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1.
J Acquir Immune Defic Syndr ; 85(1): 66-72, 2020 09 01.
Article in English | MEDLINE | ID: covidwho-1860998

ABSTRACT

BACKGROUND: COVID-19 and its social responses threaten the health of people living with HIV. We conducted a rapid-response interview to assess COVID-19 protective behaviors of people living with HIV and the impact of their responses on HIV-related health care. METHOD: Men and women living with HIV (N = 162) aged 20-37 years participating in a longitudinal study of HIV treatment and care completed routine study measures and an assessment of COVID-19-related experiences. RESULTS: At baseline, most participants demonstrated HIV viremia, markers indicative of renal disorders, and biologically confirmed substance use. At follow-up, in the first month of responding to COVID-19, engaging in more social distancing behaviors was related to difficulty accessing food and medications and increased cancelation of health care appointments, both by self and providers. We observed antiretroviral therapy adherence had improved during the initial month of COVID-19 response. CONCLUSIONS: Factors that may pose added risk for COVID-19 severity were prevalent among people living with HIV, and those with greater risk factors did not practice more COVID-19 protective behaviors. Social distancing and other practices intended to mitigate the spread of COVID-19 interfered with HIV care, and impeded access to food and medications, although an immediate adverse impact on medication adherence was not evident. These results suggest social responses to COVID-19 adversely impacted the health care of people living with HIV, supporting continued monitoring to determine the long-term effects of co-occurring HIV and COVID-19 pandemics.


Subject(s)
Betacoronavirus , Coinfection/prevention & control , Coronavirus Infections/complications , Coronavirus Infections/prevention & control , HIV Infections/complications , Pandemics/prevention & control , Pneumonia, Viral/complications , Pneumonia, Viral/prevention & control , Adult , COVID-19 , Coinfection/virology , Coronavirus Infections/epidemiology , Female , Food Supply , Georgia/epidemiology , HIV Infections/epidemiology , HIV Infections/virology , HIV-1 , Humans , Male , Pneumonia, Viral/epidemiology , Risk Factors , SARS-CoV-2 , Viremia , Young Adult
2.
J Acquir Immune Defic Syndr ; 86(1): 19-21, 2021 01 01.
Article in English | MEDLINE | ID: covidwho-1861001

ABSTRACT

INTRODUCTION: Studies to examine whether HIV predisposes to a higher incidence of COVID-19 or more severe disease are accumulating. Initial studies from New York City suggested more severe disease among people living with HIV (PLWH), but this was during a time when hospitals were over-capacity and health systems stretched. This report presents the incidence and outcomes among PLWH with COVID-19 in San Francisco over the first 6 months of the pandemic. METHODS: Community transmission of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) was first reported in San Francisco on March 5, 2020. This report examines the match of the San Francisco Department of Public Health COVID-19 testing database and the San Francisco Department of Public Health HIV Surveillance case registry from March 24, 2020, to September 3, 2020. RESULTS: Among 4252 COVID-19 tests performed among PLWH, 4.5% (N = 193) were positive for COVID-19, compared with a 3.5% (N = 9626) positivity rate among the 272,555 people without HIV tested for COVID-19 (P < 0.001). The mean age of those infected with HIV/COVID-19 was 48 years (20-76), 38.9% White, 38.3% Latinx, 11.9% Black, and 91.2% were men. Only 54.6% of coinfected PLWH were housed, with the remainder marginally housed. The rate of severe illness with COVID-19 was not increased among PLWH. DISCUSSION: In San Francisco, susceptibility to COVID-19 was increased among PLWH over the first 6 months of the pandemic, although clinical outcomes were similar to those without HIV. Homelessness and higher rates of congregate living situations among PLWH likely accounted for this disparity. Special efforts to house patients with marginal housing during the COVID-19 pandemic are needed.


