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2.
BMC Public Health ; 22(1): 1167, 2022 06 11.
Article in English | MEDLINE | ID: covidwho-1885294

ABSTRACT

BACKGROUND: Lower respiratory tract infections are among the main causes of death. Although there are many respiratory viruses, diagnostic efforts are focused mainly on influenza. The Respiratory Viruses Network (RespVir) collects infection data, primarily from German university hospitals, for a high diversity of infections by respiratory pathogens. In this study, we computationally analysed a subset of the RespVir database, covering 217,150 samples tested for 17 different viral pathogens in the time span from 2010 to 2019. METHODS: We calculated the prevalence of 17 respiratory viruses, analysed their seasonality patterns using information-theoretic measures and agglomerative clustering, and analysed their propensity for dual infection using a new metric dubbed average coinfection exclusion score (ACES). RESULTS: After initial data pre-processing, we retained 206,814 samples, corresponding to 1,408,657 performed tests. We found that Influenza viruses were reported for almost the half of all infections and that they exhibited the highest degree of seasonality. Coinfections of viruses are frequent; the most prevalent coinfection was rhinovirus/bocavirus and most of the virus pairs had a positive ACES indicating a tendency to exclude each other regarding infection. CONCLUSIONS: The analysis of respiratory viruses dynamics in monoinfection and coinfection contributes to the prevention, diagnostic, treatment, and development of new therapeutics. Data obtained from multiplex testing is fundamental for this analysis and should be prioritized over single pathogen testing.


Subject(s)
Coinfection , Respiratory Tract Infections , Virus Diseases , Viruses , Coinfection/epidemiology , Humans , Infant , Rhinovirus , Virus Diseases/epidemiology
3.
BMC Infect Dis ; 22(1): 891, 2022 Nov 28.
Article in English | MEDLINE | ID: covidwho-2139180

ABSTRACT

BACKGROUND: The impact of corticosteroids on patients with severe coronavirus disease 2019 (COVID-19)/chronic hepatitis B virus (HBV) co-infection is currently unknown. We aimed to investigate the association of corticosteroids on these patients. METHODS: This retrospective multicenter study screened 5447 confirmed COVID-19 patients hospitalized between Jan 1, 2020 to Apr 18, 2020 in seven centers in China, where the prevalence of chronic HBV infection is moderate to high. Severe patients who had chronic HBV and acute SARS-cov-2 infection were potentially eligible. The diagnosis of chronic HBV infection was based on positive testing for hepatitis B surface antigen (HBsAg) or HBV DNA during hospitalization and a medical history of chronic HBV infection. Severe patients (meeting one of following criteria: respiratory rate > 30 breaths/min; severe respiratory distress; or SpO2 ≤ 93% on room air; or oxygen index < 300 mmHg) with COVID-19/HBV co-infection were identified. The bias of confounding variables on corticosteroids effects was minimized using multivariable logistic regression model and inverse probability of treatment weighting (IPTW) based on propensity score. RESULTS: The prevalence of HBV co-infection in COVID-19 patients was 4.1%. There were 105 patients with severe COVID-19/HBV co-infections (median age 62 years, 57.1% male). Fifty-five patients received corticosteroid treatment and 50 patients did not. In the multivariable analysis, corticosteroid therapy (OR, 6.32, 95% CI 1.17-34.24, P = 0.033) was identified as an independent risk factor for 28-day mortality. With IPTW analysis, corticosteroid treatment was associated with delayed SARS-CoV-2 viral RNA clearance (OR, 2.95, 95% CI 1.63-5.32, P < 0.001), increased risk of 28-day and in-hospital mortality (OR, 4.90, 95% CI 1.68-14.28, P = 0.004; OR, 5.64, 95% CI 1.95-16.30, P = 0.001, respectively), and acute liver injury (OR, 4.50, 95% CI 2.57-7.85, P < 0.001). Methylprednisolone dose per day and cumulative dose in non-survivors were significantly higher than in survivors. CONCLUSIONS: In patients with severe COVID-19/HBV co-infection, corticosteroid treatment may be associated with increased risk of 28-day and in-hospital mortality.


