Your browser doesn't support javascript.
Show: 20 | 50 | 100
Results 1 - 20 de 1.442
Filter
1.
researchsquare; 2024.
Preprint in English | PREPRINT-RESEARCHSQUARE | ID: ppzbmed-10.21203.rs.3.rs-3940109.v1

ABSTRACT

Background Coinfections in patients with coronavirus disease 2019 (COVID-19) affect patient prognosis. Patients with hematologic malignancies (HMs) are usually immunosuppressed and may be at high risk of coinfection, but few related data have been reported. Here, we conducted a retrospective study to explore coinfections in patients with HMs and COVID-19 by next-generation sequencing (NGS) of bronchoalveolar lavage fluid (BALF).Methods The data of hospitalized patients with pneumonia who underwent NGS analysis of BALF were reviewed. COVID-19 patients with HMs were enrolled in the HM group, and those without HMs were enrolled in the non-HM group. The coinfections of the two groups identified by NGS were analyzed.Results Fifteen patients were enrolled in the HM group, and 14 patients were enrolled in the non-HM group. The coinfection rates in the HM group and non-HM group were 80.0% and 85.7%, respectively. The percentage of coinfected bacteria in the HM group was significantly lower than that in the non-HM group (20.0% vs 71.4%, p = 0.005). The coinfection rates of fungi and viruses were 60.0% and 35.7%, respectively, in the HM group and 35.7% and 78.6%, respectively, in the non-HM group, with no significant differences. The most common coexisting pathogen in patients with HMs was Pneumocystis jirovecii (33.3%), and the most common coexisting pathogen in patients without HMs was human gammaherpesvirus 4 (50%). Coinfection with herpesviruses occurred frequently in both groups.Conclusions Our study showed that hospitalized patients with COVID-19 had a high incidence of coinfection. Pneumocystis jiroveci and herpesvirus are commonly coinfected pathogens in patients with HMs. Bacterial coinfection is rare in patients with HMs but is more common in patients without HMs.


Subject(s)
Cerebrospinal Fluid Leak , Hematologic Neoplasms , Coinfection , Pneumonia , COVID-19 , Pneumocystis Infections
2.
authorea preprints; 2024.
Preprint in English | PREPRINT-AUTHOREA PREPRINTS | ID: ppzbmed-10.22541.au.170667235.57161637.v1

ABSTRACT

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), that causes coronavirus disease 2019 (COVID-19) is a public health problem and may have co-infection with other pathogens such as influenza virus.This study aims to assess the co-infection of SARS-CoV-2 with influenza among COVID-19 cases.The all relevant studies were collected from international databases. For improving the quality of the present literature, the all studies were evaluated by two reviewers in order to confirm all of the studies have inclusion criteria. Finally, all articles with sufficient quality scores were included in meta-analysis. Assessment of heterogeneity among the studies of primary studies was performed using the statistic chi‐squared test (Cochran’s Q) and I2 index. In this results, random or fixed effect model were used for determination of heterogeneity test. All statistical analyses were performed using Comprehensive Meta-Analysis (CMA), V.2 software.This meta- analysis included 9 primary studies investigating the co-infection of SARS-CoV-2 with influenza among COVID-19 cases. Pooled prevalence (95% confidence interval) of co-infection is shown that the prevalence of influenza A is higher than influenza B. 2.3(0.5-9.3) vs 0.1 (0.4-3.3). Using the fixed effect model the frequency of fever was (80.6% [95% CI 76.1–84.40, p < 0.153]) and it is shown that fever is the most prevalent symptom in patients.Patients admitted to hospital with COVID-19 also infected with influenza virus. Thus, the current research provides a better understanding about the control and treatment of co-infection with SARS-CoV-2 and the influenza virus.


Subject(s)
Coinfection , Fever , Severe Acute Respiratory Syndrome , COVID-19 , Coronavirus Infections
3.
authorea preprints; 2024.
Preprint in English | PREPRINT-AUTHOREA PREPRINTS | ID: ppzbmed-10.22541.au.170669898.85808641.v1

