An overview on viral interference during SARS-CoV-2 pandemic

Population-level respiratory virus-virus interactions, Puerto Rico, 2013-2023

BACKGROUND

Understanding virus-virus interactions is important for evaluating disease transmission and severity. Positive interactions suggest concurrent circulation, while negative interactions indicate reduced transmission of one virus when another is prevalent. This study examines interactions among seven respiratory viruses using a Bayesian approach that accounts for seasonality and long-term trends.

METHODS

We analyzed data from 43,385 acute febrile illness cases in the Sentinel Enhanced Dengue Surveillance System in Puerto Rico (2013-2023). Viruses studied included influenza A (IAV), influenza B (IBV), respiratory syncytial virus (RSV), human parainfluenza viruses 1 and 3 (HPIV-1, HPIV-3), human adenovirus (HAdV), and human metapneumovirus (HMPV). Wavelet coherence analysis investigated synchronous or asynchronous viral co-variation, while a Bayesian hierarchical model estimated pairwise interactions.

RESULTS

Among 43,385 participants, 26.0% tested positive for at least one virus, with IAV (9.5%), HAdV (4.1%), RSV (3.6%), and IBV (3.6%) being most frequent. Coinfections occurred in 0.5% of cases, often involving HAdV. Wavelet coherence identified significant synchronization among RSV/HMPV, HPIV-1/HMPV, and other virus pairs, with minimal coherence during the COVID-19 pandemic. Bayesian modeling suggested five virus-virus associations: four positive (RSV/HPIV-3, HMPV/HPIV-1, IBV/HAdV, IBV/HMPV) and one negative (IAV/HAdV). However, when restricting the analysis to the prepandemic period, fewer associations remained statistically credible.

CONCLUSION

Respiratory viruses in Puerto Rico demonstrate patterns of co-circulation that may reflect complex interactions, but these associations appear context-dependent. Findings highlight the need for continued surveillance to better understand virus-virus dynamics and their implications for public health interventions.

Trends of respiratory viruses and factors associated with severe acute respiratory infection in patients presenting at a university hospital: a 6-year retrospective study across the COVID-19 pandemic

Background

The COVID-19 pandemic significantly disrupted the epidemiology of respiratory viruses, altering seasonal patterns and reducing circulation. While recovery trends have been observed, factors associated with severe acute respiratory infections (SARIs) during pre- and post-pandemic periods remain underexplored in middle-income countries.

Objective

This study aimed to analyze the trends in respiratory virus circulation and identify factors associated with SARI in patients attending a tertiary care university hospital in western Mexico over a six-year period spanning the pre-pandemic, pandemic, and post-pandemic phases.

Methods

A retrospective study was conducted using data from 19,088 symptomatic patients tested for respiratory viruses between 2018 and 2024. Viral trends were analyzed through interrupted time series (ITS) modeling, incorporating locally estimated scatterplot smoothing (LOESS) and raw positivity rates. Additionally, ITS analysis was performed to evaluate temporal changes in SARI proportions across different phases of the pandemic. Multivariate logistic regression models were applied to determine independent risk factors for SARI across different time periods.

Results

During the pandemic (2020-2021), respiratory virus positivity rates significantly declined, particularly for influenza, which experienced a sharp reduction but rebounded post-2022. Respiratory syncytial virus (RSV) demonstrated a delayed resurgence, whereas other respiratory viruses exhibited heterogeneous rebound patterns. ITS modeling of SARI proportions revealed a significant pre-pandemic increasing trend, followed by a slower rise during the pandemic, and a sharp post-pandemic drop in early 2022, before resuming an upward trajectory. Among older adults (>65 years), a marked increase in SARI was observed at the beginning of the pandemic, while younger groups showed more stable patterns. Logistic regression identified advanced age, male sex, cardiovascular disease, obesity, and immunosuppression as major risk factors for SARI, while vaccination consistently showed a protective effect across all periods and subgroups.

