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Summary: Coinfections affecting the porcine respiratory system have often been overlooked, in favor of mono-infections, even though they are significantly more common in the field. In pigs, the term 'porcine respiratory complex' is used to describe coinfections involving both viruses, such as, for example, the swine influenza type A virus (swIAV), the porcine respiratory and reproductive syndrome virus (PRRSV), and the porcine circovirus type 2 (PCV-2), as well as bacteria. Until recently, most studies were primarily focused on clinical aspects and paid little attention to the molecular consequences of coinfections. This narrative review addresses the consequences of coinfections in the porcine respiratory system involving viruses. When possible, interactions that can occur between viruses are briefly presented. Conversely, research involving bacteria, protozoa, and fungi has not been considered at all. Finally, the main limitations complicating the interpretation of results from coinfection/superinfection studies are considered, and prospects in this exciting field of health research are presented. [ABSTRACT FROM AUTHOR]

Although frequently reported since the beginning of the pandemic, questions remain regarding the impact of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) interaction with circulating respiratory viruses in coinfected patients. We here investigated dual infections involving early-pandemic SARS-CoV-2 and the Alpha variant and three of the most prevalent respiratory viruses, rhinovirus (RV) and Influenza A and B viruses (IAV and IBV), in reconstituted respiratory airway epithelial cells cultured at air–liquid interface. We found that SARS-CoV-2 replication was impaired by primary, but not secondary, rhino- and influenza virus infection. In contrast, SARS-CoV-2 had no effect on the replication of these seasonal respiratory viruses. Inhibition of SARS-CoV-2 correlated better with immune response triggered by RV, IAV and IBV than the virus entry. Using neutralizing antibody against type I and III interferons, SARS-CoV-2 blockade in dual infections could be partly prevented. Altogether, these data suggested that SARS-CoV-2 interaction with seasonal respiratory viruses would be modulated by interferon induction and could impact SARS-CoV-2 epidemiology when circulation of other respiratory viruses is restored.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel respiratory virus that causes coronavirus disease 2019 (COVID-19). Symptoms of COVID-19 range from mild to severe illness. It was observed that disease progression in COVID-19 patients depends on their immune response, especially in elderly patients whose immune system suppression may put them at increased risk of infection. Human T-cell lymphotropic virus type-I (HTLV-I) attacks the CD4+ T cells (T cells) of the immune system and leads to immune dysfunction. Co-infection with HTLV-I and SARS-CoV-2 has been reported in recent studies. Modeling HTLV-I and SARS-CoV-2 co-infection can be a helpful tool to understand the in-host co-dynamics of these viruses. The aim of this study was to construct a model that characterizes the in-host dynamics of HTLV-I and SARS-CoV-2 co-infection. By considering the mobility of the viruses and cells, the model is represented by a system of partial differential equations (PDEs). The system contains two independent variables, time t and position x, and seven dependent variables for representing the densities of healthy epithelial cells (ECs), latent SARS-CoV-2-infected ECs, active SARS-CoV-2-infected ECs, SARS-CoV-2, healthy T cells, latent HTLV-I-infected T cells and active HTLV-I-infected T cells. We first studied the fundamental properties of the solutions of the system, then deduced all steady states and proved their global properties. We examined the global stability of the steady states by constructing appropriate Lyapunov functions. The analytical results were illustrated by performing numerical simulations. We discussed the effect of HTLV-I infection on COVID-19 progression. The results suggest that patients with HTLV-I have a weakened immune response; consequently, their risk of COVID-19 infection may be increased. [ABSTRACT FROM AUTHOR]

Background: To assess the prevalence of Herpes simplex and Cytomegalovirus infection in respiratory samples of critically-ill COVID-19 patients, its role in outcome and mortality and the influence of dexamethasone treatment in the early stage of SARS-CoV-2 infection. Methods: All mechanically ventilated COVID-19 patients treated on ICU between March 2020 and January 2021 were included. Respiratory specimens were tested for Herpes simplex virus (HSV) type 1, 2 and Cytomegalovirus (CMV) by quantitative real-time PCR. Clinical parameters were compared in the cohorts with and without HSV-1-infection. Results: 134 patients with a median age of 72.5 years (73.0% male, n=98) were included. HSV-1 reactivation occurred in 61 patients (45.5%), after median 9 (7-13) days of mechanical ventilation. The main factor for reactivation was length of stay on ICU (24 days vs 13 days, p<0.001) and duration of mechanical ventilation (417 vs 214 hours, p<0.001). Treatment with dexamethasone and a history of immunosuppression did not associate with HSV-infection in the univariate analysis (39 vs 41, p=0.462 and 27.9% vs 23.3%, p=0.561, respectively). Both ICU and hospital mortality were not significantly different in the cohorts with and without HSV-infection (57.4% vs 45.2%, p=0.219). Conclusions: Our study shows a high prevalence of HSV-infection in critically-ill COVID-19 patients which was unexpectedly higher than the prevalence of CMV-infections and unrelated to dexamethasone treatment. The main risk factors for HSV and CMV in the studied cohorts were the length of ICU stay and duration of mechanical ventilation. Therefore, we recommend routine monitoring of critically ill COVID-19 patients for these viral co-infections and consider treatment in those patients. [ABSTRACT FROM AUTHOR]

