveillance, including simultaneous testing where concurrent circulation is detected, and note that combining pathogen data with information on population immunity, mobility and weather could improve early-warning capacity. These recommendations are prospective implications of the study rather than evidence that the reported interventions have already reduced transmission.

Subject of Research: Seasonal patterns and coinfection of SARS-CoV-2 and influenza virus in Sichuan sentinel surveillance

Article Title: Analysis of multiplex pathogen sentinel surveillance results of SARS-CoV-2 and influenza virus in Sichuan Province, 2024–2026

Article References: Hu, F., Zhou, X., Zhou, L., Li, Z., Dong, S., & Xiao, C. (2026). Analysis of multiplex pathogen sentinel surveillance results of SARS-CoV-2 and influenza virus in Sichuan Province, 2024–2026. Frontiers in Public Health, 14, Article 1961515. https://doi.org/10.3389/fpubh.2026.1961515

Image Credits: AI Generated

DOI: 10.3389/fpubh.2026.1961515

Keywords: SARS-CoV-2, influenza virus, viral coinfection, seasonal surveillance, multiplex RT-PCR, Sichuan Province, acute respiratory infection, sentinel hospitals, population-level association, viral interference, Analysis, multiplex