Conclusion

The COVID-19 pandemic induced persistent shifts in respiratory virus circulation, disrupting seasonal dynamics and modifying the burden of SARI. The findings underscore the importance of continuous surveillance, targeted vaccination programs, and early diagnostics to mitigate severe outcomes. These results highlight the need for adaptive public health strategies in middle-income countries to address evolving respiratory disease threats.

Impact of COVID-19 on Respiratory Virus Infections in Children, Japan, 2018-2023

BACKGROUND

COVID-19, caused by SARS-CoV-2, was first documented in Japan in January 2020. We previously reported an increased risk of rhinovirus infections among children during the early phase of the COVID-19 pandemic. Here, we assessed the impact of COVID-19 on respiratory virus infections after SARS-CoV-2 spread nationwide.

METHODS

We analyzed clinical specimens from 4012 patients with respiratory infections in Yokohama, Japan from January 2018 to April 2023.

RESULTS

Among 15 representative respiratory viruses we detected (influenza virus, rhinovirus, coxsackievirus, echovirus, enterovirus, human coronavirus 229E, HKU1, NL63, and OC43, human metapneumovirus, human parainfluenza virus, human parechovirus, RSV, human adenovirus, human bocavirus, human parvovirus B19, herpes simplex virus type 1, and varicella-zoster virus), influenza was most affected by the COVID-19 pandemic, with no influenza viruses detected for nearly 3 years.

CONCLUSIONS

The decrease in influenza infections following the emergence of SARS-CoV-2 may have contributed to the previously reported increase in rhinovirus infections. The rhinovirus outbreak, rather than SARS-CoV-2, may have contributed to the decrease in enveloped virus infections (RSV, parainfluenza viruses, metapneumovirus, and coronavirus 229E, HKU1, NL63, and OC43), possibly due to negative virus-virus interactions.

Severe Acute Respiratory Syndrome Coronavirus 2 Antibody Prevalence and Associated Risk Factors in a Large Cohort of US Children

Background

Household transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) may play a key role in times of increased infection, particularly among children. We aimed to determine the prevalence of SARS-CoV-2 antibodies and identify risk factors associated with SARS-CoV-2 antibody positivity in children.

Methods

Unvaccinated children aged 18 months to 11 years between August 2022 and June 2023 underwent oral fluid testing for SARS-CoV-2 antibodies. Caregivers completed electronic surveys at 4 major healthcare practices in Northern and Central New Jersey. Information was collected on demographics, household size, vaccination status, and prior SARS-CoV-2-related illness. Multivariable logistic regression determined individual and household-level factors associated with SARS-CoV-2 antibody positivity.

Results

A total of 870 children provided tests and corresponding surveys. Children were predominantly Hispanic (37%) or non-Hispanic Black (30%), and on average 5.7 years old. Overall SARS-CoV-2 antibody positivity was 68%. Risk factors for SARS-CoV-2 positivity include Hispanic or non-Hispanic Black race/ethnicity (adjusted odds ratios [aOR], 2.29 and 1.95 vs. White race/ethnicity; P < .01) and later enrollment in the study period. Children from households with ≥1 vaccinated adult were 52% less likely to be antibody positive than those from households with no vaccinated adults (aOR: 0.38, [95% confidence interval 0.2 to 0.69]).

Conclusions

There is high burden of SARS-CoV-2 infection among children over time. Adult vaccination appears to be a protective factor in helping to mitigate coronavirus disease 2019 (COVID-19) infection among children. Increased vaccination of adults in the community can help inform COVID-19 prevention strategies for minors in the household.

