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1.
AIDS Res Ther ; 19(1): 3, 2022 01 14.
Article in English | MEDLINE | ID: covidwho-1631500

ABSTRACT

BACKGROUND: Data on the association of human immunodeficiency virus (HIV) infection with adverse outcomes in patients with COVID-19 are conflicting. This systematic review and meta-analysis aimed to summarize the available information on the risk of hospitalization, severe disease, and death attributable to HIV in patients with COVID-19. METHODS: PubMed, EMBASE, Web of Science, and SCOPUS were searched through October 25, 2021, to identify relevant studies, without language restriction. A random-effects model was used to pool estimates. RESULTS: We included 44 studies reporting information from 38,971,065 patients with COVID-19. The pooled prevalence of HIV among COVID-19 patients was 26.9 ‰ (95% CI 22.7-31.3) and was significantly higher in studies conducted in Africa compared to those conducted elsewhere (118.5‰ [95% CI 84.8-156.9, 11 studies] vs 10.9‰ [95% CI 8.8-13.2, 27 studies]). In pooled analyses of unadjusted odds ratio, HIV-positive individuals were more likely to be admitted to hospital (OR: 1.49; 95% CI 1.01-2.21, 6 studies) compared to HIV-negative individuals. In the adjusted (for age and sex) analyses, HIV was associated with an increased risk of death (hazard ratio: 1.76, 95% CI 1.31-2.35, 2 studies). However, HIV was not associated with the severity of the disease (OR: 1.28; 95% CI 0.77-2.13, 13 studies), or death (OR: 0.81; 95% CI 0.47; 1.41, 23 studies) in patients with COVID-19 in the meta-analysis of unadjusted odds ratio. CONCLUSION: Our findings suggest that patients with HIV have an increased risk of hospital admission for COVID-19. HIV seems to be independently associated with increased risk of mortality in COVID-19 patient in adjusted analysis. However, this evidence was derived from only two studies.


Subject(s)
COVID-19 , Coinfection , HIV Infections , Coinfection/epidemiology , HIV Infections/complications , HIV Infections/epidemiology , Humans , Odds Ratio , SARS-CoV-2
2.
PLoS One ; 16(12): e0261849, 2021.
Article in English | MEDLINE | ID: covidwho-1623664

ABSTRACT

BACKGROUND: Tuberculosis (TB) and COVID-19 pandemics are both diseases of public health threat globally. Both diseases are caused by pathogens that infect mainly the respiratory system, and are involved in airborne transmission; they also share some clinical signs and symptoms. We, therefore, took advantage of collected sputum samples at the early stage of COVID-19 outbreak in Ghana to conduct differential diagnoses of long-standing endemic respiratory illness, particularly tuberculosis. METHODOLOGY: Sputum samples collected through the enhanced national surveys from suspected COVID-19 patients and contact tracing cases were analyzed for TB. The sputum samples were processed using Cepheid's GeneXpert MTB/RIF assay in pools of 4 samples to determine the presence of Mycobacterium tuberculosis complex. Positive pools were then decoupled and analyzed individually. Details of positive TB samples were forwarded to the NTP for appropriate case management. RESULTS: Seven-hundred and seventy-four sputum samples were analyzed for Mycobacterium tuberculosis in both suspected COVID-19 cases (679/774, 87.7%) and their contacts (95/774, 12.3%). A total of 111 (14.3%) were diagnosed with SARS CoV-2 infection and six (0.8%) out of the 774 individuals tested positive for pulmonary tuberculosis: five (83.3%) males and one female (16.7%). Drug susceptibility analysis identified 1 (16.7%) rifampicin-resistant tuberculosis case. Out of the six TB positive cases, 2 (33.3%) tested positive for COVID-19 indicating a coinfection. Stratifying by demography, three out of the six (50%) were from the Ayawaso West District. All positive cases received appropriate treatment at the respective sub-district according to the national guidelines. CONCLUSION: Our findings highlight the need for differential diagnosis among COVID-19 suspected cases and regular active TB surveillance in TB endemic settings.


Subject(s)
COVID-19/diagnosis , COVID-19/epidemiology , Coinfection/diagnosis , Coinfection/epidemiology , Mycobacterium tuberculosis/genetics , Pandemics/prevention & control , SARS-CoV-2/genetics , Tuberculosis, Pulmonary/diagnosis , Tuberculosis, Pulmonary/epidemiology , Antibiotics, Antitubercular/pharmacology , COVID-19/prevention & control , COVID-19/virology , Coinfection/virology , Diagnosis, Differential , Drug Resistance, Bacterial/drug effects , Female , Ghana/epidemiology , Humans , Male , Microbial Sensitivity Tests , Mycobacterium tuberculosis/drug effects , Rifampin/pharmacology , Sputum/microbiology , Tuberculosis, Pulmonary/microbiology
3.
Virol J ; 18(1): 205, 2021 10 12.
Article in English | MEDLINE | ID: covidwho-1619949

ABSTRACT

Co-infections have a key role in virus transmission in wild reservoir hosts. We investigated the simultaneous presence of astroviruses, coronaviruses, and paramyxoviruses in bats from Madagascar, Mayotte, Mozambique, and Reunion Island. A total of 871 samples from 28 bat species representing 8 families were tested by polymerase chain reactions (PCRs) targeting the RNA-dependent RNA-polymerase genes. Overall, 2.4% of bats tested positive for the presence of at least two viruses, only on Madagascar and in Mozambique. Significant variation in the proportion of co-infections was detected among bat species, and some combinations of co-infection were more common than others. Our findings support that co-infections of the three targeted viruses occur in bats in the western Indian Ocean region, although further studies are needed to assess their epidemiological consequences.