ABSTRACT

Objectives: This study aimed to assess the impact of COVID-19 on the prevalence of respiratory pathogens among hospitalized children with lower respiratory tract infections (LTRIs) in Shanghai. Methods: Respiratory specimens were collected from children with LTRIs in Children’s Hospital of Fudan University from February 2019 to January 2021 and common respiratory pathogens were detected using multiplex PCR. The data of 13 respiratory pathogens were analyzed and compared between the year of 2020 (from February 2020 to January 2021) and 2019 (from February 2019 to January 2020). Results: A total of 1049 patients were enrolled, including 417 patients in 2019 and 632 patients in 2020. In 2020, 27.53% of patients were tested positive for at least one pathogens, which was significantly lower than that in 2019 (78.66%). The top three pathogens were Mp, ADV and RV in 2019, whereas RV, RSV and PIV were the predominant ones in 2020. The positive rates of Mp, ADV, RV, PIV, InfB, H3N2 and H1N1 were significantly decreased in 2020. RV was the most detectable respiratory pathogen in 2020, and become the most frequent pathogen in all five age groups. PIV had a high prevalence from October to December 2020 which was even higher than that in 2019. InfA was not detected in 2020. Co-infection was significantly less frequent in 2020. Conclusions: The public health interventions aiming to eliminate COVID-19 have great impact on the prevalence of common respiratory pathogens. The prevalence of RV and PIV reminds us a possible resurgence of some pathogens.


Subject(s)
Coinfection , COVID-19 , Respiratory Tract Infections
4.
authorea preprints; 2024.
Preprint in English | PREPRINT-AUTHOREA PREPRINTS | ID: ppzbmed-10.22541.au.170670568.86897254.v1

ABSTRACT

Measles is an acute infectious disease which is highly contagious. This illness is caused by a negative sense, single-stranded RNA virus belonging to the Paramyxoviridae family. In spite of having a highly effective vaccine, measles is still a public health concern. In October 2019, Iran has achieved the status of measles elimination using effective vaccination strategies and surveillance system based on WHO recommendations. However, recent COVID-19 pandemic disrupted impeccable immunization services and altered health-seeking behaviors worldwide. Herein, we report a case of measles and influenza co-infection in a nine month-old infant from Bushehr province of Iran


Subject(s)
Communicable Diseases , Coinfection , COVID-19
5.
researchsquare; 2024.
Preprint in English | PREPRINT-RESEARCHSQUARE | ID: ppzbmed-10.21203.rs.3.rs-3910065.v1

ABSTRACT

This study aimed to investigate the association between disease severity and demographic characteristics, clinical features, and prevalence of intestinal parasite carriage among patients with COVID-19 in Addis Ababa, Ethiopia. A cross-sectional study was conducted at St. Paul's Hospital Millennium Medical College, involving 337 COVID-19 patients. Patient data were collected during hospitalization to assess clinical outcomes, including demographic information, clinical features, and associated factors. Blood and stool samples were collected and analyzed for hematological and biochemical tests, as well as the presence of intestinal parasites. Statistical analysis was performed using the Statistical Packages for Social Sciences v. 26, employing descriptive statistics, chi-square tests, and logistic regression. A p-value of < 0.05 was considered statistically significant. Among the 337 patients with confirmed SARS-CoV-2 infection through PCR testing, 96(28.5%) were found to have co-infections with one or more intestinal parasites. Multivariate analysis revealed that patients aged ≥ 60 years [Adjusted Odds Ratio (AOR) 3.943 (95% CI: 1.792–8.673), p < 0.001], elevated creatinine levels [AOR 2.254 (95% CI: 1.041–4.881), p = 0.039], increased glutamate oxaloacetate transaminase levels [AOR 2.219 (95% CI: 1.234–3.991), p = 0.008], decreased hematocrit levels [AOR 8.839 (95% CI: 4.914–15.900), p < 0.001], and co-infection with intestinal parasites [AOR 2.419 (95% CI: 1.278–4.579), p = 0.007] were significantly associated with increased disease severity in COVID-19 patients. These findings suggest a potential link between co-infection with intestinal parasites and a more severe form of COVID-19, indicating that parasite-induced immunomodulatory responses may hinder the essential immune response against SARS-CoV-2.


Subject(s)
Intestinal Diseases, Parasitic , Coinfection , COVID-19
6.
researchsquare; 2024.
Preprint in English | PREPRINT-RESEARCHSQUARE | ID: ppzbmed-10.21203.rs.3.rs-3869323.v1