Subject(s)
COVID-19 , Coinfection , Hepatitis B, Chronic , Hepatitis B , Humans , Male , Middle Aged , Female , SARS-CoV-2 , Hepatitis B, Chronic/complications , Hepatitis B, Chronic/drug therapy , COVID-19/drug therapy , Coinfection/drug therapy , Coinfection/epidemiology , Hepatitis B virus , Adrenal Cortex Hormones/therapeutic use , Hepatitis B Surface Antigens
4.
Saudi Med J ; 43(9): 1000-1006, 2022 Sep.
Article in English | MEDLINE | ID: covidwho-2111186

ABSTRACT

OBJECTIVES: To investigate the seroprevalence of the community-acquired bacterial that causes atypical pneumonia among confirmed severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) patients. METHODS: In this cohort study, we retrospectively investigated the seroprevalence of Chlamydia pneumoniae, Mycoplasma pneumoniae, and Legionella pneumophila among randomly selected 189 confirmed COVID-19 patients at their time of hospital presentation via commercial immunoglobulin M (IgM) antibodies against these bacteria. We also carried out quantitative measurements of procalcitonin in patients' serum. RESULTS: The seropositivity for L. pneumophila was 12.6%, with significant distribution among patientsolder than 50 years (χ2 test, p=0.009), while those of M. pneumoniae was 6.3% and C. pneumoniae was 2.1%, indicating an overall co-infection rate of 21% among COVID-19 patients. No significant difference (χ2 test, p=0.628) in the distribution of bacterial co-infections existed between male and female patients. Procalcitonin positivity was confirmed amongst 5% of co-infected patients. CONCLUSION: Our study documented the seroprevalence of community-acquired bacteria co-infection among COVID-19 patients. In this study, procalcitonin was an inconclusive biomarker for non-severe bacterial co-infections among COVID-19 patients. Consideration and proper detection of community-acquired bacterial co-infection may minimize misdiagnosis during the current pandemic and positively reflect disease management and prognosis.


Subject(s)
COVID-19 , Coinfection , Community-Acquired Infections , Pneumonia, Bacterial , Adult , COVID-19/epidemiology , Cohort Studies , Coinfection/epidemiology , Community-Acquired Infections/diagnosis , Community-Acquired Infections/epidemiology , Female , Humans , Immunoglobulin M , Male , Mycoplasma pneumoniae , Pneumonia, Bacterial/epidemiology , Pneumonia, Bacterial/microbiology , Procalcitonin , Retrospective Studies , SARS-CoV-2 , Saudi Arabia/epidemiology , Seroepidemiologic Studies
5.
J Clin Virol ; 157: 105300, 2022 Dec.
Article in English | MEDLINE | ID: covidwho-2105314

ABSTRACT

BACKGROUND: Viral conjunctivitis (pink eye) can be highly contagious and is of public health importance. There remains significant debate whether SARS-CoV-2 can present as a primary conjunctivitis. The aim of this study was to identify pathogens associated with outpatient infectious conjunctivitis during the COVID-19 Delta surge. METHODS: This prospective study was conducted in the spring and summer months of 2021. 106 patients with acute conjunctivitis who presented to the Aravind Eye Center in Madurai, India were included. One anterior nasal swab and one conjunctival swab of each eye were obtained for each enrolled patient. Samples were subsequently processed for unbiased metagenomic RNA deep sequencing (RNA-seq). Outcomes included clinical findings and codetection of other pathogens with SARS-CoV-2 in patients with conjunctivitis. RESULTS: Among the 13 patients identified with human coronavirus RNA fragments in their swabs, 6 patients had SARS-CoV-2 infection, 5 patients had coinfections of SARS-CoV-2 and human adenovirus (HAdV), 1 patient had a coinfection with human coronavirus OC43 and HAdV, and 1 patient had a coinfection of Vittaforma corneae and SARS-CoV-2. 30% had bilateral disease and symptoms on presentation. Petechial hemorrhage was noted in 33% of patients with SARS-CoV-2 infection. No patients with SARS-CoV-2 or SARS-CoV-2 and HAdV infections had subepithelial infiltrates on presentation. All patients denied systemic symptoms. CONCLUSIONS: Among the patients presented with conjunctivitis associated with human coronavirus infection, over 50% of the patients had co-infections with other circulating pathogens, suggesting the public-health importance of broad pathogen testing and surveillance in the outpatient conjunctivitis population.