Subject(s)
COVID-19/epidemiology , Disease Susceptibility/virology , HIV Infections/epidemiology , Adolescent , Adult , Aged , Coinfection/epidemiology , Coinfection/virology , Female , Homeless Persons , Housing , Humans , Incidence , Male , Middle Aged , San Francisco/epidemiology , Young Adult
3.
West J Emerg Med ; 22(6): 1262-1269, 2021 Oct 26.
Article in English | MEDLINE | ID: covidwho-1761083

ABSTRACT

INTRODUCTION: Coinfection with severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) and another virus may influence the clinical trajectory of emergency department (ED) patients. However, little empirical data exists on the clinical outcomes of coinfection with SARS-CoV-2 METHODS: In this retrospective cohort analysis, we included adults presenting to the ED with confirmed, symptomatic coronavirus 2019 who also underwent testing for additional viral pathogens within 24 hours. To investigate the association between coinfection status with each of the outcomes, we performed logistic regression. RESULTS: Of 6,913 ED patients, 5.7% had coinfection. Coinfected individuals were less likely to experience index visit or 30-day hospitalization (odds ratio [OR] 0.57; 95% confidence interval [CI], 0.36-0.90 and OR 0.39; 95% CI, 0.25-0.62, respectively). CONCLUSION: Coinfection is relatively uncommon in symptomatic ED patients with SARS-CoV-2 and the clinical short- and long-term outcomes are more favorable in coinfected individuals.


Subject(s)
COVID-19/therapy , Coinfection/virology , Emergency Service, Hospital/statistics & numerical data , Hospitalization/statistics & numerical data , Adult , Aged , Aged, 80 and over , COVID-19/epidemiology , COVID-19/mortality , Coinfection/epidemiology , Female , Humans , Male , Middle Aged , Retrospective Studies , SARS-CoV-2 , Severity of Illness Index
4.
Microb Genom ; 8(3)2022 03.
Article in English | MEDLINE | ID: covidwho-1746155

ABSTRACT

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has infected almost 200 million people worldwide by July 2021 and the pandemic has been characterized by infection waves of viral lineages showing distinct fitness profiles. The simultaneous infection of a single individual by two distinct SARS-CoV-2 lineages may impact COVID-19 disease progression and provides a window of opportunity for viral recombination and the emergence of new lineages with differential phenotype. Several hundred SARS-CoV-2 lineages are currently well phylogenetically defined, but two main factors have precluded major coinfection/codetection and recombination analysis thus far: (i) the low diversity of SARS-CoV-2 lineages during the first year of the pandemic, which limited the identification of lineage defining mutations necessary to distinguish coinfecting/recombining viral lineages; and the (ii) limited availability of raw sequencing data where abundance and distribution of intrasample/intrahost variability can be accessed. Here, we assembled a large sequencing dataset from Brazilian samples covering a period of 18 May 2020 to 30 April 2021 and probed it for unexpected patterns of high intrasample/intrahost variability. This approach enabled us to detect nine cases of SARS-CoV-2 coinfection with well characterized lineage-defining mutations, representing 0.61 % of all samples investigated. In addition, we matched these SARS-CoV-2 coinfections with spatio-temporal epidemiological data confirming its plausibility with the cocirculating lineages at the timeframe investigated. Our data suggests that coinfection with distinct SARS-CoV-2 lineages is a rare phenomenon, although it is certainly a lower bound estimate considering the difficulty to detect coinfections with very similar SARS-CoV-2 lineages and the low number of samples sequenced from the total number of infections.