ABSTRACT

Background Lower respiratory tract infections (LRTIs) are one of the leading causes of hospital admissions among children. In this study, we aimed to describe the epidemiological characteristics of viral pathogens associated with LRTIs in hospitalized children in Yan'an; this has yet to be reported in the literature and may guide public health interventions and resource allocation in this region. Methods Between June 2021 and May 2023, we conducted a retrospective analysis of the results of viral detection using oral pharyngeal swabs from 4565 children with LRTIs in the Inpatient Department of Yan'an University Affiliated Hospital. Eleven respiratory viruses, including influenza A virus (Flu A), influenza A H1N1 virus (H1N1), seasonal influenza A H3N2 virus (H3N2), influenza B virus (Flu B), parainfluenza virus (HPIV), adenovirus (HADV), bocavirus (HBoV), rhinovirus (HRV), metapneumovirus (HNPV), coronavirus (HCoV), and respiratory syncytial virus (HRSV), were confirmed by applying a multiplex real-time polymerase chain reaction (PCR) kit for respiratory viruses. We evaluated the epidemiological features of infections caused by respiratory pathogens, including aging and the seasonal variations of different pathogens, and explored the high-risk factors associated with virus-caused pneumonia. Results At least one virus was detected in all 4565 cases; the positivity rate was 27.95%. We also detected a total of 1,276 cases with mixed infections (with two or more viruses). Of the positive cases, 59.3% were male and 40.7% were female (x2 = 0.41, P = 0.68). The highest positivity rates for respiratory pathogens were observed for HRSV, HRV, and HADV, at 5.98%, 5.67%, and 4.38%, respectively. We also observed variations in the number and positivity rates of respiratory pathogen infections by season and age. HPIV (x2 = 12.05,P < 0.05) and HADV (x2 = 11.73,P < 0.05) were more common in children under 3 years-of-age. Conclusions In conclusion, our analysis revealed that respiratory pathogen infections varied by gender, season, and age in the enrolled population of children.


Subject(s)
Respiratory Syncytial Virus Infections , Pneumonia , Coinfection , Respiratory Tract Infections
7.
biorxiv; 2023.
Preprint in English | bioRxiv | ID: ppzbmed-10.1101.2023.12.21.572736

ABSTRACT

School closures were used as strategies to mitigate transmission in the COVID-19 pandemic. Understanding the nature of SARS-CoV-2 outbreaks and the distribution of infections in classrooms could help inform targeted or precision preventive measures and outbreak management in schools, in response to future pandemics. In this work, we derive an analytical model of Probability Density Function (PDF) of SARS-CoV-2 secondary infections and compare the model with infection data from all public schools in Ontario, Canada between September-December, 2021. The model accounts for major sources of variability in airborne transmission like viral load and dose-response (i.e., the human bodys response to pathogen exposure), air change rate, room dimension, and classroom occupancy. Comparisons between reported cases and the modeled PDF demonstrated the intrinsic overdispersed nature of the real-world and modeled distributions, but uncovered deviations stemming from an assumption of homogeneous spread within a classroom. The inclusion of near-field transmission effects resolved the discrepancy with improved quantitative agreement between the data and modeled distributions. This study provides a practical tool for predicting the size of outbreaks from one index infection, in closed spaces such as schools, and could be applied to inform more focused mitigation measures. Author summaryAt the start of the COVID-19 pandemic, there was huge uncertainty around the risks of SARS-CoV-2 spread in classrooms. In the absence of early predictions surrounding classroom risks, many jurisdictions across countries closed in-person education. There is great interest in adopting a more precision approach to better inform future interventions in the context of airborne virus risks. For this purpose, we need tools that can predict the probability of the size of outbreaks within classrooms along with the impact of interventions including masks, better ventilation, and physical distancing by limiting the number of students per classroom. To this end, we have developed a robust but practical model that yields the probability of secondary infections stemming from index cases occurring within schools on a given day. During model development, the major underlying physical and biological factors that dictate the disease transmission process, both at long-range and close-range, have been accounted for. This enables our model to modify its predictions for different scenarios - and possibly allows its use beyond schools. Finally, the models predictive capability has been verified by comparing its outputs with publicly available data on SARS-CoV-2 diagnoses in Ontario public schools. To our knowledge, this is the first time an analytical model derived from mostly first principles describes real-world infection distributions, satisfactorily. The quantitative match between the theoretical prediction and real-world data offers the proposed model as a possible powerful tool for better-informed precision pandemic mitigation strategies in indoor environments like schools.