Subject(s)
Astroviridae Infections/epidemiology , Chiroptera/virology , Coinfection/epidemiology , Coronavirus Infections/epidemiology , Paramyxoviridae Infections/epidemiology , Animals , Madagascar , Mozambique , Reunion
4.
Proc Biol Sci ; 289(1966): 20212358, 2022 01 12.
Article in English | MEDLINE | ID: covidwho-1621738

ABSTRACT

There is growing experimental evidence that many respiratory viruses-including influenza and SARS-CoV-2-can interact, such that their epidemiological dynamics may not be independent. To assess these interactions, standard statistical tests of independence suggest that the prevalence ratio-defined as the ratio of co-infection prevalence to the product of single-infection prevalences-should equal unity for non-interacting pathogens. As a result, earlier epidemiological studies aimed to estimate the prevalence ratio from co-detection prevalence data, under the assumption that deviations from unity implied interaction. To examine the validity of this assumption, we designed a simulation study that built on a broadly applicable epidemiological model of co-circulation of two emerging or seasonal respiratory viruses. By focusing on the pair influenza-SARS-CoV-2, we first demonstrate that the prevalence ratio systematically underestimates the strength of interaction, and can even misclassify antagonistic or synergistic interactions that persist after clearance of infection. In a global sensitivity analysis, we further identify properties of viral infection-such as a high reproduction number or a short infectious period-that blur the interaction inferred from the prevalence ratio. Altogether, our results suggest that ecological or epidemiological studies based on co-detection prevalence data provide a poor guide to assess interactions among respiratory viruses.


Subject(s)
COVID-19 , Coinfection , Influenza, Human , Coinfection/epidemiology , Humans , Influenza, Human/epidemiology , Prevalence , SARS-CoV-2
5.
MMWR Morb Mortal Wkly Rep ; 70(5152): 1766-1772, 2021 Dec 31.
Article in English | MEDLINE | ID: covidwho-1599145

ABSTRACT

During June 2021, the highly transmissible† B.1.617.2 (Delta) variant of SARS-CoV-2, the virus that causes COVID-19, became the predominant circulating strain in the United States. U.S. pediatric COVID-19-related hospitalizations increased during July-August 2021 following emergence of the Delta variant and peaked in September 2021.§ As of May 12, 2021, CDC recommended COVID-19 vaccinations for persons aged ≥12 years,¶ and on November 2, 2021, COVID-19 vaccinations were recommended for persons aged 5-11 years.** To date, clinical signs and symptoms, illness course, and factors contributing to hospitalizations during the period of Delta predominance have not been well described in pediatric patients. CDC partnered with six children's hospitals to review medical record data for patients aged <18 years with COVID-19-related hospitalizations during July-August 2021.†† Among 915 patients identified, 713 (77.9%) were hospitalized for COVID-19 (acute COVID-19 as the primary or contributing reason for hospitalization), 177 (19.3%) had incidental positive SARS-CoV-2 test results (asymptomatic or mild infection unrelated to the reason for hospitalization), and 25 (2.7%) had multisystem inflammatory syndrome in children (MIS-C), a rare but serious inflammatory condition associated with COVID-19.§§ Among the 713 patients hospitalized for COVID-19, 24.7% were aged <1 year, 17.1% were aged 1-4 years, 20.1% were aged 5-11 years, and 38.1% were aged 12-17 years. Approximately two thirds of patients (67.5%) had one or more underlying medical conditions, with obesity being the most common (32.4%); among patients aged 12-17 years, 61.4% had obesity. Among patients hospitalized for COVID-19, 15.8% had a viral coinfection¶¶ (66.4% of whom had respiratory syncytial virus [RSV] infection). Approximately one third (33.9%) of patients aged <5 years hospitalized for COVID-19 had a viral coinfection. Among 272 vaccine-eligible (aged 12-17 years) patients hospitalized for COVID-19, one (0.4%) was fully vaccinated.*** Approximately one half (54.0%) of patients hospitalized for COVID-19 received oxygen support, 29.5% were admitted to the intensive care unit (ICU), and 1.5% died; of those requiring respiratory support, 14.5% required invasive mechanical ventilation (IMV). Among pediatric patients with COVID-19-related hospitalizations, many had severe illness and viral coinfections, and few vaccine-eligible patients hospitalized for COVID-19 were vaccinated, highlighting the importance of vaccination for those aged ≥5 years and other prevention strategies to protect children and adolescents from COVID-19, particularly those with underlying medical conditions.