Subject(s)
COVID-19 , Coinfection , Conjunctivitis , Humans , SARS-CoV-2 , Coinfection/epidemiology , Outpatients , Prospective Studies , India/epidemiology , RNA
6.
Infect Control Hosp Epidemiol ; 42(1): 89-92, 2021 01.
Article in English | MEDLINE | ID: covidwho-2096391
7.
Acta Biomed ; 93(5): e2022313, 2022 Oct 26.
Article in English | MEDLINE | ID: covidwho-2091393

ABSTRACT

BACKGROUND AND AIM: The pandemic caused by SARS-COV-2 has increased Semi-Intensive Care Unit (SICU) admission, causing an increase in healthcare-associated infection (HAI). Mostly HAI reveals the same risk factors, but fewer studies have analyzed the possibility of multiple coinfections in these patients. The study aimed was to identify patterns of co-presence of different species describing at the same time the association between such patterns and patient demographics and, finally, comparing the patterns between the two cohorts of COVID-19 patients admitted at Policlinico during the first wave and the second one). METHODS: All the patients admitted to SICUs during two COVID-19 waves, from March to June 2020 months and from October to December 2020, were screened following the local infection control surveillance program; whoever manifested fever has undergone on microbiological culture to detect bacterial species. Statistical analysis was performed to observe the existence of microbiological patterns through DBSCAN method. RESULTS: 246 patients were investigated and 83 patients were considered in our study because they presented infection symptoms with a mean age of 67 years and 33.7% of female patients. During the first and second waves were found respectively 10 and 8 bacterial clusters with no difference regarding the most frequent species. CONCLUSIONS: The results show the importance of an analysis which considers the risk factors for the possibility of co- and superinfection (such as age and gender) to structure a good prognostic tool to predict which patients will encounter severe coinfections during hospitalization.


Subject(s)
COVID-19 , Coinfection , Cross Infection , Humans , Female , Aged , SARS-CoV-2 , Coinfection/epidemiology , Intensive Care Units , Hospitalization , Hospitals , Retrospective Studies
9.
Nat Commun ; 13(1): 6316, 2022 Oct 23.
Article in English | MEDLINE | ID: covidwho-2087201

ABSTRACT

From December 2021-February 2022, an intense and unprecedented co-circulation of SARS-CoV-2 variants with high genetic diversity raised the question of possible co-infections between variants and how to detect them. Using 11 mixes of Delta:Omicron isolates at different ratios, we evaluated the performance of 4 different sets of primers used for whole-genome sequencing and developed an unbiased bioinformatics method for the detection of co-infections involving genetically distinct SARS-CoV-2 lineages. Applied on 21,387 samples collected between December 6, 2021 to February 27, 2022 from random genomic surveillance in France, we detected 53 co-infections between different lineages. The prevalence of Delta and Omicron (BA.1) co-infections and Omicron lineages BA.1 and BA.2 co-infections were estimated at 0.18% and 0.26%, respectively. Among 6,242 hospitalized patients, the intensive care unit (ICU) admission rates were 1.64%, 4.81% and 15.38% in Omicron, Delta and Delta/Omicron patients, respectively. No BA.1/BA.2 co-infections were reported among ICU admitted patients. Among the 53 co-infected patients, a total of 21 patients (39.6%) were not vaccinated. Although SARS-CoV-2 co-infections were rare in this study, their proper detection is crucial to evaluate their clinical impact and the risk of the emergence of potential recombinants.


Subject(s)
COVID-19 , Coinfection , Humans , SARS-CoV-2/genetics , COVID-19/diagnosis , COVID-19/epidemiology , Prevalence , Coinfection/epidemiology
10.
BMC Infect Dis ; 22(1): 792, 2022 Oct 19.
Article in English | MEDLINE | ID: covidwho-2079396