Subject(s)
Coinfection , Severe Acute Respiratory Syndrome , COVID-19
8.
preprints.org; 2023.
Preprint in English | PREPRINT-PREPRINTS.ORG | ID: ppzbmed-10.20944.preprints202312.0800.v1

ABSTRACT

During the COVID-19 pandemic, the circulation of non–SARS-CoV-2 respiratory viruses changed throughout the world. This study aimed to analyze the effect of respiratory syncytial virus (RSV), metapneumovirus (MPV), rhinovirus (RV), and parainfluenza (PIV)-3 single infection, dual co-infection, and viral load on cytokine and chemokine expression in 300 Mexican patients with ARIs negative for SARS-CoV-2. Molecular detection and viral load were performed by RT-qPCR. Cytokine and chemokine expression was determined in samples positive for single RSV, MPV, RV, or PIV-3 infection, and in the most frequent dual co-infections, by a cytokine panel using a magnetic-bead-based multiplex immunoassay. Of the patients positive for viral infection, 91.7% had a single infection and 8.3% had dual co-infections. In this study, RSV was the respiratory virus with the highest prevalence, and the most common dual co-infection was RV+RSV. On the other hand, RV infections had the highest viral loads compared to the other viruses detected. FGF basic, MIP-1α IL-8, IP-10, MCP-1, IFN-γ, and RANTES showed differential expression between single infections and dual co-infections compared to healthy patients. We report, for the first time, the circulation of non-SARS-CoV-2 viruses in the south of Mexico and the cytokine and chemokine profiles associated with these viruses.


Subject(s)
Respiratory Syncytial Virus Infections , Coinfection , COVID-19 , Virus Diseases , Infections
9.
researchsquare; 2023.
Preprint in English | PREPRINT-RESEARCHSQUARE | ID: ppzbmed-10.21203.rs.3.rs-3716276.v1

ABSTRACT

Introduction Directly-acting antivirals (DAA) are the cornerstone to reach HCV elimination. In men who have sex with men (MSM) with HIV coinfection, recently acquired HCV infection (RAHCV) is common. Sexual practices and reinfection rates may hamper micro-elimination despite high treatment rates. Methods The cohort included MSM with RAHCV from 2014 to 2021. The patients’ demographic, clinical, behavioral, and laboratory data were documented, as well as treatment and reinfection outcomes.  Results 237 men with RAHCV were included, 216 (91%) were PLWH. Median age was 46 years (IQR: 39–52), median CD4 count was 660/mm3 (IQR: 527–835). The annual incidence of RAHCV remained between 0.28% and 0.43%, but dropped to 0.02% in 2021 during the onset of the COVID-pandemic almost reaching micro-elimination. The reinfection incidence was 15.5 per 100 patient-years (95%-CI: 12.6-18.8), reinfection was associated with use of crystal methamphetamine (p=0.032) and ketamine (p=0.042). 31.3% had multiple reinfections, four reinfections occurred in PrEP users. Conclusions High treatment and cure rates did not lead to HCV elimination. A change in sexual behavior, potentially imposed by COVID-19 restrictions, led to micro-elimination in the NoCo cohort. As RAHCV is prevalent in HIV-positive and -negative MSM, surveillance is necessary to consolidate elimination goals.


Subject(s)
Coinfection , COVID-19 , Hepatitis C
10.
medrxiv; 2023.
Preprint in English | medRxiv | ID: ppzbmed-10.1101.2023.12.04.23299372

ABSTRACT

Background: COVID-19 disruptions in Africa in 2020-2022 contributed to reductions in malaria control activities including antimalarial surveillance programs. This study investigated the malaria burden and distribution on the background of active transmission of SARS-CoV-2 in Southern Ghana. Specifically, it aimed to identify epidemiological factors that can maximise programmatic control for both diseases, utilising community health education and medical screening (CHEMS). Methods: Between October-December 2022, prospective cross-sectional surveys, with CHEMS were conducted in Greater Accra and Central regions, where 994 participants enrolled either at a hospital or community setting provided demographic and clinical data including history of clinical malaria infection and antimalarial treatment in the past two weeks. Of this study population, 953 provided nasal/throat swabs for COVID-19 RT-PCR testing, with a subset of 136 participants also providing finger-prick blood for malaria RDT testing. Results: The study population comprised of 73.6% adults, with 54.6% COVID-19 vaccination rate. Overall, 18.1% of participants had a history of clinical malaria, which was associated (adjusted odds ratio > 1.50, P-value [≤] 0.022) with COVID-19 symptoms and positivity, study area and hospital setting, suggestive of overlaps in the epidemiological risk for malaria. On a background of widespread SARS-CoV-2 infections (12-37%), malaria parasitaemia was detected in 6%, with 2% being co-infections. Among the malaria positives, 9.5% had a history of antimalarial treatment, which suggested that their infections were recrudescent parasitaemia. Conclusion: The overlaps in the epidemiological risk for malaria and COVID-19 indicate that innovative surveillance programs, with community engagement are needed to maximise control interventions including treatment of asymptomatic malaria infections.