Burden of Acute Respiratory Infections Caused by Influenza Virus, Respiratory Syncytial Virus, and SARS-CoV-2 with Consideration of Older Adults: A Narrative Review

Influenza virus, respiratory syncytial virus (RSV), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are acute respiratory infections (ARIs) that can cause substantial morbidity and mortality among at-risk individuals, including older adults. In this narrative review, we summarize themes identified in the literature regarding the epidemiology, seasonality, immunity after infection, clinical presentation, and transmission for these ARIs, along with the impact of the COVID-19 pandemic on seasonal patterns of influenza and RSV infections, with consideration of data specific to older adults when available. As the older adult population increases globally, it is of paramount importance to fully characterize the true disease burden of ARIs in order to develop appropriate mitigation strategies to minimize their impact in vulnerable populations. Challenges associated with characterizing the burden of these diseases include the shared symptomology and clinical presentation of influenza virus, RSV, and SARS-CoV-2, which complicate accurate diagnosis and highlight the need for improved testing and surveillance practices. To this end, multiple regional, national, and global virologic and disease surveillance systems have been established to provide accurate knowledge of viral epidemiology, support appropriate preparedness and response to potential outbreaks, and help inform prevention strategies to reduce disease severity and transmission. Beyond the burden of acute illness, long-term health consequences can also result from influenza virus, RSV, and SARS-CoV-2 infection. These include cardiovascular and pulmonary complications, worsening of existing chronic conditions, increased frailty, and reduced life expectancy. ARIs among older adults can also place a substantial financial burden on society and healthcare systems. Collectively, the existing data indicate that influenza virus, RSV, and SARS-CoV-2 infections in older adults present a substantial global health challenge, underscoring the need for interventions to improve health outcomes and reduce the disease burden of respiratory illnesses.Graphical abstract and video abstract available for this article.

Exploring the epidemiological burden of RSV pre- and post-COVID-19 pandemic: A Jordanian tertiary hospital experience

OBJECTIVES

To describe changes in respiratory syncytial virus (RSV) epidemiology, its associated clinical outcomes and predictors of severe acute lower respiratory tract infection (ALRTI) pre- and post-COVID-19.

METHODS

In this retrospective cohort, we analysed data from electronic medical record of children <5 years who were hospitalized at Jordan University Hospital with RSV-associated ALRTI from 2018 to 2022.

RESULTS

325 inpatients with respiratory infections were included. Rate of RSV infections decreased from 74% pre-pandemic to 30% post-pandemic. Patients diagnosed with ALRTI post-COVID had significantly higher SpO2, less chronic disease, lower temperature and respiratory rate at admission and fewer days in hospital compared with those diagnosed pre-COVID. Furthermore, patients diagnosed pre-pandemic were significantly more likely to have abnormal X-rays, used more antibiotics and antivirals, and had higher rates of severe disease than those with infection post-COVID.

CONCLUSION

COVID-19 and its associated social restriction measures led to changes in RSV epidemiology, characterized by a decline in rates and clinical severity in the post-pandemic period. However, further studies are needed to characterize the impact of COVID-19 on subsequent RSV seasons.

Attrition in serum anti-DENV antibodies correlates with high anti-SARS-CoV-2 IgG levels and low DENV positivity in mosquito vectors-Findings from a state-wide cluster-randomized community-based study in Tamil Nadu, India

The decline in dengue incidence and/or prevalence during the COVID-19 pandemic (2020-22) appears to be attributed to reduced treatment-seeking rates, under-reporting, misdiagnosis, disrupted health services and reduced exposure to mosquito vectors due to prevailing lockdowns. There is limited scientific data on dengue virus (DENV) disease during the COVID-19 pandemic. Here, we conducted a community-based, cross-sectional, cluster-randomized survey to assess anti-DENV and anti-SARS-CoV-2 seroprevalence, and also estimated the spatial distribution of DENV-positive aedine mosquito vectors during the COVID-19 pandemic across all the 38 districts of Tamil Nadu, India. Using real-time PCR, the prevalence of DENV in mosquito pools during 2021 was analyzed and compared with the previous and following years of vector surveillance, and correlated with anti-DENV IgM and IgG levels in the population. Results implicate that both anti-DENV IgM and IgG seroprevalence and DENV positivity in mosquito pools were reduced across all the districts. A total of 13464 mosquito pools and 5577 human serum samples from 186 clusters were collected. Of these, 3.76% of the mosquito pools were positive for DENV. In the human sera, 4.12% were positive for anti-DENV IgM and 6.4% for anti-DENV IgG. While the anti-SARS-CoV-2 levels significantly correlated with overall DENV seropositivity, COVID-19 vaccination status significantly correlated with anti-DENV IgM levels. The study indicates a profound impact of anti-SARS-CoV-2 levels on DENV-positive mosquito pools and seropositivity. Continuous monitoring of anti-DENV antibody levels, especially with the evolving variants of SARS-CoV-2 and the surge in COVID-19 cases will shed light on the distribution, transmission and therapeutic attributes of DENV infection.

