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Prevalence of non-influenza respiratory viruses in acute respiratory infection cases in Mexico.

ABSTRACT: Acute respiratory infections are the leading cause of morbidity and mortality worldwide. Although a viral aetiological agent is estimated to be involved in up to 80% of cases, the majority of these agents have never been specifically identified. Since 2009, diagnostic and surveillance efforts for influenza virus have been applied worldwide. However, insufficient epidemiological information is available for the many other respiratory viruses that can cause Acute respiratory infections.This study evaluated the presence of 14 non-influenza respiratory viruses in 872 pharyngeal exudate samples using RT-qPCR. All samples met the operational definition of a probable case of an influenza-like illness or severe acute respiratory infection and had a previous negative result for influenza by RT-qPCR.The presence of at least one non-influenza virus was observed in 312 samples (35.8%). The most frequent viruses were rhinovirus (RV; 33.0%), human respiratory syncytial virus (HRSV; 30.8%) and human metapneumovirus (HMPV; 10.6%). A total of 56 cases of co-infection (17.9%) caused by 2, 3, or 4 viruses were identified. Approximately 62.5% of all positive cases were in children under 9 years of age.In this study, we identified 13 non-influenza respiratory viruses that could occur in any season of the year. This study provides evidence for the prevalence and seasonality of a wide range of respiratory viruses that circulate in Mexico and constitute a risk for the population. Additionally, our data suggest that including these tests more widely in the diagnostic algorithm for influenza may reduce the use of unnecessary antibiotics, reduce the hospitalisation time, and enrich national epidemiological data with respect to the infections caused by these viruses.

SUBMITTER: Fernandes-Matano L

PROVIDER: S-EPMC5415110 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature

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Prevalence of non-influenza respiratory viruses in acute respiratory infection cases in Mexico.

Fernandes-Matano Larissa L Monroy-Muñoz Irma Eloísa IE Angeles-Martínez Javier J Sarquiz-Martinez Brenda B Palomec-Nava Iliana Donají ID Pardavé-Alejandre Hector Daniel HD Santos Coy-Arechavaleta Andrea A Santacruz-Tinoco Clara Esperanza CE González-Ibarra Joaquín J González-Bonilla Cesar Raúl CR Muñoz-Medina José Esteban JE

PloS one 20170503 5

<h4>Background</h4>Acute respiratory infections are the leading cause of morbidity and mortality worldwide. Although a viral aetiological agent is estimated to be involved in up to 80% of cases, the majority of these agents have never been specifically identified. Since 2009, diagnostic and surveillance efforts for influenza virus have been applied worldwide. However, insufficient epidemiological information is available for the many other respiratory viruses that can cause Acute respiratory inf ...[more]

PMID: 28467515

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Project description:Respiratory diseases in weaned pigs are a common problem, with a complex etiology involving both viruses and bacteria. In the present study, we investigated the presence of eleven viruses in nasal swabs, collected from nurseries (55 cases) under the suspicion of swine influenza A virus (swIAV) and submitted by swine veterinarians for diagnosis. The other ten viruses included in the study were influenza B (IBV) and D (IDV), Porcine reproductive and respiratory syndrome virus (PRRSV), Porcine respiratory coronavirus (PRCV), Porcine cytomegalovirus (PCMV), Porcine circovirus 2 (PCV2), 3 (PCV3) and 4 (PCV), Porcine parainfluenza 1 (PPIV1) and Swine orthopneumovirus (SOV). Twenty-six swIAV-positive cases and twenty-nine cases of swIAV-negative respiratory disease were primarily established. While IBV, IDV, PCV4 and PPIV1 were not found in any of the cases, PRCV, SOV, and PCMV were more likely to be found in swIAV-positive nurseries with respiratory disease (p < 0.05). Overall, PCV3, PRRSV, and PCMV were the most frequently detected agents at herd level. Taken individually, virus prevalence was: swIAV, 48.6%; PRCV, 48.0%; PRRSV, 31.6%; SOV, 33.8%; PCMV, 48.3%, PCV2, 36.0%; and PCV3, 33.0%. Moreover, low Ct values (<30) were common for all agents, except PCV2 and PCV3. When the correlation between pathogens was individually examined, the presence of PRRSV was negatively correlated with swIAV and PRCV, while was positively associated to PCMV (p < 0.05). Also, PRCV and SOV were positively correlated between them and negatively with PCMV. Besides, the analysis of suckling pig samples, collected in subclinically infected farrowing units under an influenza monitoring program, showed that circulation of PRCV, PCMV, SOV, and PCV3 started during the early weeks of life. Interestingly, in those subclinically infected units, none of the pathogens was found to be correlated to any other. Overall, our data may contribute to a better understanding of the complex etiology and epidemiology of respiratory diseases in weaners. This is the first report of SOV in Spain and shows, for the first time, the dynamics of this pathogen in swine farms.

Project description:Some respiratory viruses can cause a viral interference through the activation of the interferon (IFN) pathway that reduces the replication of another virus. Epidemiological studies of coinfections between SARS-CoV-2 and other respiratory viruses have been hampered by non-pharmacological measures applied to mitigate the spread of SARS-CoV-2 during the COVID-19 pandemic. With the ease of these interventions, SARS-CoV-2 and influenza A viruses can now co-circulate. It is thus of prime importance to characterize their interactions. In this work, we investigated viral interference effects between an Omicron variant and a contemporary influenza A/H3N2 strain, in comparison with an ancestral SARS-CoV-2 strain and the 2009 pandemic influenza A/H1N1 virus. We infected nasal human airway epitheliums with SARS-CoV-2 and influenza, either simultaneously or 24 h apart. Viral load was measured by RT-qPCR and IFN-α/β/λ1/λ2 proteins were quantified by immunoassay. Expression of four interferon-stimulated genes (ISGs; OAS1/IFITM3/ISG15/MxA) was also measured by RT-droplet digital PCR. Additionally, susceptibility of each virus to IFN-α/β/λ2 recombinant proteins was determined. Our results showed that influenza A, and especially A/H3N2, interfered with both SARS-CoV-2 viruses, but that SARS-CoV-2 did not significantly interfere with A/H3N2 or A/H1N1. Consistently with these results, influenza, and particularly the A/H3N2 strain, caused a higher production of IFN proteins and expression of ISGs than SARS-CoV-2. SARS-CoV-2 induced a marginal IFN production and reduced the IFN response during coinfections with influenza. All viruses were susceptible to exogenous IFNs, with the ancestral SARS-CoV-2 and Omicron being less susceptible to type I and type III IFNs, respectively. Thus, influenza A causes a viral interference towards SARS-CoV-2 most likely through an IFN response. The opposite is not necessarily true, and a concurrent infection with both viruses leads to a lower IFN response. Taken together, these results help us to understand how SARS-CoV-2 interacts with another major respiratory pathogen.

Dataset Information

Prevalence of non-influenza respiratory viruses in acute respiratory infection cases in Mexico.

Publications

Prevalence of non-influenza respiratory viruses in acute respiratory infection cases in Mexico.

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