Subject(s)
Coinfection , Severe Acute Respiratory Syndrome , COVID-19 , Malaria , Communication Disorders , Recurrence
11.
biorxiv; 2023.
Preprint in English | bioRxiv | ID: ppzbmed-10.1101.2023.11.20.567923

ABSTRACT

The emergence of the COVID-19 pandemic prompted increased interest in seasonal human coronaviruses. 229E, OC43, NL63 and HKU1 are endemic seasonal coronaviruses that cause the common cold and are associated with generally mild respiratory symptoms. In this study, we identified cell lines that exhibited cytopathic effects (CPE) upon infection by three of these coronaviruses and characterized their viral replication kinetics and the effect of infection on host surface receptor expression. We found that NL63 produced CPE in LLC-MK2 cells, while OC43 produced CPE in MRC-5, HCT-8 and WI-38 cell lines, while 229E produced CPE in MRC-5 and WI-38 by day 3 post-infection. We observed a sharp increase in nucleocapsid and spike viral RNA (vRNA) from day 3 to day 5 post-infection for all viruses, however the abundance and the proportion of vRNAs copies measured in the supernatants and cell lysates of infected cells varied considerably depending on the virus-host cell pair. Importantly, we observed modulation of coronavirus entry and attachment receptors upon infection. Infection with 229E and OC43 led to a downregulation of CD13 and GD3, respectively. In contrast, infection with NL63, and also with OC43, lead to an increase in ACE2 expression. Attempts to block entry of NL63 using either soluble ACE2 or anti-ACE2 monoclonal antibodies demonstrated the potential of these strategies to greatly reduce infection. Overall, our results enable a better understanding of seasonal coronaviruses infection kinetics in permissive cell lines, and reveal entry receptor modulation that may have implications in facilitating co-infections with multiple coronaviruses in humans. IMPORTANCESeasonal human coronavirus are an important cause of the common cold associated with generally mild upper respiratory tract infections that can result in respiratory complications for some individuals. There are no vaccines available for these viruses, with only limited antiviral therapeutic options to treat the most severe cases. A better understanding of how these viruses interact with host cells is essential to identify new strategies to prevent infection-related complications. By analyzing viral replication kinetics in different permissive cell lines, we find that cell-dependent host factors influence how viral genes are expressed and virus particles released. We also analyzed entry receptor expression on infected cells and found that these can be up or down modulated depending on the infecting coronavirus. Our findings raise concerns over the possibility of infection enhancement upon co-infection by some coronaviruses, which may facilitate genetic recombination and the emergence of new variants and strains.


Subject(s)
Coinfection , Seasonal Affective Disorder , COVID-19 , Respiratory Tract Infections
12.
researchsquare; 2023.
Preprint in English | PREPRINT-RESEARCHSQUARE | ID: ppzbmed-10.21203.rs.3.rs-3625807.v1

ABSTRACT

Purpose: During the autumn/winter respiratory syncytial virus (RSV) epidemics, bacterial co-infection is common and affects the severity of the disease. We aimed to understand the relationship between RSV-bacterial co-infections and clinical severity since the change of RSV seasonality after the COVID-19 pandemic. Methods: We conducted a prospective, sentinel surveillance study at 20 sites in Portugal in children under two years old hospitalized with RSV, between April 2021 and January 2023. The effect of co-infection with potentially pathogenic bacteria (PPB) on the length of hospitalization and disease severity (defined by the need for ventilation or admission to an intensive care unit-ICU) was investigated using multivariate linear and log-binomial regression models. Age group (<6 months/≥6 months) and prematurity (yes/no) were included in models as potential confounders. Results: We report two RSV off-season epidemics: June 2021-February 2022 and May-October 2022. Among 678 RSV hospitalizations, 67.4 % occurred in children under 6 months old and 15.3 % in pre-term; 20.4 % tested positive for PPB; median length of hospitalization was five days (IQR: 3-7days); 5.8 % had at least one underlying condition. The most common bacteria were Haemophilus influenzae and Streptococcus pneumoniae. Children co-infected with PPB had a higher rate of ICU admission (29.7 % versus 3.5 %, p<0.001), resulting in more prolonged hospitalizations (median of 7 days versus 5 days, p<0.001) and a 13-fold risk of having severe disease (RR: 13.2, 95 CI: 7.3-23.9). Conclusion: RSV-bacterial co-infection was associated with increased length of hospitalization and severe illness during off-season epidemics. This risk is probably overestimated, as laboratory testing for bacterial infections is usually higher in severely ill-appearing children. Measures to prevent outgrowth of pathogenic bacteria within the respiratory tract should be discussed.