ABSTRACT

BACKGROUND: SARS-CoV-2 infections have a wide spectrum of clinical manifestations whose causes are not completely understood. Some human conditions predispose to severe outcome, like old age or the presence of comorbidities, but many other facets, including coinfections with other viruses, remain poorly characterized. METHODS: In this study, the eukaryotic fraction of the respiratory virome of 120 COVID-19 patients was characterized through whole metagenomic sequencing. RESULTS: Genetic material from respiratory viruses was detected in 25% of all samples, whereas human viruses other than SARS-CoV-2 were found in 80% of them. Samples from hospitalized and deceased patients presented a higher prevalence of different viruses when compared to ambulatory individuals. Small circular DNA viruses from the Anneloviridae (Torque teno midi virus 8, TTV-like mini virus 19 and 26) and Cycloviridae families (Human associated cyclovirus 10), Human betaherpesvirus 6, were found to be significantly more abundant in samples from deceased and hospitalized patients compared to samples from ambulatory individuals. Similarly, Rotavirus A, Measles morbillivirus and Alphapapilomavirus 10 were significantly more prevalent in deceased patients compared to hospitalized and ambulatory individuals. CONCLUSIONS: Results show the suitability of using metagenomics to characterize a broader peripheric virological landscape of the eukaryotic virome in SARS-CoV-2 infected patients with distinct disease outcomes. Identified prevalent viruses in hospitalized and deceased patients may prove important for the targeted exploration of coinfections that may impact prognosis.


Subject(s)
COVID-19 , Coinfection , Viruses , Humans , SARS-CoV-2/genetics , Coinfection/epidemiology , Viruses/genetics , DNA, Circular , Severity of Illness Index
11.
Virology ; 576: 105-110, 2022 11.
Article in English | MEDLINE | ID: covidwho-2061964

ABSTRACT

As SARS-CoV-2 and influenza viruses co-circulate, co-infections with these viruses generate an increasing concern to public health. To evaluate the prevalence and clinical impacts of SARS-CoV-2 and influenza A virus co-infections during the 2021-2022 influenza season, SARS-CoV-2-positive samples from 462 individuals were collected from October 2021 to January 2022. Of these individuals, 152 tested positive for influenza, and the monthly co-infection rate ranged from 7.1% to 48%. Compared to the Delta variant, individuals infected with Omicron were less likely to be co-infected and hospitalized, and individuals who received influenza vaccines were less likely to become co-infected. Three individuals had two samples collected on different dates, and all three developed a co-infection after their initial SARS-CoV-2 infection. This study demonstrates high prevalence of co-infections in central Missouri during the 2021-2022 influenza season, differences in co-infection prevalence between the Delta and the Omicron waves, and the importance of influenza vaccinations against co-infections.


Subject(s)
COVID-19 , Coinfection , Influenza A virus , Influenza Vaccines , Influenza, Human , Humans , Influenza, Human/epidemiology , SARS-CoV-2 , Coinfection/epidemiology , Cross-Sectional Studies , Seasons , Missouri/epidemiology , COVID-19/epidemiology , Influenza A virus/genetics
12.
Emerg Infect Dis ; 28(11): 2285-2289, 2022 Nov.
Article in English | MEDLINE | ID: covidwho-2054895

ABSTRACT

We analyzed epidemiologic characteristics and distribution of 492 deaths related to Chagas disease and coronavirus disease (COVID-19) co-infection in Brazil during March‒December 2020. Cumulative co-infected death rates were highest among advanced age groups, persons of Afro-Brazilian ethnicity and with low education levels, and geographically distributed mainly in major Chagas disease‒endemic areas.


Subject(s)
COVID-19 , Chagas Disease , Coinfection , Humans , Brazil/epidemiology , Coinfection/epidemiology , Chagas Disease/epidemiology
13.
BMC Infect Dis ; 22(1): 760, 2022 Sep 29.
Article in English | MEDLINE | ID: covidwho-2053870