Circulation and Codetections of Influenza Virus, SARS-CoV-2, Respiratory Syncytial Virus, Rhinovirus, Adenovirus, Bocavirus, and Other Respiratory Viruses During 2022-2023 Season in Latvia

This retrospective study analysed the routine data obtained by multiplex real-time RT-qPCR methods for respiratory virus detection. A total of 4814 respiratory specimens collected during 1 September 2022-31 August 2023 were included in the study. A total of 38% of the specimens were positive for at least one target, with the incidence maximum (82%) for the small children (age group 0-4 years). The five dominant virus groups were rhinovirus (RV, 12%), influenza virus A (IAV, 7%), adenovirus (AdV, 6%), respiratory syncytial virus (RSV, 5%), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, 5%). The specimens with multi-detections represented 19% of the positives, unevenly distributed (n = 225, 56, 43, 24) among the age groups 0-4, 5-14, 15-64, and 65< years, respectively. The dominant virus groups in multi-positive specimens were RV (53%), AdV (43%), and bocavirus (BoV, 35%)-in mutual pairs as well as all three together-followed by RSV (21%), and IAV (15%). Our study focused on the specimens with codetections and provides an insight into the variety of the respiratory virus interactions in Latvia during the first year since pandemic-related social restriction measures were eased. The observations also emphasise the need to consider the differentiation between rhinoviruses and enteroviruses, especially for the youngest patients in the age group 0-4.

Risk factors for severe disease in pediatric respiratory syncytial virus infections

OBJECTIVES

To assess factors associated with the risk of severe disease in children aged 5 years or younger with laboratory-confirmed respiratory syncytial virus (RSV) infection.

STUDY DESIGN

We conducted a nationwide retrospective cohort study in Mexico.

METHODS

Eligible participants included children aged 5 years or younger with laboratory-confirmed RSV infection January 1, 2023, and May 15, 2024. We collected relevant clinical and epidemiological data. Risk ratios (RR) and 95% confidence intervals (CI) were employed to identify factors associated with the risk of severe disease, characterized by clinical and radiographic evidence of bronchiolitis or pneumonia requiring hospital admission.

RESULTS

Data from 2022 children were analyzed and the overall risk of severe disease was 21.0% (n = 424/2022). In multiple generalized linear regression analysis, a personal history of immunosuppression (due to any cause) showed a protective effect (RR = 0.14, 95% CI 0.05-0.42, P = 0.001) against severe RSV disease, while an increased risk was documented for each additional day elapsed between the date of symptom onset and the date of seeking healthcare RR = 1.06, 95% CI 1.02-1.10, P = 0.004).

CONCLUSION

These findings provide insights into risk stratification and suggest specific directions for future research. This information informs the development of targeted intervention strategies to mitigate the impact of RSV infections in this vulnerable population.