Subject(s)
Bacterial Infections , Respiratory Syncytial Virus Infections , Coinfection , COVID-19
13.
medrxiv; 2023.
Preprint in English | medRxiv | ID: ppzbmed-10.1101.2023.09.12.23295464

ABSTRACT

The impact of COVID-19 in Africa has been a big concern since the beginning of the pandemic. However, low incidence of COVID-19 case severity and mortality has been reported in many African countries, although data are highly heterogeneous and, in some regions, like Sub-Saharan Africa, very scarce. Many of these regions are also the cradle of endemic infectious diseases like malaria. The aim of this study was to determine the prevalence of SARS-CoV-2, the diversity and origin of circulating variants as well as the frequency of co-infections with malaria in Equatorial Guinea. For this purpose, we conducted antigen diagnostic tests for SARS-CoV-2, and microscopy examinations for malaria of 1,556 volunteers at six health centres in Bioko and Bata from June to October 2021. Nasopharyngeal swab samples were also taken for molecular detection of SARS-CoV-2 by RT-qPCR and whole genome viral sequencing. We report 3.0% of SARS-CoV-2 and 24.4% of malaria prevalence over the sampling in Equatorial Guinea. SARS-CoV-2 cases were found at a similar frequency in all age groups, whereas the age groups most frequently affected by malaria were children (36.8% [95% CI 30.9-42.7]) and teenagers (34.7% [95% CI 29.5-39.9]). We found six cases of confirmed co-infection of malaria and SARS-CoV-2 distributed among all age groups, representing a 0.4% frequency of co-infection in the whole sampled population. Interestingly, the majority of malaria and SARS-CoV-2 co-infections were mild. We obtained the genome sequences of 43 SARS-CoV-2 isolates, most of which belong to the lineage Delta (AY.43) and that according to our pandemic-scale phylogenies were introduced from Europe in multiple occasions (7 transmission groups and 17 unique introductions). This study is relevant in providing first-time estimates of the actual prevalence of SARS-CoV-2 in this malaria-endemic country, with the identification of circulating variants, their origin, and the occurrence of SARS-CoV-2 and malaria co-infection.


Subject(s)
Coinfection , COVID-19 , Malaria
14.
medrxiv; 2023.
Preprint in English | medRxiv | ID: ppzbmed-10.1101.2023.08.20.23294345

ABSTRACT

Background: B-cell hypo-responsiveness has been associated with intestinal parasitic co-infection. The effect of parasite co-infection on antibody response to SARS-CoV-2 is unknown. Here, we aimed to determine antibody response to SARS-CoV-2 among COVID-19 patients co-infected with intestinal parasites and those without parasite co-infection. Methods: In this prospective cohort study, a total of 589 samples were serially collected from 72 RT-PCR-confirmed patients. Anti-SARS-CoV-2 nucleocapsid protein (NP) antibody titers were measured longitudinally during hospitalization. SARS-CoV-2 infection was confirmed by RT-PCR on samples obtained from nasopharyngeal swabs, while direct microscopic examination, modified Ritchie concentration, and Kato-Katz methods were used to identify parasites and ova from fresh stool samples. Data were analyzed using STATA version 14. Results: Of the 72 COVID-19 patients, 39 (54.2%) were co-infected with intestinal parasites while 33 (45.8%) had no parasitic co-infection. Overall, the median cut-off index (COI) for anti-NP antibody titer among COVID-19 patients co-infected with parasites was 6.91 (IQR: 0.55-40.7) compared to 7.51 (IQR: 0.21-59.21) in those without parasites (p=0.764). In addition, 174/261 [66.7% (95% CI: 60.68-72.16)] and 231/328 [70.4% (95% CI: 65.23-75.14)] specimens from COVID-19 patients with parasite co-infection and without parasites, respectively, had anti-SARS-CoV-2 antibody above the cut-off COI value (p=0.328). The positivity rate for anti-SARS-CoV-2 NP < 14 days after symptom onset was 66.3% (95% CI: 60.21-71.85) and 70.0% (95% CI: 64.72-74.74) for those not infected and co-infected with parasites, respectively (p=0.343). In addition, 31/72 (41.9%) of the patients who were negative at the time of enrollment were seroconverted. The trend in anti-NP antibodies among seroconverted individuals with and without parasites is also similar. Conclusions: Co-infection with parasitic infection has very little effect on the anti-SARS-CoV-2 antibody immune response. Further studies on the profile of neutralizing antibodies in parasite-endemic areas are warranted to ascertain vaccine efficacy.