Subject(s)
COVID-19/therapy , Adolescent , COVID-19/epidemiology , COVID-19 Vaccines/administration & dosage , Child , Child, Preschool , Coinfection/epidemiology , Female , Hospitalization , Hospitals , Humans , Infant , Male , Pediatric Obesity/epidemiology , Treatment Outcome , United States/epidemiology , Vaccination/statistics & numerical data
6.
Viruses ; 13(12)2021 12 16.
Article in English | MEDLINE | ID: covidwho-1580428

ABSTRACT

BACKGROUND: We aimed to compare the clinical severity in patients who were coinfected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and rhinovirus or monoinfected with a single one of these viruses. METHODS: The study period ranged from 1 March 2020 to 28 February 2021 (one year). SARS-CoV-2 and other respiratory viruses were identified by real-time reverse-transcription-PCR as part of the routine work at Marseille University hospitals. Bacterial and fungal infections were detected by standard methods. Clinical data were retrospectively collected from medical files. This study was approved by the ethical committee of our institute. RESULTS: A total of 6034/15,157 (40%) tested patients were positive for at least one respiratory virus. Ninety-three (4.3%) SARS-CoV-2-infected patients were coinfected with another respiratory virus, with rhinovirus being the most frequent (62/93, 67%). Patients coinfected with SARS-CoV-2 and rhinovirus were significantly more likely to report a cough than those with SARS-CoV-2 monoinfection (62% vs. 31%; p = 0.0008). In addition, they were also significantly more likely to report dyspnea than patients with rhinovirus monoinfection (45% vs. 36%; p = 0.02). They were also more likely to be transferred to an intensive care unit and to die than patients with rhinovirus monoinfection (16% vs. 5% and 7% vs. 2%, respectively) but these differences were not statistically significant. CONCLUSIONS: A close surveillance and investigation of the co-incidence and interactions of SARS-CoV-2 and other respiratory viruses is needed. The possible higher risk of increased clinical severity in SARS-CoV-2-positive patients coinfected with rhinovirus warrants further large scale studies.


Subject(s)
COVID-19/epidemiology , Coinfection/epidemiology , Coinfection/virology , Picornaviridae Infections/epidemiology , Adolescent , Adult , Aged , COVID-19/diagnosis , Child , Coinfection/diagnosis , Female , Humans , Incidence , Male , Middle Aged , Picornaviridae Infections/diagnosis , Picornaviridae Infections/virology , Real-Time Polymerase Chain Reaction , Respiratory Tract Infections/epidemiology , Respiratory Tract Infections/virology , Retrospective Studies , Rhinovirus , SARS-CoV-2 , Severity of Illness Index , Young Adult
7.
J Med Virol ; 94(1): 99-109, 2022 01.
Article in English | MEDLINE | ID: covidwho-1544351

ABSTRACT

A severe pandemic of Coronavirus Disease (COVID-19) has been sweeping the globe since 2019, and this time, it did not stop, with frequent mutations transforming into virulent strains, for instance, B.1.1.7, B.1.351, and B.1.427. In recent months, a fungal infection, mucormycosis has emerged with more fatal responses and significantly increased mortality rate. To measure the severity and potential alternative approaches against black fungus coinfection in COVID-19 patients, PubMed, Google Scholar, World Health Organization (WHO) newsletters, and other online resources, based on the cases reported and retrospective observational analysis were searched from the years 2015-2021. The studies reporting mucormycosis with Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) coinfection and/or demonstrating potential risk factors, such as a history of diabetes mellitus or suppressed immune system were included, and reports published in non-English language were excluded. More than 20 case reports and observational studies on black fungus coinfection in COVID-19 patients were eligible for inclusion. The results indicated that diabetes mellitus, hyperglycemic, and immunocompromised COVID-19 patients with mucormycosis were at a higher risk. We found that it was prudent to assess the potential risk factors and severity of invasive mycosis via standardized diagnostic and clinical settings. Large-scale studies need to be conducted to identify early biomarkers and optimization of diagnostic methods has to be established per population and geographical variation. This will not only help clinicians around the world to detect the coinfection in time but also will prepare them for future outbreaks of other potential pandemics.


Subject(s)
COVID-19/epidemiology , Coinfection/epidemiology , Mucormycosis/epidemiology , Mucormycosis/mortality , SARS-CoV-2/isolation & purification , Diabetes Mellitus/pathology , Humans , Hyperglycemia/pathology , Immunocompromised Host/physiology , Mucorales/growth & development , Mucorales/isolation & purification , Mucormycosis/pathology , Retrospective Studies , Risk Factors
8.
J Med Virol ; 94(1): 366-371, 2022 01.
Article in English | MEDLINE | ID: covidwho-1544350