Influenza-like illness (ILI) can be caused by a range of respiratory viruses. The present study investigates the contribution of influenza and other respiratory viruses, the occurrence of viral co-infections, and the persistence of the viruses after ILI onset in older adults. During the influenza season 2014–2015, 2366 generally healthy community-dwelling older adults (≥60 years) were enrolled in the study. Viruses were identified by multiplex ligation–dependent probe-amplification assay in naso- and oropharyngeal swabs taken during acute ILI phase, and 2 and 8 weeks later. The ILI incidence was 10.7%, which did not differ between vaccinated and unvaccinated older adults; influenza virus was the most frequently detected virus (39.4%). Other viruses with significant contribution were: rhinovirus (17.3%), seasonal coronavirus (9.8%), respiratory syncytial virus (6.7%), and human metapneumovirus (6.3%). Co-infections of influenza virus with other viruses were rare. The frequency of ILI cases in older adults in this 2014–2015 season with low vaccine effectiveness was comparable to that of the 2012–2013 season with moderate vaccine efficacy. The low rate of viral co-infections observed, especially for influenza virus, suggests that influenza virus infection reduces the risk of simultaneous infection with other viruses. Viral persistence or viral co-infections did not affect the clinical outcome of ILI. [ABSTRACT FROM AUTHOR]

Relevance. In recent years, there has been a steady increase in the incidence of children morbidity, in the structure of which infectious pathology occupies a leading position. The development of minimal persistent inflammation of the upper respiratory tract mucosa is the basis for the persistence of microflora, the entrance gate for allergens and irritants, and creates conditions for the timing of the inflammation. The aim of the study: based on the study of the features of the immune system and interferon system in immunocompromised children of early age suffering from co-infections: return ARVI associated with atypical chronic herpes virus infections, to develop a new program of local and systemic interferon therapy and evaluate its effectiveness. Materials and methods: We observed 30 children aged 1-4 years, 16 boys and 14 girls suffering from recurrent ARVI associated with various atypical chronic active herpes virus infections (ACHA-HVI) (HSV I/II, EBV, CMV, HHV VI). The comparison group was 20 conditionally healthy children, comparable by sex and age. We used clinical and immunological methods: ELISA, PCR, cytofluorimetry. Results: A clinical and anamnestic investigation showed that young children had clinical features of immunocomprometization: a high rate of recurrent ARVI of 10-15 or more episodes per year, and the duration of these episodes ranged from 7 to 12 days, while in 100 % of cases there were recurrent monoand/or mixed ACHA-HVI. A study of the state of the immune system and the interferon system showed that children of the study group were deficient in T cytotoxic lymphocytes, natural killer cells, serum IFN, serum IgA, and various disorders of neutrophil granulocytes (NG). A new immunopathogenetically based program of local and systemic therapy with recombinant IFN2b in combination with antioxidants has been developed. This program demonstrated a high clinical-immunological effectiveness, providing in a significant reduction of ARVI episode rates, a reduction in the duration of IRVI, as well as the number of complicated ARVI, a decrease in the replicative activity of herpes viruses in a field of restoration of the interferon system, a significant improvement of antiviral and antibacterial immune response. Conclusions: A new immunopathogenetically based program of systemic and local IFNtherapy for immunocompromised young children has been created. The high clinical-immunological effectiveness and immunoprophylactic orientation of the developed local and systemic program of interferonotherapy have been demonstrated.