Subject(s)
Coinfection , Intestinal Diseases, Parasitic , COVID-19 , Lung Diseases, Parasitic
15.
biorxiv; 2023.
Preprint in English | bioRxiv | ID: ppzbmed-10.1101.2023.07.28.551035

ABSTRACT

SARS-CoV-2 patients have been reported to have high rates of secondary Klebsiella pneumoniae infections. Klebsiella pneumoniae is a commensal that is typically found in the respiratory and gastrointestinal tracts. However, it can cause severe disease when a person's immune system is compromised. Despite a high number of K. pneumoniae cases reported in SARS-CoV-2 patients, a co-infection animal model evaluating the pathogenesis is not available. We describe a mouse model to study disease pathogenesis of SARS-CoV-2 and K. pneumoniae co-infection. BALB/cJ mice were inoculated with mouse-adapted SARS-CoV-2 followed by a challenge with K. pneumoniae. Mice were monitored for body weight change, clinical signs, and survival during infection. The bacterial load, viral titers, immune cell accumulation and phenotype, and histopathology were evaluated in the lungs. The co-infected mice showed severe clinical disease and a higher mortality rate within 48 h of K. pneumoniae infection. The co-infected mice had significantly elevated bacterial load in the lungs, however, viral loads were similar between co-infected and single-infected mice. Histopathology of co-infected mice showed severe bronchointerstitial pneumonia with copious intralesional bacteria. Flow cytometry analysis showed significantly higher numbers of neutrophils and macrophages in the lungs. Collectively, our results demonstrated that co-infection of SARS-CoV-2 with K. pneumoniae causes severe disease with increased mortality in mice.


Subject(s)
Klebsiella Infections , Pneumonia , Severe Acute Respiratory Syndrome , Coinfection
16.
biorxiv; 2023.
Preprint in English | bioRxiv | ID: ppzbmed-10.1101.2023.07.21.550109

ABSTRACT

The opportunistic fungus Aspergillus fumigatus has been found to cause coinfections in patients with severe SARS-CoV-2 virus infection, leading to COVID-19-associated pulmonary aspergillosis (CAPA). The CAPA all-cause mortality rate is approximately 50% and may be complicated by azole-resistance. Genomic epidemiology can help shed light on the genetics of A. fumigatus causing CAPA including the prevalence of alleles that are associated with azole-resistance. Here, a population genomic analysis of 21 CAPA isolates from four European countries is presented. The CAPA isolates were compared with A. fumigatus from a wider population of 167 non-CAPA clinical isolates and 73 environmental isolates. Bioinformatic analysis and antifungal susceptibility testing were performed to quantify resistance and identify possible genetically-encoded azole-resistant mechanisms. Phylogenetic analysis of the 21 CAPA isolates showed a lack of genetic distinction from the wider A. fumigatus population, with isolates distributed within two distinct clades (A and B), with the majority of the CAPA isolates in clade B (71.4%). The prevalence of phenotypic azole-resistance in CAPA was 14.3% (n=3/21); all three CAPA isolates contained a known resistance-associated cyp51A polymorphism. CAPA isolates are drawn from the wider A. fumigatus population rather than forming a unique genetic background showing that COVID-19 patients are susceptible to the entire A. fumigatus population. However, the relatively high prevalence of azole-resistance alleles that we document poses a threat to treatment success rates, warranting enhanced detection and surveillance of A. fumigatus genotypes in these patients. Furthermore, potential changes to antifungal first-line treatment guidelines may be needed to improve patient outcomes.


Subject(s)
Pulmonary Aspergillosis , Severe Acute Respiratory Syndrome , Coinfection , COVID-19
17.
preprints.org; 2023.
Preprint in English | PREPRINT-PREPRINTS.ORG | ID: ppzbmed-10.20944.preprints202307.0921.v1

ABSTRACT

We provide a summary of various epidemiological parameters related to COVID-19 such as incubation period, serial interval and other parameters. Understanding these parameters is important for developing prevention strategies. SARS-CoV-2 can be transmitted by droplets and close contact, but there is evidence of airborne transmission. Aerosol-generating procedures have been identified as one of the specific risk factors for healthcare workers. Super-spreading events refer to situations where a small number of individuals cause the majority of infections. The basic reproductive number (R0) and the spread parameter (k) are used to characterise the transmissibility of the disease. Estimated values for R0 range from 2 to 3 and the estimated value for k is 0.1.The duration of infectiousness depends on viral load and shedding. Viral load varies according to factors such as clinical spectrum, type of variant and vaccination status. The relationship between viral load and infectivity is not fully understood.With regard to the frequency of symptoms and signs of COVID-19, fever, cough, fatigue and dyspnoea are common. The prevalence of olfactory and gustatory dysfunction (OGD) varies between studies and countries. Age and comorbidities are factors associated with olfactory dysfunction.Estimates of the proportion of asymptomatic patients range from 6% to 96%. Asymptomatic transmission is considered likely and is important for control measures.We reviewed the quantitative semiology of COVID-19 is reported on sensitivity, specificity and likelihood ratios of signs.Finally, we also review risk factors for COVID-19 (including health care workers), co-infections, and epidemiology of variants..