Prevalence and Seasonal Patterns of 16 Common Viral Respiratory Pathogens during the COVID-19 Pandemic in Gauteng Province, South Africa, 2020-2021

Coronavirus disease 2019 (COVID-19) is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The COVID-19 pandemic resulted in widespread morbidity and mortality, but generally, the diagnosis of other respiratory viruses was limited. This study aimed to assess the prevalence of other respiratory viruses during the 2020/2021 pandemic among patients of all ages who accessed care at public healthcare facilities in Gauteng Province, South Africa. Laboratory diagnosis for respiratory viruses, with or without SARS-CoV-2, was conducted via multiplex real-time polymerase chain reactions using respiratory specimens. A total of 1776 patients were included from 1 April 2020 to 31 March 2021, of which 766 (43.1%) were positive for respiratory viruses other than SARS-CoV-2. RV (368/1776; 20.7%) was the most prevalent, followed by RSV (304/1776; 17.1%), AdV (112/1776; 6.3%) and EV (105/1776; 5.9%). hCoV-OC43 (39/1776; 2.2%) was the most prevalent common coronavirus. SARS-CoV-2 co-infections were detected in 4.8% (24/500) of patients. Only 27.1% (482/1776) of patients were admitted to high-care or intensive care units. A decrease in respiratory virus detections was observed, except for RSV, EV and hCoV-OC43. RSV prevalence increased in 2021, while influenza A/B viruses remained undetected.

Prevalence of Co-Infections in Primary Care Patients with Medically Attended Acute Respiratory Infection in the 2022/2023 Season

In the post-pandemic period, an endemic circulation of respiratory viruses has been re-established. Respiratory viruses are co-circulating with SARS-CoV-2. We performed a retrospective analysis of co-infections in primary care patients with medically attended acute respiratory infections (MAARI) who consulted from week 40/2022 to week 39/2023 and were tested for a panel of respiratory viruses. Out of 2099 samples tested, 1260 (60.0%) were positive for one virus. In 340 samples, co-infection was detected: two viruses in 281 (13.4%), three viruses in 51 (2.4%), and four viruses in eight (0.4%) samples. Respiratory viruses co-infected the patients with MAARI at very different rates. The lowest rates of co-infections were confirmed for influenza B (13.8%) and influenza A (22.9%) and the highest for human bocaviruses (84.0%) and human parechoviruses (82.1%). Co-infections were detected in 28.2% of SARS-CoV-2 positive samples. SARS-CoV-2 has never been co-infected with influenza B virus, enterovirus or adenovirus, although the latter was found as a co-infecting virus with all other respiratory viruses tested. The rate of co-infections decreased significantly with increasing age (p-value 0.000), and no difference was found regarding gender (p-value 0.672). It is important to understand the epidemiology of respiratory co-infections for prevention and management decisions in patients with MAARI.

Sequencing and characterization of human bocavirus genomes from patients diagnosed in Southern France between 2017 and 2022

The diversity and evolution of the genomes of human bocavirus (HBoV), which causes respiratory diseases, have been scarcely studied. Here, we aimed to obtain and characterize HBoV genomes from patients's nasopharyngeal samples collected between 2017 and 2022 period (5 years and 7 months). Next-generation sequencing (NGS) used Illumina technology after having implemented using GEMI an in-house multiplex PCR amplification strategy. Genomes were assembled and analyzed with CLC Genomics, Mafft, BioEdit, MeV, Nextclade, MEGA, and iTol. A total of 213 genomes were obtained. Phylogeny classified them all as of Bocavirus 1 (HBoV1) species. Five HBoV1 genotypic clusters determined by hierarchical clustering analysis of 27 variable genome positions were scattered over the study period although with differences in yearly prevalence. A total of 167 amino acid substitutions were detected. Besides, coinfection was observed for 52% of the samples, rhinoviruses then adenoviruses (HAdVs) being the most common viruses. Principal component analysis showed that HBoV1 genotypic cluster α tended to be correlated with HAdV co-infection. Subsequent HAdV typing for HBoV1-positive samples and negative controls demonstrated that HAdVC species predominated but HAdVB was that significantly HBoV1-associated. Overall, we described here the first HBoV1 genomes sequenced for France. HBoV1 and HAdVB association deserves further investigation.