ABSTRACT

Co-epidemics happening simultaneously can generate a burden on healthcare systems. The co-occurrence of SARS-CoV-2 with vector-borne diseases (VBD), such as malaria and dengue in resource-limited settings represents an additional challenge to the healthcare systems. Herein, we assessed the coinfection rate between SARS-CoV-2 and VBD to highlight the need to carry out an accurate diagnosis and promote timely measures for these infections in Luanda, the capital city of Angola. This was a cross-sectional study conducted with 105 subjects tested for the SARS-CoV-2 and VBD with a rapid detection test in April 2021. The participants tested positive for SARS-CoV-2 (3.80%), malaria (13.3%), and dengue (27.6%). Low odds related to testing positivity to SARS-CoV-2 or VBD were observed in participants above or equal to 40 years (odds ratio [OR]: 0.60, p = 0.536), while higher odds were observed in male (OR: 1.44, p = 0.392) and urbanized areas (OR: 3.78, p = 0.223). The overall co-infection rate between SARS-CoV-2 and VBD was 11.4%. Our findings showed a coinfection between SARS-CoV-2 with malaria and dengue, which could indicate the need to integrate the screening for VBD in the SARS-CoV-2 testing algorithm and the adjustment of treatment protocols. Further studies are warranted to better elucidate the relationship between COVID-19 and VBD in Angola.


Subject(s)
COVID-19/epidemiology , Coinfection/epidemiology , Dengue/epidemiology , Malaria/epidemiology , Vector Borne Diseases/epidemiology , Adolescent , Adult , Age Factors , Angola/epidemiology , Antibodies, Protozoan/blood , Antibodies, Viral/blood , COVID-19 Testing , Chikungunya Fever/epidemiology , Child , Child, Preschool , Cross-Sectional Studies , Female , Humans , Infant , Infant, Newborn , Male , Mass Screening , Middle Aged , RNA, Viral/blood , SARS-CoV-2/isolation & purification , Sex Factors , Young Adult , Zika Virus Infection/epidemiology
9.
J Med Virol ; 94(1): 303-309, 2022 01.
Article in English | MEDLINE | ID: covidwho-1544346

ABSTRACT

Emerging evidence shows co-infection with atypical bacteria in coronavirus disease 2019 (COVID-19) patients. Respiratory illness caused by atypical bacteria such as Mycoplasma pneumoniae, Chlamydia pneumoniae, and Legionella pneumophila may show overlapping manifestations and imaging features with COVID-19 causing clinical and laboratory diagnostic issues. We conducted a prospective study to identify co-infections with SARS-CoV-2 and atypical bacteria in an Indian tertiary hospital. From June 2020 to January 2021, a total of 194 patients with laboratory-confirmed COVID-19 were also tested for atypical bacterial pathogens. For diagnosing M. pneumoniae, a real-time polymerase chain reaction (PCR) assay and serology (IgM ELISA) were performed. C. pneumoniae diagnosis was made based on IgM serology. L. pneumophila diagnosis was based on PCR or urinary antigen testing. Clinical and epidemiological features of SARS-CoV-2 and atypical bacteria-positive and -negative patient groups were compared. Of the 194 patients admitted with COVID-19, 17 (8.8%) were also diagnosed with M. pneumoniae (n = 10) or C. pneumoniae infection (n = 7). Confusion, headache, and bilateral infiltrate were found more frequently in the SARS CoV-2 and atypical bacteria co-infection group. Patients in the M. pneumoniae or C. pneumoniae co-infection group were more likely to develop ARDS, required ventilatory support, had a longer hospital length of stay, and higher fatality rate compared to patients with only SARS-CoV-2. Our report highlights co-infection with bacteria causing atypical pneumonia should be considered in patients with SARS-CoV-2 depending on the clinical context. Timely identification of co-existing pathogens can provide pathogen-targeted treatment and prevent fatal outcomes of patients infected with SARS-CoV-2 during the current pandemic.


Subject(s)
Atypical Bacterial Forms/isolation & purification , COVID-19/pathology , Chlamydophila Infections/epidemiology , Coinfection/epidemiology , Legionnaires' Disease/epidemiology , Pneumonia, Mycoplasma/epidemiology , Adolescent , Adult , Aged , Aged, 80 and over , Chlamydophila pneumoniae/isolation & purification , Female , Humans , India , Legionella pneumophila/isolation & purification , Length of Stay , Male , Middle Aged , Mycoplasma pneumoniae/isolation & purification , Prospective Studies , SARS-CoV-2 , Severity of Illness Index , Young Adult
10.
J Med Virol ; 93(12): 6798-6802, 2021 Dec.
Article in English | MEDLINE | ID: covidwho-1530182

ABSTRACT

Viral infections have been on the rise for the past decades. The impact of the viruses worsened amidst the pandemic burdening the already overwhelmed health care system in African countries. This article sheds light on how the coronavirus together with the already existing viral infections, some of which re-emerged, impacted the continent. The strategies in place such as immunization, education, will have to be strengthened in all African countries to reduce the burden. Furthermore, governments can further collaborate with other countries in creating guidelines to reduce co-infection of the diseases.