Subject(s)
COVID-19/virology , Coinfection/virology , SARS-CoV-2/genetics , Superinfection/virology , Brazil , Genome, Viral , Humans , Mutation , Phylogeny , Polymorphism, Single Nucleotide
5.
J Med Virol ; 93(9): 5310-5322, 2021 09.
Article in English | MEDLINE | ID: covidwho-1733920

ABSTRACT

The most consequential challenge raised by coinfection is perhaps the inappropriate generation of recombinant viruses through the exchange of genetic material among different strains. These genetically similar viruses can interfere with the replication process of each other and even compete for the metabolites required for the maintenance of the replication cycle. Due to the similarity in clinical symptoms of most viral respiratory tract infections, and their coincidence with COVID-19, caused by SARS-CoV-2, it is recommended to develop a comprehensive diagnostic panel for detection of respiratory and nonrespiratory viruses through the evaluation of patient samples. Given the resulting changes in blood markers, such as coagulation factors and white blood cell count following virus infection, these markers can be of diagnostic value in the detection of mixed infection in individuals already diagnosed with a certain viral illness. In this review, we seek to investigate the coinfection of SARS-CoV-2 with other respiratory and nonrespiratory viruses to provide novel insights into the development of highly sensitive diagnostics and effective treatment modalities.


Subject(s)
COVID-19/epidemiology , Coinfection , Virus Diseases/epidemiology , Coinfection/epidemiology , Coinfection/virology , Humans
6.
J Med Virol ; 94(4): 1670-1688, 2022 04.
Article in English | MEDLINE | ID: covidwho-1718413

ABSTRACT

Bangladesh is experiencing a second wave of COVID-19 since March 2021, despite the nationwide vaccination drive with ChAdOx1 (Oxford-AstraZeneca) vaccine from early February 2021. Here, we characterized 19 nasopharyngeal swab (NPS) samples from COVID-19 suspect patients using genomic and metagenomic approaches. Screening for SARS-CoV-2 by reverse transcriptase polymerase chain reaction and metagenomic sequencing revealed 17 samples of COVID-19 positive (vaccinated = 10, nonvaccinated = 7) and 2 samples of COVID-19 negative. We did not find any significant correlation between associated factors including vaccination status, age or sex of the patients, diversity or abundance of the coinfected organisms/pathogens, and the abundance of SARS-CoV-2. Though the first wave of the pandemic was dominated by clade 20B, Beta, V2 (South African variant) dominated the second wave (January 2021 to May 2021), while the third wave (May 2021 to September 2021) was responsible for Delta variants of the epidemic in Bangladesh including both vaccinated and unvaccinated infections. Noteworthily, the receptor binding domain (RBD) region of S protein of all the isolates harbored similar substitutions including K417N, E484K, and N501Y that signify the Beta, while D614G, D215G, D80A, A67V, L18F, and A701V substitutions were commonly found in the non-RBD region of Spike proteins. ORF7b and ORF3a genes underwent a positive selection (dN/dS ratio 1.77 and 1.24, respectively), while the overall S protein of the Bangladeshi SARS-CoV-2 isolates underwent negative selection pressure (dN/dS = 0.621). Furthermore, we found different bacterial coinfections like Streptococcus agalactiae, Neisseria meningitidis, Elizabethkingia anophelis, Stenotrophomonas maltophilia, Klebsiella pneumoniae, and Pseudomonas plecoglossicida, expressing a number of antibiotic resistance genes such as tetA and tetM. Overall, this approach provides valuable insights on the SARS-CoV-2 genomes and microbiome composition from both vaccinated and nonvaccinated patients in Bangladesh.


Subject(s)
COVID-19/virology , Metagenomics , SARS-CoV-2/genetics , Adolescent , Adult , Aged , Bacteria/classification , Bacteria/genetics , Bacterial Infections/epidemiology , Bacterial Infections/microbiology , Bacterial Infections/virology , Bangladesh/epidemiology , COVID-19/epidemiology , COVID-19/microbiology , COVID-19/prevention & control , Coinfection/epidemiology , Coinfection/microbiology , Coinfection/virology , Drug Resistance, Bacterial/genetics , Female , Genome, Bacterial/genetics , Genome, Viral/genetics , Humans , Male , Microbiota/genetics , Middle Aged , Mutation , Phylogeny , SARS-CoV-2/classification , SARS-CoV-2/isolation & purification , Selection, Genetic , Vaccination , Viral Proteins/genetics , Young Adult
7.
Viruses ; 14(2)2022 02 21.
Article in English | MEDLINE | ID: covidwho-1705332