ABSTRACT

BACKGROUND: Patients with COVID-19 receiving mechanical ventilation may become aggravated with a secondary respiratory infection. The aim of this study was to describe secondary respiratory infections, their predictive factors, and outcomes in patients with COVID-19 requiring mechanical ventilation. METHODS: A cohort study was carried out in a single tertiary hospital in Santiago, Chile, from 1st June to 31st July 2020. All patients with COVID-19 admitted to the intensive care unit that required mechanical ventilation were included. RESULTS: A total of 175 patients were enrolled, of which 71 (40.6%) developed at least one secondary respiratory infection during follow-up. Early and late secondary infections were diagnosed in 1.7% and 31.4% respectively. Within late secondary infections, 88% were bacterial, 10% were fungal, and 2% were of viral origin. One-third of isolated bacteria were multidrug-resistant. Bivariate analysis showed that the history of corticosteroids used before admission and the use of dexamethasone during hospitalization were associated with a higher risk of secondary infections (p = 0.041 and p = 0.019 respectively). Multivariate analysis showed that for each additional day of mechanical ventilation, the risk of secondary infection increases 1.1 times (adOR = 1.07; 95% CI 1.02-1.13, p = 0.008) CONCLUSIONS: Patients with COVID-19 admitted to the intensive care unit and requiring mechanical ventilation had a high rate of secondary infections during their hospital stay. The number of days on MV was a risk factor for acquiring secondary respiratory infections.


Subject(s)
COVID-19 , Coinfection , Respiratory Tract Infections , Cohort Studies , Coinfection/epidemiology , Dexamethasone , Humans , Intensive Care Units , Respiration, Artificial
14.
Transbound Emerg Dis ; 69(5): e3393-e3399, 2022 Sep.
Article in English | MEDLINE | ID: covidwho-2053038

ABSTRACT

Flaviviruses such as West Nile (WNV), Usutu (USUV) and Bagaza (BAGV) virus and avian malaria parasites are vector borne pathogens that circulate naturally between avian and mosquito hosts. WNV and USUV and potentially also BAGV constitute zoonoses. Temporal and spatial cocirculation and coinfection with Plasmodium spp., and West Nile virus has been documented in birds and mosquito vectors, and fatally USUV-infected passerines coinfected with Plasmodium spp. had more severe lesions. Also, WNV, USUV and BAGV have been found to cocirculate. Yet little is known about the interaction of BAGV and malaria parasites during consecutive or coinfections of avian hosts. Here we report mortality of free-living red-legged partridges in a hunting estate in Southern Spain that were coinfected with BAGV and Plasmodium spp. The outbreak occurred in the area where BAGV first emerged in Europe in 2010 and where cocirculation of BAGV, USUV and WNV was confirmed in 2011 and 2013. Partridges were found dead in early October 2019. Birds had mottled locally pale pectoral muscles, enlarged, congestive greenish-black tinged livers and enlarged kidneys. Microscopically congestion and predominantly mononuclear inflammatory infiltrates were evident and Plasmodium phanerozoites were present in the liver, spleen, kidneys, muscle and skin. Molecular testing and sequencing detected Plasmodium spp. and BAGV in different tissues of the partridges, and immunohistochemistry confirmed the presence and colocalization of both pathogens in the liver and spleen. Due to the importance of the red-legged partridge in the ecosystem of the Iberian Peninsula and as driver of regional economy such mortalities are of concern. Such outbreaks may reflect climate change related shifts in host, vector and pathogen ecology and interactions that could emerge similarly for other pathogens.


Subject(s)
Bird Diseases , Coinfection , Flavivirus Infections , Flavivirus , Galliformes , Plasmodium , West Nile Fever , West Nile virus , Animals , Coinfection/epidemiology , Coinfection/veterinary , Ecosystem , Flavivirus/physiology , Flavivirus Infections/epidemiology , Flavivirus Infections/veterinary , Quail , Spain/epidemiology , West Nile Fever/epidemiology , West Nile Fever/veterinary
15.
Influenza Other Respir Viruses ; 16(4): 780-788, 2022 07.
Article in English | MEDLINE | ID: covidwho-2052612