Subject(s)
COVID-19/enzymology , COVID-19/virology , Coinfection/epidemiology , Coinfection/virology , Virus Diseases/epidemiology , Africa/epidemiology , COVID-19/immunology , Coinfection/immunology , Humans , Pandemics/prevention & control , SARS-CoV-2/immunology , Vaccination/methods , Virus Diseases/immunology , Virus Diseases/virology
11.
Emerg Infect Dis ; 27(11): 2923-2926, 2021 11.
Article in English | MEDLINE | ID: covidwho-1504649

ABSTRACT

During September 1, 2020-April 30, 2021, the California Department of Public Health, Richmond, California, USA, received 255 positive influenza molecular test results that matched with severe acute respiratory syndrome coronavirus 2 molecular test results; 58 (23%) persons were co-infected. Influenza activity was minimal in California, and co-infections were sporadic.


Subject(s)
COVID-19 , Coinfection , Influenza, Human , Coinfection/epidemiology , Humans , Influenza, Human/epidemiology , Public Health , SARS-CoV-2
12.
Western Pac Surveill Response J ; 12(3): 65-70, 2021.
Article in English | MEDLINE | ID: covidwho-1497710

ABSTRACT

Objective: Bacterial co-infections in cases of coronavirus disease 2019 (COVID-19) can lead to less favourable outcomes. The aim of this study was to determine the prevalence of primary bacterial co-infections among patients with COVID-19 in Brunei Darussalam. Methods: Seventy-one of 180 patients admitted to the National Isolation Centre between 9 March 2020 and 4 February 2021 were screened for primary bacterial co-infection (infection occurring £48 hour from admission). We compared patients with a primary bacterial co-infection to those without. Results: Of the 71 screened patients, 8 (11.2%) had a primary bacterial co-infection (sputum 37.5% [6/16], blood 2.8% [1/36], urine 1.7% [1/60]), for a period prevalence rate of 4.4% (respiratory tract infection 3.3% [6/180], bloodstream 0.6% [1/180], urine 0.6% [1/180]) among all COVID-19 patients. Older age, presence of comorbidity, symptoms at admission (fever, dyspnoea, nausea/vomiting), abnormal chest X-ray (CXR) and more severe COVID-19 (P < 0.05) were associated with primary bacterial co-infection. Primary bacterial co-infection was also associated with development of secondary infection and death (all P < 0.05). Only one patient with primary bacterial co-infection died (methicillin-sensitive Staphylococcus aureus septicaemia and multiorgan failure). Conclusion: Our study showed that primary bacterial co-infection affected 4.4% of patients with COVID-19 in Brunei Darussalam. Older age, presence of comorbidity, symptoms and abnormal CXR at admission and more severe disease were associated with a primary bacterial co-infection. Lower respiratory tract infection was the most common co-infection.


Subject(s)
COVID-19 , Coinfection , Staphylococcal Infections , Aged , Brunei , Coinfection/epidemiology , Humans , Prevalence , SARS-CoV-2
13.
Antimicrob Resist Infect Control ; 10(1): 155, 2021 10 30.
Article in English | MEDLINE | ID: covidwho-1496232

ABSTRACT

BACKGROUND: We defined the frequency of respiratory community-acquired bacterial co-infection in patients with COVID-19, i.e. patients with a positive SARS-CoV-2 PCR or a COVID-19 Reporting and Data System (CO-RADS) score ≥ 4, based on a complete clinical assessment, including prior antibiotic use, clinical characteristics, inflammatory markers, chest computed tomography (CT) results and microbiological test results. METHODS: Our retrospective study was conducted within a cohort of prospectively included patients admitted for COVID-19 in our tertiary medical centres between 1-3-2020 and 1-6-2020. A multidisciplinary study team developed a diagnostic protocol to retrospectively categorize patients as unlikely, possible or probable bacterial co-infection based on clinical, radiological and microbiological parameters in the first 72 h of admission. Within the three categories, we summarized patient characteristics and antibiotic consumption. RESULTS: Among 281 included COVID-19 patients, bacterial co-infection was classified as unlikely in 233 patients (82.9%), possible in 35 patients (12.4%) and probable in 3 patients (1.1%). Ten patients (3.6%) could not be classified due to inconclusive data. Within 72 h of hospital admission, 81% of the total study population and 78% of patients classified as unlikely bacterial co-infection received antibiotics. CONCLUSIONS: COVID-19 patients are unlikely to have a respiratory community-acquired bacterial co-infection. This study underpins recommendations for restrictive use of antibacterial drugs in patients with COVID-19.


Subject(s)
Bacterial Infections/epidemiology , COVID-19/diagnosis , Coinfection/epidemiology , Community-Acquired Infections/epidemiology , Hospitalization/statistics & numerical data , Pneumonia/epidemiology , Adult , Anti-Bacterial Agents/therapeutic use , Antimicrobial Stewardship , Bacterial Infections/drug therapy , Bacterial Infections/microbiology , COVID-19/complications , Cohort Studies , Coinfection/drug therapy , Community-Acquired Infections/microbiology , Female , Humans , Male , Middle Aged , Retrospective Studies , SARS-CoV-2
14.
Virol J ; 18(1): 159, 2021 08 03.
Article in English | MEDLINE | ID: covidwho-1496199