BackgroundLittle is known about viral co-infections in African human immunodeficiency virus (HIV)-infected children. We examined the prevalence of seromarkers for cytomegalovirus (CMV), herpes simplex virus type 2 (HSV-2) and hepatitis B virus (HBV) infections among HIV-infected, antiretroviral treatment (ART)-naïve children in Lilongwe, Malawi.MethodsNinety-one serum samples were tested for IgG and IgM antibodies to CMV, and IgG antibodies to HSV-2 and hepatitis B surface antigen (HBsAg). Baseline demographic, clinical and laboratory data were abstracted from electronic records.ResultsCMV IgG was the most common positive result in all age groups (in 73% of children

Background: To assess the prevalence of Herpes simplex and Cytomegalovirus infection in respiratory samples of critically-ill COVID-19 patients, its role in outcome and mortality and the influence of dexamethasone treatment in the early stage of SARS-CoV-2 infection. Methods: All mechanically ventilated COVID-19 patients treated on ICU between March 2020 and January 2021 were included. Respiratory specimens were tested for Herpes simplex virus (HSV) type 1, 2 and Cytomegalovirus (CMV) by quantitative real-time PCR. Clinical parameters were compared in the cohorts with and without HSV-1- infection. Results: 134 patients with a median age of 72.5 years (73.0% male, n=98) were included. HSV-1 reactivation occurred in 61 patients (45.5%), after median 9 (7-13) days of mechanical ventilation. The main factor for reactivation was length of stay on ICU (24 days vs 13 days, p<0.001) and duration of mechanical ventilation (417 vs 214 hours, p<0.001). Treatment with dexamethasone and a history of immunosuppression did not associate with HSV-infection in the univariate analysis (39 vs 41, p=0.462 and 27.9% vs 23.3%, p=0.561, respectively). Both ICU and hospital mortality were not significantly different in the cohorts with and without HSV-infection (57.4% vs 45.2%, p=0.219). Conclusions: Our study shows a high prevalence of HSV-infection in critically-ill COVID-19 patients which was unexpectedly higher than the prevalence of CMV-infections and unrelated to dexamethasone treatment. The main risk factors for HSV and CMV in the studied cohorts were the length of ICU stay and duration of mechanical ventilation. Therefore, we recommend routine monitoring of critically ill COVID-19 patients for these viral co-infections and consider treatment in those patients. [ABSTRACT FROM AUTHOR]

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel respiratory virus that causes coronavirus disease 2019 (COVID-19). Symptoms of COVID-19 range from mild to severe illness. It was observed that disease progression in COVID-19 patients depends on their immune response, especially in elderly patients whose immune system suppression may put them at increased risk of infection. Human T-cell lymphotropic virus type-I (HTLV-I) attacks the CD4+ T cells (T cells) of the immune system and leads to immune dysfunction. Co-infection with HTLV-I and SARS-CoV-2 has been reported in recent studies. Modeling HTLV-I and SARS-CoV-2 co-infection can be a helpful tool to understand the in-host co-dynamics of these viruses. The aim of this study was to construct a model that characterizes the in-host dynamics of HTLV-I and SARS-CoV-2 co-infection. By considering the mobility of the viruses and cells, the model is represented by a system of partial differential equations (PDEs). The system contains two independent variables, time t and position x, and seven dependent variables for representing the densities of healthy epithelial cells (ECs), latent SARS-CoV-2-infected ECs, active SARS-CoV-2-infected ECs, SARS-CoV-2, healthy T cells, latent HTLV-I-infected T cells and active HTLV-I-infected T cells. We first studied the fundamental properties of the solutions of the system, then deduced all steady states and proved their global properties. We examined the global stability of the steady states by constructing appropriate Lyapunov functions. The analytical results were illustrated by performing numerical simulations. We discussed the effect of HTLV-I infection on COVID-19 progression. The results suggest that patients with HTLV-I have a weakened immune response; consequently, their risk of COVID-19 infection may be increased.

Influenza-like illness (ILI) can be caused by a range of respiratory viruses. The present study investigates the contribution of influenza and other respiratory viruses, the occurrence of viral co-infections, and the persistence of the viruses after ILI onset in older adults. During the influenza season 2014–2015, 2366 generally healthy community-dwelling older adults (≥60 years) were enrolled in the study. Viruses were identified by multiplex ligation–dependent probe-amplification assay in naso- and oropharyngeal swabs taken during acute ILI phase, and 2 and 8 weeks later. The ILI incidence was 10.7%, which did not differ between vaccinated and unvaccinated older adults; influenza virus was the most frequently detected virus (39.4%). Other viruses with significant contribution were: rhinovirus (17.3%), seasonal coronavirus (9.8%), respiratory syncytial virus (6.7%), and human metapneumovirus (6.3%). Co-infections of influenza virus with other viruses were rare. The frequency of ILI cases in older adults in this 2014–2015 season with low vaccine effectiveness was comparable to that of the 2012–2013 season with moderate vaccine efficacy. The low rate of viral co-infections observed, especially for influenza virus, suggests that influenza virus infection reduces the risk of simultaneous infection with other viruses. Viral persistence or viral co-infections did not affect the clinical outcome of ILI.