Genetic Diversity of Human Respiratory Syncytial Virus during COVID-19 Pandemic in Yaoundé, Cameroon, 2020-2021

Worldwide, human respiratory syncytial virus (HRSV) is a major cause of severe infections of the lower respiratory system, affecting individuals of all ages. This study investigated the genetic variability of HRSV during the COVID-19 outbreak in Yaoundé; nasopharyngeal samples positive for HRSV were collected from different age groups between July 2020 and October 2021. A semi-nested RT-PCR was performed on the second hypervariable region of the G gene of detected HRSV, followed by sequencing and phylogenetic assessment. Throughout the study, 40 (37.7%) of the 106 HRSV-positive samples successfully underwent G-gene amplification. HRSV A and HRSV B co-circulated at rates of 47.5% and 52.5%, respectively. HRSV A clustered in the GA2.3.5 genetic lineage (ON1) and HRSV B clustered in the GB5.0.5a genetic lineage (BA9). Differences in circulating genotypes were observed between pre- and post-pandemic years for HRSV A. Predictions revealed potential N-glycosylation sites at positions 237-318 of HRSV A and positions 228-232-294 of HRSV B. This study reports the molecular epidemiology of HRSV in Cameroon during the COVID-19 pandemic. It describes the exclusive co-circulation of two genetic lineages. These findings highlight the importance of implementing comprehensive molecular surveillance to prevent the unexpected emergence of other diseases.

The coevolution of Covid-19 and host immunity

The dynamic of the virus-host interaction is subject to constant evolution, which makes it difficult to predict when the SARS-CoV-2 pandemic will become endemic. Vaccines in conjunction with efforts around masking and social distancing have reduced SARS-CoV-2 infection rates, however, there are still significant challenges to contend with before the pandemic shifts to endemic, such as the coronavirus acquiring mutations that allow the virus to dodge the immunity acquired by hosts. SARS-CoV-2 variants deploy convergent evolutionary mechanisms to sharpen their ability to impede the host’s innate immune response. The continued emergence of variants and sub-variants poses a significant hurdle to reaching endemicity. This underscores the importance of continued public health measures to control SARS-CoV-2 transmission and the need to develop better second-generation vaccines and effective treatments that would tackle current and future variants. We hypothesize that the hosts’ immunity to the virus is also evolving, which is likely to abet the process of reaching endemicity.

Human respiratory syncytial virus subgroups A and B outbreak in a kindergarten in Zhejiang Province, China, 2023

BACKGROUND

In May-June 2023, an unprecedented outbreak of human respiratory syncytial virus (HRSV) infections occurred in a kindergarten, Zhejiang Province, China. National, provincial, and local public health officials investigated the cause of the outbreak and instituted actions to control its spread.

METHODS

We interviewed patients with the respiratory symptoms by questionnaire. Respiratory samples were screened for six respiratory pathogens by real-time quantitative polymerase chain reaction (RT-PCR). The confirmed cases were further sequenced of G gene to confirm the HRSV genotype. A phylogenetic tree was reconstructed by maximum likelihood method.

RESULTS

Of the 103 children in the kindergarten, 45 were classified as suspected cases, and 25 cases were confirmed by RT-PCR. All confirmed cases were identified from half of classes. 36% (9/25) were admitted to hospital, none died. The attack rate was 53.19%. The median ages of suspected and confirmed cases were 32.7 months and 35.8 months, respectively. Nine of 27 confirmed cases lived in one community. Only two-family clusters among 88 household contacts were HRSV positive. A total of 18 of the G gene were obtained from the confirmed cases. Phylogenetic analyses revealed that 16 of the sequences belonged to the HRSV B/BA9 genotype, and the other 2 sequences belonged to the HRSV A/ON1 genotype. The school were closed on June 9 and the outbreak ended on June 15.

CONCLUSION

These findings suggest the need for an increased awareness of HRSV coinfections outbreak in the kindergarten, when HRSV resurges in the community after COVID-19 pandemic.