ABSTRACT

BACKGROUND: The multifaceted non-pharmaceutical interventions (NPIs) taken during the COVID-19 pandemic not only decrease the spreading of the SARS-CoV-2, but have impact on the prevalence of other viruses. This study aimed to explore the prevalence of common respiratory viruses among hospitalized children with lower respiratory tract infections (LRTI) in China during the COVID-19 pandemic. METHODS: Respiratory specimens were obtained from children with LRTI at Children's Hospital of Fudan University for detection of respiratory syncytial virus (RSV), adenovirus (ADV), parainfluenza virus (PIV) 1 to 3, influenza virus A (FluA), influenza virus B (FluB), human metapneumovirus (MPV) and rhinovirus (RV). The data were analyzed and compared between the year of 2020 (COVID-19 pandemic) and 2019 (before COVID-19 pandemic). RESULTS: A total of 7107 patients were enrolled, including 4600 patients in 2019 and 2507 patients in 2020. Compared with 2019, we observed an unprecedented reduction of RSV, ADV, FluA, FluB, and MPV infections in 2020, despite of reopening of schools in June, 2020. However, the RV infection was significantly increased in 2020 and a sharp increase was observed especially after reopening of schools. Besides, the PIV infection showed resurgent characteristic after September of 2020. The mixed infections were significantly less frequent in 2020 compared with the year of 2019. CONCLUSIONS: The NPIs during the COVID-19 pandemic have great impact on the prevalence of common respiratory viruses in China. Meanwhile, we do need to be cautious of a possible resurgence of some respiratory viruses as the COVID-19 restrictions are relaxed.


Subject(s)
COVID-19/epidemiology , Respiratory Tract Infections/epidemiology , Respiratory Tract Infections/virology , Age Distribution , COVID-19/prevention & control , Child , Child, Preschool , China/epidemiology , Coinfection/epidemiology , Coinfection/virology , Female , Hospitalization , Hospitals, Pediatric , Humans , Infant , Male , Prevalence , SARS-CoV-2 , Seasons , Viruses/classification , Viruses/isolation & purification
15.
J Antimicrob Chemother ; 76(Supplement_3): iii12-iii19, 2021 Sep 23.
Article in English | MEDLINE | ID: covidwho-1493834

ABSTRACT

BACKGROUND: The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) claimed over 4 million lives by July 2021 and continues to pose a serious public health threat. OBJECTIVES: Our retrospective study utilized respiratory pathogen panel (RPP) results in patients with SARS-CoV-2 to determine if coinfection (i.e. SARS-CoV-2 positivity with an additional respiratory virus) was associated with more severe presentation and outcomes. METHODS: All patients with negative influenza/respiratory syncytial virus testing who underwent RPP testing within 7 days of a positive SARS-CoV-2 test at a large, academic medical centre in New York were examined. Patients positive for SARS-CoV-2 with a negative RPP were compared with patients positive for SARS-CoV-2 and positive for a virus by RPP in terms of biomarkers, oxygen requirements and severe COVID-19 outcome, as defined by mechanical ventilation or death within 30 days. RESULTS: Of the 306 SARS-CoV-2-positive patients with RPP testing, 14 (4.6%) were positive for a non-influenza virus (coinfected). Compared with the coinfected group, patients positive for SARS-CoV-2 with a negative RPP had higher inflammatory markers and were significantly more likely to be admitted (P = 0.01). Severe COVID-19 outcome occurred in 111 (36.3%) patients in the SARS-CoV-2-only group and 3 (21.4%) patients in the coinfected group (P = 0.24). CONCLUSIONS: Patients infected with SARS-CoV-2 along with a non-influenza respiratory virus had less severe disease on presentation and were more likely to be admitted-but did not have more severe outcomes-than those infected with SARS-CoV-2 alone.


Subject(s)
COVID-19 , Coinfection , Coinfection/epidemiology , Humans , Pandemics , Retrospective Studies , SARS-CoV-2
16.
Int J Adolesc Med Health ; 33(3): 41-51, 2021 Apr 29.
Article in English | MEDLINE | ID: covidwho-1484890

ABSTRACT

OBJECTIVES: Tuberculosis (TB) is a leading infectious cause of death globally. Of the estimated 10 million people who developed active TB in 2019, 1.8 million (18%) were adolescents and young adults aged 15-24 years. Adolescents have poorer rates of TB screening, treatment initiation and completion compared to adults. Unfortunately, there is relatively less programme, research and policy focus on TB for adolescents aged 10-19 years. This article reviews the scope of health services and the relevant policy landscape for TB case notification and care/treatment, TB/HIV management, and latent TB infection for adolescents in Nigeria. Additionally, it discusses considerations for TB vaccines in this population. CONTENT: All Nigeria Federal Ministry of Health policy documents relevant to adolescent health services and TB, and published between 2000 and 2020 underwent narrative review. Findings were reported according to the service areas outlined in the Objectives. SUMMARY AND OUTLOOK: Nine policy documents were identified and reviewed. While multiple policies acknowledge the needs of adolescents in public health and specifically in TB programming, these needs are often not addressed in policy, nor in program integration and implementation. The lack of age-specific epidemiologic and clinical outcomes data for adolescents contributes to these policy gaps. Poor outcomes are driven by factors such as HIV co-infection, lack of youth-friendly health services, and stigma and discrimination. Policy guidelines and innovations should include adaptations tailored to adolescent needs. However, these adaptations cannot be developed without robust epidemiological data on adolescents at risk of, and living with TB. Gaps in TB care integration into primary reproductive, maternal-child health and nutrition services should be addressed across multiple policies, and mechanisms for supervision, and monitoring and evaluation of integration be developed to guide comprehensive implementation. Youth-friendly TB services are recommended to improve access to quality care delivered in a patient-centered approach.