ABSTRACT

Coinfection rates with other pathogens in coronavirus disease 2019 (COVID-19) varied during the pandemic. We assessed the latest prevalence of coinfection with viruses, bacteria, and fungi in COVID-19 patients for more than one year and its impact on mortality. A total of 436 samples were collected between August 2020 and October 2021. Multiplex real-time PCR, culture, and antimicrobial susceptibility testing were performed to detect pathogens. The coinfection rate of respiratory viruses in COVID-19 patients was 1.4%. Meanwhile, the rates of bacteria and fungi were 52.6% and 10.5% in hospitalized COVID-19 patients, respectively. Respiratory syncytial virus, rhinovirus, Acinetobacter baumannii, Escherichia coli, Pseudomonas aeruginosa, and Candida albicans were the most commonly detected pathogens. Ninety percent of isolated A. baumannii was non-susceptible to carbapenem. Based on a multivariate analysis, coinfection (odds ratio [OR] = 6.095), older age (OR = 1.089), and elevated lactate dehydrogenase (OR = 1.006) were risk factors for mortality as a critical outcome. In particular, coinfection with bacteria (OR = 11.250), resistant pathogens (OR = 11.667), and infection with multiple pathogens (OR = 10.667) were significantly related to death. Screening and monitoring of coinfection in COVID-19 patients, especially for hospitalized patients during the pandemic, are beneficial for better management and survival.


Subject(s)
Bacterial Infections/epidemiology , COVID-19/epidemiology , Coinfection/microbiology , Coinfection/virology , Mycoses/epidemiology , Virus Diseases/epidemiology , Adolescent , Adult , Bacteria/classification , Bacteria/pathogenicity , COVID-19/microbiology , COVID-19/virology , Coinfection/epidemiology , Coinfection/mortality , Cross Infection/epidemiology , Cross Infection/microbiology , Cross Infection/virology , Female , Fungi/classification , Fungi/pathogenicity , Humans , Male , Middle Aged , Prevalence , Republic of Korea/epidemiology , Viruses/classification , Viruses/pathogenicity , Young Adult
8.
Pediatr Infect Dis J ; 41(3): e95-e101, 2022 03 01.
Article in English | MEDLINE | ID: covidwho-1615776

ABSTRACT

BACKGROUND: The clinical impact of common human coronavirus (cHCoV) remains unclear. We studied the clinical manifestations of pediatric cHCoV infections and the possible modifying effects of codetected human rhinovirus (RV) and respiratory syncytial virus (RSV). METHODS: We used data from an 11-year-long prospective study of hospitalized children with community-acquired respiratory tract infections. Nasopharyngeal aspirates were analyzed with real-time polymerase chain reaction assay for cHCoV OC43, NL63, HKU1 and 229E, and 15 other respiratory viruses. We assessed disease severity based on the clinical factors hospitalization length, oxygen requirement, other respiratory support and supplementary fluids. RESULTS: cHCoV was detected in 341 (8%) of 4312 children. Among 104 children with single cHCoV detections, 58 (56%) had lower respiratory tract infection (LRTI) and 20 (19%) developed severe disease. The proportion with severe disease was lower among single cHCoV detections compared with single RSV detections (338 of 870; 39%), but similar to single RV detections (136 of 987; 14%). Compared with single cHCoV, codetected cHCoV-RSV was more often associated with LRTI (86 of 89; 97%) and severe disease (adjusted odds ratio, 3.3; 95% confidence interval: 1.6-6.7). LRTI was more frequent in codetected cHCoV-RV (52 of 68; 76%) than single cHCoV, but the risk of severe disease was lower (adjusted odds ratios, 0.3; 95% confidence interval: 0.1-1.0). CONCLUSIONS: cHCoV was associated with severe LRTI in hospitalized children. Viral codetections were present in two-thirds. Codetections of cHCoV-RV were associated with lower proportions of severe disease, suggesting a modifying effect of RV on HCoV.