Canine coronavirus (CCoV) strains with the ability to spread to internal organs, also known as pantropic CCoVs (pCCoVs), have been detected in domestic dogs and wild carnivores. Our study focused on the detection and molecular characterization of pCCoV strains circulating in Italy during the period 2014–2017 in autochthonous dogs, in dogs imported from eastern Europe or illegally imported from an unknown country. Samples from the gut and internal organs of 352 dogs were screened for CCoV; putative pCCoV strains, belonging to subtype CCoV‐IIa, were identified in the internal organs of 35 of the examined dogs. Fifteen pCCoV strains were subjected to sequence and phylogenetic analyses, showing that three strains (98960‐1/2016, 98960‐3/2016, 98960‐4/2016) did not cluster either with Italian or European CCoVs, being more closely related to alphacoronaviruses circulating in Asia with which they displayed a 94%–96% nucleotide identity in partial spike protein gene sequences. The pCCoV‐positive samples were also tested for other canine viruses, showing co‐infections mainly with canine parvovirus. [ABSTRACT FROM AUTHOR]

Purpose of Review: This investigation aims to understand the role and burden of viral co-infections for acute respiratory illnesses in children. Co-infection can be either viral-viral or viral-bacterial and with new technology there is more information on the role they play on the health of children. Recent Findings: With the proliferation of multiplex PCR for rapid diagnosis of multiple viruses as well as innovations on identification of bacterial infections, research has been attempting to discover how these co-infections affect each other and the host. Studies are aiming to discern if the epidemiology of viruses seen at a population level is related to the interaction between different viruses on a host level. Studies are also attempting to discover the burden of morbidity and mortality of these viral-viral co-infections on the pediatric population. It is also becoming important to understand the interplay of certain viruses with specific bacteria and understanding the impact of viral-bacterial co-infections. Summary: RSV continues to contribute to a large burden of disease for pediatric patients with acute respiratory illnesses. However, recent literature suggests that viral-viral co-infections do not add to this burden and might, in some cases, be protective of severe disease. Viral-bacterial co-infections, on the other hand, are most likely adding to the burden of morbidity in pediatric patients because of the synergistic way they can infect the nasopharyngeal space. Future research needs to focus on confirming these conclusions as it could affect hospital cohorting, role of molecular testing, and therapeutic interventions. [ABSTRACT FROM AUTHOR]