ABSTRACT

BACKGROUND: Influenza causes significant morbidity and mortality in the United States. Among patients infected with influenza, the presence of bacterial co-infection is associated with worse clinical outcomes; less is known regarding the clinical importance of viral co-infections. The objective of this study was to determine rates of viral co-infections in emergency department (ED) patients with confirmed influenza and association of co-infection with disease severity. METHODS: Secondary analysis of a biorepository and clinical database from a parent study where rapid influenza testing was implemented in four U.S. academic EDs, during the 2014-2015 influenza season. Patients were systematically tested for influenza virus using a validated clinical decision guideline. Demographic and clinical data were extracted from medical records; nasopharyngeal specimens from influenza-positive patients were tested for viral co-infections (ePlex, Genmark Diagnostics). Patterns of viral co-infections were evaluated using chi-square analysis. The association of viral co-infection with hospital admission was assessed using univariate and multivariate regression. RESULTS: The overall influenza A/B positivity rate was 18.1% (1071/5919). Of the 999 samples with ePlex results, the prevalence of viral co-infections was 7.9% (79/999). The most common viral co-infection was rhinovirus/enterovirus (RhV/EV), at 3.9% (39/999). The odds of hospital admission (OR 2.33, 95% CI: 1.01-5.34) increased significantly for those with viral co-infections (other than RhV/EV) versus those with influenza A infection only. CONCLUSION: Presence of viral co-infection (other than RhV/EV) in ED influenza A/B positive patients was independently associated with increased risk of hospital admission. Further research is needed to determine clinical utility of ED multiplex testing.


Subject(s)
Coinfection , Influenza, Human , Orthomyxoviridae , Respiratory Tract Infections , Virus Diseases , Viruses , Coinfection/epidemiology , Hospitalization , Humans , Influenza, Human/complications , Influenza, Human/epidemiology , Respiratory Tract Infections/epidemiology , Virus Diseases/complications , Virus Diseases/epidemiology
16.
Clin Infect Dis ; 75(Supplement_2): S294-S297, 2022 Oct 03.
Article in English | MEDLINE | ID: covidwho-2051353

ABSTRACT

We described bacterial/fungal coinfections and antibiotic-resistant infections among inpatients with a diagnosis of coronavirus disease 2019 (COVID-19) and compared findings in those with a diagnosis of influenza like illness. Less than 10% of inpatients with COVID-19 had bacterial/fungal coinfection. Longer lengths of stay, critical care stay, and mechanical ventilation contribute to increased incidence of hospital-onset infections among inpatients with COVID-19.


Subject(s)
COVID-19 , Coinfection , Anti-Bacterial Agents/therapeutic use , Coinfection/epidemiology , Hospitals , Humans , Inpatients , SARS-CoV-2 , United States
19.
Medicina (Kaunas) ; 58(9)2022 Sep 12.
Article in English | MEDLINE | ID: covidwho-2033055

ABSTRACT

Background: This study aimed to investigate the clinical form, risk factors, and outcomes of patients with COVID-19 and Clostridioides difficile co-infections. Methods: This retrospective study (2 September 2021-1 April 2022) included all patients with Clostridioides difficile infection (CDI) and COVID-19 infection who were admitted to the Covid Hospital of the University Clinical Center of Vojvodina. Results: A total of 5124 COVID-19 patients were admitted to the Covid Hospital, and 326 of them (6.36%) developed hospital-onset CDI. Of those, 326 of the CDI patients (88.65%) were older than 65 years. The median time of CDI onset was 12.88 days. Previous hospitalizations showed 69.93% of CDI patients compared to 38.81% in the non-CDI group (p = 0.029). The concomitant antibiotics exposure was higher among the CDI group versus the non-CDI group (88.65% vs. 68.42%, p = 0.037). Albumin levels were ≤ 25 g/L among 39.57% of the CDI patients and 21.71% in the non-CDI patients (p = 0.021). The clinical manifestations of CDI ranged from mild diarrhea (26.9%) to severe diarrhea (63.49%) and a complicated form of colitis (9.81%). Regarding outcomes, 79.14% of the CDI patients recovered and 20.86% had fatal outcomes in-hospital. Although a minority of the patients were in the non-CDI group, the difference in mortality rate between the CDI and non-CDI group was not statistically significant (20.86% vs. 15.13%, p = 0.097). Conclusions: Elderly patients on concomitant antibiotic treatments with hypoalbuminemia and with previous healthcare exposures were the most affected by COVID-19 and CD co-infections.


Subject(s)
COVID-19 , Clostridioides difficile , Clostridium Infections , Coinfection , Aged , Albumins , Anti-Bacterial Agents/therapeutic use , COVID-19/complications , Clostridium Infections/complications , Clostridium Infections/drug therapy , Clostridium Infections/epidemiology , Coinfection/epidemiology , Diarrhea/epidemiology , Diarrhea/etiology , Hospitals , Humans , Retrospective Studies , Serbia/epidemiology , Universities , Yugoslavia
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