Subject(s)
Health Policy , Public Health , Tuberculosis , Adolescent , COVID-19 , Coinfection/epidemiology , HIV Infections/epidemiology , Humans , Nigeria/epidemiology , Patient Acceptance of Health Care , Risk Factors , SARS-CoV-2 , Tuberculosis/drug therapy , Tuberculosis/epidemiology , Tuberculosis/prevention & control , Young Adult
17.
Antimicrob Resist Infect Control ; 10(1): 151, 2021 10 21.
Article in English | MEDLINE | ID: covidwho-1484323

ABSTRACT

Concomitant prevention of SARS-CoV-2 and extensively drug-resistant bacteria transmission is a difficult challenge in intensive care units dedicated to COVID-19 patients. We report a nosocomial cluster of four patients carrying NDM-1 plasmid-encoded carbapenemase-producing Enterobacter cloacae. Two main factors may have contributed to cross-transmission: misuse of gloves and absence of change of personal protective equipment, in the context of COVID-19-associated shortage. This work highlights the importance of maintaining infection control measures to prevent CPE cross-transmission despite the difficult context and that this type of outbreak can potentially involve several species of Enterobacterales.


Subject(s)
Carbapenem-Resistant Enterobacteriaceae/isolation & purification , Coinfection/epidemiology , Cross Infection/epidemiology , Enterobacter cloacae/isolation & purification , Enterobacteriaceae Infections/epidemiology , Infection Control/methods , Bacterial Proteins , COVID-19 , Carbapenem-Resistant Enterobacteriaceae/genetics , Disease Outbreaks , Enterobacter cloacae/genetics , Enterobacteriaceae Infections/microbiology , Enterobacteriaceae Infections/transmission , Humans , Intensive Care Units , Personal Protective Equipment , SARS-CoV-2 , beta-Lactamases
18.
Infection ; 49(6): 1299-1306, 2021 Dec.
Article in English | MEDLINE | ID: covidwho-1482322

ABSTRACT

PURPOSE: Thorough knowledge of the nature and frequency of co-infections is essential to optimize treatment strategies and risk assessment in cases of coronavirus disease 2019 (COVID-19). This study aimed to evaluate the multiplex polymerase chain reaction (PCR) screening approach for community-acquired bacterial pathogens (CABPs) at hospital admission, which could facilitate identification of bacterial co-infections in hospitalized COVID-19 patients. METHODS: Clinical data and biomaterials from 200 hospitalized COVID-19 patients from the observational cohort of the Competence Network for community-acquired pneumonia (CAPNETZ) prospectively recruited between March 17, 2020, and March 12, 2021 in 12 centers in Germany and Switzerland, were included in this study. Nasopharyngeal swab samples were analyzed on hospital admission using multiplex real-time reverse transcription (RT)-PCR for a broad range of CABPs. RESULTS: In total of 200 patients Staphylococcus aureus (27.0%), Haemophilus influenzae (13.5%), Streptococcus pneumoniae (5.5%), Moraxella catarrhalis (2.5%), and Legionella pneumophila (1.5%) were the most frequently detected bacterial pathogens. PCR detection of bacterial pathogens correlated with purulent sputum, and showed no correlation with ICU admission, mortality, and inflammation markers. Although patients who received antimicrobial treatment were more often admitted to the ICU and had a higher mortality rate, PCR pathogen detection was not significantly related to antimicrobial treatment. CONCLUSION: General CABP screening using multiplex PCR with nasopharyngeal swabs may not facilitate prediction or identification of bacterial co-infections in the early phase of COVID-19-related hospitalization. Most patients with positive PCR results appear to be colonized rather than infected at that time, questioning the value of routine antibiotic treatment on admission in COVID-19 patients.


Subject(s)
COVID-19 , Coinfection , Community-Acquired Infections , Legionella pneumophila , Pneumonia , Cohort Studies , Coinfection/diagnosis , Coinfection/epidemiology , Community-Acquired Infections/diagnosis , Humans , Multiplex Polymerase Chain Reaction , Prospective Studies , SARS-CoV-2
19.
Front Immunol ; 12: 715023, 2021.
Article in English | MEDLINE | ID: covidwho-1477819

ABSTRACT

Emerging evidence has unveiled the secondary infection as one of the mortal causes of post-SARS-CoV-2 infection, but the factors related to secondary bacterial or fungi infection remains largely unexplored. We here systematically investigated the factors that might contribute to secondary infection. By clinical examination index analysis of patients, combined with the integrative analysis with RNA-seq analysis in the peripheral blood mononuclear cell isolated shortly from initial infection, this study showed that the antibiotic catabolic process and myeloid cell homeostasis were activated while the T-cell response were relatively repressed in those with the risk of secondary infection. Further monitoring analysis of immune cell and liver injury analysis showed that the risk of secondary infection was accompanied by severe lymphocytopenia at the intermediate and late stages and liver injury at the early stages of SARS-CoV-2. Moreover, the metagenomics analysis of bronchoalveolar lavage fluid and the microbial culture analysis, to some extent, showed that the severe pneumonia-related bacteria have already existed in the initial infection.