Purpose: The aim of the study was to determine and evaluate the clinical usefulness of pathogen specific semi-quantitative cut-offs in stool samples with multiple pathogen detections.The PCR (Seegene Allplex Gastrointestinal Virus Assay) data from 4527 positive samples received over 16 months were retrospectively analyzed to investigate the distribution of the Ct values of each individual viral pathogen. By using interquartile ranges for each viral pathogen, pathogen specific semi-quantitative cut-offs were determined.After a thorough analysis of the Ct values, a well-founded decision to exclude all results with a Ct value higher than 35 was made. This approach made it possible to generate a more nuanced report and to facilitate clinical interpretation in case of mixed infections by linking a lower Ct value of a pathogen to a greater likelihood of being a relevant causative pathogen. Moreover, not reporting viral pathogens with a Ct value higher than 35 led to a significant reduction (p < 0.0001) of reported mixed infections compared to oversimplified qualitative or qualitative reporting.By omitting very high Ct values and reporting semi-quantitatively, value was added to the syndromic reports, leading to an easier to read lab report, especially in mixed infections.Methods: The aim of the study was to determine and evaluate the clinical usefulness of pathogen specific semi-quantitative cut-offs in stool samples with multiple pathogen detections.The PCR (Seegene Allplex Gastrointestinal Virus Assay) data from 4527 positive samples received over 16 months were retrospectively analyzed to investigate the distribution of the Ct values of each individual viral pathogen. By using interquartile ranges for each viral pathogen, pathogen specific semi-quantitative cut-offs were determined.After a thorough analysis of the Ct values, a well-founded decision to exclude all results with a Ct value higher than 35 was made. This approach made it possible to generate a more nuanced report and to facilitate clinical interpretation in case of mixed infections by linking a lower Ct value of a pathogen to a greater likelihood of being a relevant causative pathogen. Moreover, not reporting viral pathogens with a Ct value higher than 35 led to a significant reduction (p < 0.0001) of reported mixed infections compared to oversimplified qualitative or qualitative reporting.By omitting very high Ct values and reporting semi-quantitatively, value was added to the syndromic reports, leading to an easier to read lab report, especially in mixed infections.Results: The aim of the study was to determine and evaluate the clinical usefulness of pathogen specific semi-quantitative cut-offs in stool samples with multiple pathogen detections.The PCR (Seegene Allplex Gastrointestinal Virus Assay) data from 4527 positive samples received over 16 months were retrospectively analyzed to investigate the distribution of the Ct values of each individual viral pathogen. By using interquartile ranges for each viral pathogen, pathogen specific semi-quantitative cut-offs were determined.After a thorough analysis of the Ct values, a well-founded decision to exclude all results with a Ct value higher than 35 was made. This approach made it possible to generate a more nuanced report and to facilitate clinical interpretation in case of mixed infections by linking a lower Ct value of a pathogen to a greater likelihood of being a relevant causative pathogen. Moreover, not reporting viral pathogens with a Ct value higher than 35 led to a significant reduction (p < 0.0001) of reported mixed infections compared to oversimplified qualitative or qualitative reporting.By omitting very high Ct values and reporting semi-quantitatively, value was added to the syndromic reports, leading to an easier to read lab report, especially in mixed infections.Conclusion: The aim of the study was to determine and evaluate the clinical usefulness of pathogen specific semi-quantitative cut-offs in stool samples with multiple pathogen detections.The PCR (Seegene Allplex Gastrointestinal Virus Assay) data from 4527 positive samples received over 16 months were retrospectively analyzed to investigate the distribution of the Ct values of each individual viral pathogen. By using interquartile ranges for each viral pathogen, pathogen specific semi-quantitative cut-offs were determined.After a thorough analysis of the Ct values, a well-founded decision to exclude all results with a Ct value higher than 35 was made. This approach made it possible to generate a more nuanced report and to facilitate clinical interpretation in case of mixed infections by linking a lower Ct value of a pathogen to a greater likelihood of being a relevant causative pathogen. Moreover, not reporting viral pathogens with a Ct value higher than 35 led to a significant reduction (p < 0.0001) of reported mixed infections compared to oversimplified qualitative or qualitative reporting.By omitting very high Ct values and reporting semi-quantitatively, value was added to the syndromic reports, leading to an easier to read lab report, especially in mixed infections. [ABSTRACT FROM AUTHOR]

Coinfections affecting the porcine respiratory system have often been overlooked, in favor of mono-infections, even though they are significantly more common in the field. In pigs, the term 'porcine respiratory complex' is used to describe coinfections involving both viruses, such as, for example, the swine influenza type A virus (swIAV), the porcine respiratory and reproductive syndrome virus (PRRSV), and the porcine circovirus type 2 (PCV-2), as well as bacteria. Until recently, most studies were primarily focused on clinical aspects and paid little attention to the molecular consequences of coinfections. This narrative review addresses the consequences of coinfections in the porcine respiratory system involving viruses. When possible, interactions that can occur between viruses are briefly presented. Conversely, research involving bacteria, protozoa, and fungi has not been considered at all. Finally, the main limitations complicating the interpretation of results from coinfection/superinfection studies are considered, and prospects in this exciting field of health research are presented.

Although frequently reported since the beginning of the pandemic, questions remain regarding the impact of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) interaction with circulating respiratory viruses in coinfected patients. We here investigated dual infections involving early-pandemic SARS-CoV-2 and the Alpha variant and three of the most prevalent respiratory viruses, rhinovirus (RV) and Influenza A and B viruses (IAV and IBV), in reconstituted respiratory airway epithelial cells cultured at air-liquid interface. We found that SARS-CoV-2 replication was impaired by primary, but not secondary, rhino- and influenza virus infection. In contrast, SARS-CoV-2 had no effect on the replication of these seasonal respiratory viruses. Inhibition of SARS-CoV-2 correlated better with immune response triggered by RV, IAV and IBV than the virus entry. Using neutralizing antibody against type I and III interferons, SARS-CoV-2 blockade in dual infections could be partly prevented. Altogether, these data suggested that SARS-CoV-2 interaction with seasonal respiratory viruses would be modulated by interferon induction and could impact SARS-CoV-2 epidemiology when circulation of other respiratory viruses is restored.