Subject(s)
Fever , Coinfection , COVID-19 , Cough , Fatigue , Seizures
18.
researchsquare; 2023.
Preprint in English | PREPRINT-RESEARCHSQUARE | ID: ppzbmed-10.21203.rs.3.rs-3159433.v1

ABSTRACT

Systematic monitoring of SARS-CoV-2 co-infections between different lineages and assessing the risk of intra-host recombinant emergence are crucial for forecasting viral evolution. Here we present a comprehensive analysis of more than 2 million SARS-CoV-2 raw read datasets submitted to the European COVID-19 Data Portal to identify co-infections and intra-host recombination. Co-infection was observed in 0.35% of the investigated cases. Two independent procedures were implemented to detect intra-host recombination. We show that sensitivity is predominantly determined by the density of lineage-defining mutations along the genome, thus we used an expanded list of mutually exclusive defining mutations of specific variant combinations to increase statistical power. We call attention to multiple challenges rendering recombinant detection difficult and provide guidelines for the reduction of false positives arising from chimeric sequences produced during PCR amplification. Additionally, we identify three recombination hotspots of Delta – Omicron BA.1 intra-host recombinants.


Subject(s)
Coinfection , COVID-19
19.
researchsquare; 2023.
Preprint in English | PREPRINT-RESEARCHSQUARE | ID: ppzbmed-10.21203.rs.3.rs-3089476.v1

ABSTRACT

Background H5N1 influenza is a cause of severe pneumonia. Co-infection with influenza and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) may lead to poor prognosis in the epidemic of COVID-19. However, few studies have reported regarding patients co-infected with avian influenza and SARS-CoV-2. Case presentation A 52-year-old woman presented with fever for eight days and worsening shortness of breath and decreased blood pressure. Computed tomography (CT) revealed air bronchogram, lung consolidation and bilateral pleural effusion. Furthermore, polymerase chain reaction (PCR) of the bronchoalveolar lavage fluid (BALF) showed positivity for H5N1 and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Conclusion H5N1 influenza is a cause of severe pneumonia. The clinical presentation of the patient had a predomination of H5N1 influenza rather than COVID-19. A viral PCR analysis is necessary to demonstrate the pathogen of severe pneumonia. The patient exhibited an excellent prognosis upon the appropriate use of antiviral medicine.


Subject(s)
Coinfection , Fever , Pneumonia , Pleural Effusion , COVID-19 , Coronavirus Infections , Dyspnea
20.
Postgrad Med J ; 96(1137): 417-421, 2020 Jul.
Article in English | MEDLINE | ID: covidwho-20244607

ABSTRACT

All animal life on earth is thought to have a common origin and have common genetic mechanisms. Evolution has enabled differentiation of species. Pathogens likewise have evolved within various species and mostly come to a settled dynamic equilibrium such that co-existence results (pathogens ideally should not kill their hosts). Problems arise when pathogens jump species because the new host had not developed any resistance. These infections from related species are known as zoonoses. COVID-19 is the latest example of a virus entering another species but HIV (and various strains of influenza) were previous examples. HIV entered the human population from monkeys in Africa. These two papers outline the underlying principle of HIV and the differing epidemiologies in Africa, the USA and in Edinburgh. The underlying immunosuppression of HIV in Africa was initially hidden behind common infections and HIV first came to world awareness in focal areas of the USA as a disease seemingly limited to gay males. The epidemic of intravenous drug abuse in Edinburgh was associated with overlapping epidemics of bloodborne viruses like hepatitis B, hepatitis C and HIV.


Subject(s)
Coinfection/virology , HIV Infections/physiopathology , Hepatitis B/physiopathology , Hepatitis C/physiopathology , Animals , Disease Outbreaks , HIV Infections/genetics , HIV Infections/virology , HIV-1/genetics , HIV-1/pathogenicity , Hepatitis B/genetics , Hepatitis C/genetics , Humans , Needle Sharing/statistics & numerical data , Phylogeny , Substance Abuse, Intravenous/epidemiology , Zoonoses
SELECTION OF CITATIONS
SEARCH DETAIL