Subject(s)
Bacterial Infections/epidemiology , COVID-19/pathology , Coinfection/epidemiology , Coinfection/mortality , Mycoses/epidemiology , Adult , Aged , Aged, 80 and over , Bacterial Infections/mortality , Bronchoalveolar Lavage Fluid/microbiology , CD4 Lymphocyte Count , Female , Humans , Leukocytes, Mononuclear/immunology , Liver/injuries , Liver/virology , Lymphopenia/immunology , Male , Middle Aged , Mycoses/mortality , Retrospective Studies , Risk Factors , SARS-CoV-2/immunology , T-Lymphocytes/immunology
20.
Microbiol Spectr ; 9(2): e0113821, 2021 10 31.
Article in English | MEDLINE | ID: covidwho-1476402

ABSTRACT

The aim of this study was to evaluate diagnostic means, host factors, delay of occurrence, and outcome of patients with COVID-19 pneumonia and fungal coinfections in the intensive care unit (ICU). From 1 February to 31 May 2020, we anonymously recorded COVID-19-associated pulmonary aspergillosis (CAPA), fungemia (CA-fungemia), and pneumocystosis (CA-PCP) from 36 centers, including results on fungal biomarkers in respiratory specimens and serum. We collected data from 154 episodes of CAPA, 81 of CA-fungemia, 17 of CA-PCP, and 5 of other mold infections from 244 patients (male/female [M/F] ratio = 3.5; mean age, 64.7 ± 10.8 years). CA-PCP occurred first after ICU admission (median, 1 day; interquartile range [IQR], 0 to 3 days), followed by CAPA (9 days; IQR, 5 to 13 days), and then CA-fungemia (16 days; IQR, 12 to 23 days) (P < 10-4). For CAPA, the presence of several mycological criteria was associated with death (P < 10-4). Serum galactomannan was rarely positive (<20%). The mortality rates were 76.7% (23/30) in patients with host factors for invasive fungal disease, 45.2% (14/31) in those with a preexisting pulmonary condition, and 36.6% (34/93) in the remaining patients (P = 0.001). Antimold treatment did not alter prognosis (P = 0.370). Candida albicans was responsible for 59.3% of CA-fungemias, with a global mortality of 45.7%. For CA-PCP, 58.8% of the episodes occurred in patients with known host factors of PCP, and the mortality rate was 29.5%. CAPA may be in part hospital acquired and could benefit from antifungal prescription at the first positive biomarker result. CA-fungemia appeared linked to ICU stay without COVID-19 specificity, while CA-PCP may not really be a concern in the ICU. Improved diagnostic strategy for fungal markers in ICU patients with COVID-19 should support these hypotheses. IMPORTANCE To diagnose fungal coinfections in patients with COVID-19 in the intensive care unit, it is necessary to implement the correct treatment and to prevent them if possible. For COVID-19-associated pulmonary aspergillosis (CAPA), respiratory specimens remain the best approach since serum biomarkers are rarely positive. Timing of occurrence suggests that CAPA could be hospital acquired. The associated mortality varies from 36.6% to 76.7% when no host factors or host factors of invasive fungal diseases are present, respectively. Fungemias occurred after 2 weeks in ICUs and are associated with a mortality rate of 45.7%. Candida albicans is the first yeast species recovered, with no specificity linked to COVID-19. Pneumocystosis was mainly found in patients with known immunodepression. The diagnosis occurred at the entry in ICUs and not afterwards, suggesting that if Pneumocystis jirovecii plays a role, it is upstream of the hospitalization in the ICU.


Subject(s)
COVID-19/epidemiology , Coinfection/mortality , Fungemia/epidemiology , Pneumonia, Pneumocystis/epidemiology , Pulmonary Aspergillosis/epidemiology , Aged , Antifungal Agents/therapeutic use , COVID-19/mortality , COVID-19/pathology , Coinfection/epidemiology , Critical Care , Female , France/epidemiology , Fungemia/drug therapy , Fungemia/mortality , Galactose/analogs & derivatives , Galactose/blood , Humans , Intensive Care Units/statistics & numerical data , Male , Mannans/blood , Middle Aged , Pneumonia, Pneumocystis/drug therapy , Pneumonia, Pneumocystis/mortality , Pulmonary Aspergillosis/drug therapy , Pulmonary Aspergillosis/mortality , Retrospective Studies , SARS-CoV-2 , Treatment Outcome
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