Respiratory infections represent a major cause of morbidity and mortality in children. The roles of viruses such as respiratory syncytial virus, paraflu and adenovirus are well known in the etiology of respiratory infections. Lately, many studies displayed the implication of Rhinoviruses and Coronaviruses in inferior tract infections, where, sometimes, they can lead to a severe form of illness. Within the last decade, new respiratory viruses were discovered: human metapneumovirus, NL63 and HKU1 coronaviruses and human bocavirus. Viral co-infections are often seen in children hospitalized for acute respiratory infections, this causing more serious forms of disease that require hospital days. Multiplex PCR tests allow a simultaneous detection from the same sample of a large spectrum of viral and bacterial agents, which lay at the basis of respiratory infections [ABSTRACT FROM AUTHOR]

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To assess the prevalence of viral co-infections in HIV infected children. Children born to HIV seropositive parents and those children who were suspected to be HIV infected based on clinical presentation by the pediatrician were screened for HIV −1 and 2 antibodies as per National Aids Control Organization (NACO) guidelines. Those found to be seropositive for HIV infection were further tested for Hepatitis B&C, Herpes simplex virus and Human cytomegalovirus infection. Among 803 children screened, 101 were found positive for HIVantibodies. Among the five viral markers tested, HCMV IgG was positive in 88 children (87.1%). HCMV IgM was positive in 35 cases (34.6%). HBsAg tested positive in 30 children, while anti-HCV IgM was reactive in 27 cases. IgM anti- HSV antibodies were observed positive in 59 (58.4%) cases. Both hepatitis virus coinfection (HBsAg and anti- HCV IgM antibodies) was observed in 10 HIV positive children, while both Herpesviridae family viruses (HCMV -IgM antibodies and HSV -IgM antibodies) were positive in 30 cases (29.7%). Viral co-infections are significantly higher in HIV positive children, which adds to significant mortality and morbidity and should therefore be screened in all HIV positive children for timely treatment in order to improve the quality of life and better survival of HIV infected children. [ABSTRACT FROM AUTHOR]

• SARS-CoV-2 accompanied by >20 common seasonal acute viral respiratory infections in March-June 2020 in a Russian population. • 56.68% and 70.67% of SARS-CoV-2-positive individuals were asymptomatic in March and June 2020, respectively. • The population is gradually adapting to the novel pathogen, even in the absence of a vaccine. • 92.6% of COVID-19-related fatalities were associated with at least one clinically identified comorbidity. • Human respiratory syncytial virus and rhinoviruses accounted for the largest proportion of viral co-infections with SARS-CoV-2. This study was conducted to assess the spread of SARS-CoV-2 in Russia and the adaptation of the population to the virus in March to June 2020. Two groups were investigated: 1) 12 082 individuals already proven positive for SARS-CoV-2 (clinical information was studied); 2) 7864+4458 individuals with suspected respiratory infections (polymerase chain reaction [PCR] tests and clinical information were studied). In the latter, SARS-CoV-2-positive individuals comprised 5.37% in March and 11.42% in June 2020. Several viral co-infections were observed for SARS-CoV-2. Rhinoviruses accounted for the largest proportion of co-infections (7.91% of samples were SARS-CoV-2-positive); followed by respiratory syncytial virus (7.03%); adenoviruses (4.84%); metapneumoviruses (3.29%); parainfluenza viruses (2.42%); enterovirus D68 (1.10%) and other viruses (entero-, echo-, parecho-) (<1%). Average SARS-CoV-2 case fatality rate in the group of 12 537 individuals was determined to be 0.6% (in contrast to official Russian government statistics of 1.5% mortality). This rate is within the range of mortality caused by other common seasonal respiratory viruses (0.01-2.21% in Russia in 2012 to 2020). Most fatalities occurred in individuals with comorbidities, as for other respiratory viruses. The proportion of SARS-CoV-2 asymptomatic carriers was 56.68% in March and 70.67% in June 2020. This new pathogen presents a substantial risk to human beings as it was not contained at the start of its outbreak in Wuhan and spread worldwide. However, surveillance, prevention and treatment must be strictly evidence-based and not dictated by fear. [ABSTRACT FROM AUTHOR]