Subject(s)
Coinfection/virology , Coronavirus Infections/virology , Picornaviridae Infections/virology , Respiratory Syncytial Virus Infections/virology , Adolescent , Child , Child, Hospitalized , Child, Preschool , Coinfection/epidemiology , Coinfection/therapy , Coronavirus Infections/epidemiology , Coronavirus Infections/therapy , Female , Humans , Infant , Infant, Newborn , Male , Norway/epidemiology , Picornaviridae Infections/epidemiology , Picornaviridae Infections/therapy , Prospective Studies , Respiratory Syncytial Virus Infections/epidemiology , Respiratory Syncytial Virus Infections/therapy
9.
J Med Virol ; 93(8): 4748-4755, 2021 08.
Article in English | MEDLINE | ID: covidwho-1610624

ABSTRACT

Respiratory infections are one of the most frequent reasons for medical consultations in children. In low resource settings such as in Lao People's Democratic Republic, knowledge gaps and the dearth of laboratory capacity to support differential diagnosis may contribute to antibiotic overuse. We studied the etiology, temporal trends, and genetic diversity of viral respiratory infections in children to provide evidence for prevention and treatment guidelines. From September 2014 to October 2015, throat swabs and nasopharyngeal aspirates from 445 children under 10 years old with symptoms of acute respiratory infection were collected at the Children Hospital in Vientiane. Rapid antigen tests were performed for influenza A and B and respiratory syncytial virus. Real-time reverse-transcription polymerase chain reactions (RT-PCRs) were performed to detect 16 viruses. Influenza infections were detected with a higher sensitivity using PCR than with the rapid antigen test. By RT-PCR screening, at least one pathogen could be identified for 71.7% of cases. Human rhinoviruses were most frequently detected (29.9%), followed by influenza A and B viruses combined (15.9%). We identify and discuss the seasonality of some of the infections. Altogether these data provide a detailed characterization of respiratory pathogens in Lao children and we provide recommendations for vaccination and further studies.


Subject(s)
Coinfection/epidemiology , Respiratory Tract Infections/epidemiology , Virus Diseases/epidemiology , Viruses/genetics , Acute Disease/epidemiology , Child , Child, Preschool , Coinfection/virology , Female , Humans , Infant , Infant, Newborn , Influenza, Human/diagnosis , Influenza, Human/epidemiology , Influenza, Human/virology , Laos/epidemiology , Male , Prevalence , Respiratory Syncytial Virus Infections/diagnosis , Respiratory Syncytial Virus Infections/epidemiology , Respiratory Syncytial Virus Infections/virology , Respiratory Tract Infections/virology , Viruses/classification , Viruses/isolation & purification
10.
Future Microbiol ; 17: 161-167, 2022 02.
Article in English | MEDLINE | ID: covidwho-1638319

ABSTRACT

The authors describe a case series of co-infection with COVID-19 and scrub typhus in two Indian patients. Clinical features like fever, cough, dyspnea and altered sensorium were common in both patients. Case 1 had lymphopenia, elevated IL-6 and history of hypertension, while case 2 had leukocytosis and an increased liver enzymes. Both patients had hypoalbuminemia and required admission to the intensive care unit; one of them succumbed to acute respiratory distress syndrome further complicated by multiple organ dysfunction syndrome. Seasonal tropical infections in COVID-19 patients in endemic settings may lead to significant morbidity and mortality. Therefore, high clinical suspicion and an early diagnosis for co-infections among COVID-19 patients are essential for better patient management.


Subject(s)
COVID-19/complications , COVID-19/diagnosis , Coinfection/diagnosis , Scrub Typhus/complications , Scrub Typhus/diagnosis , Adult , COVID-19/blood , Coinfection/microbiology , Coinfection/virology , Cough , Diagnosis, Differential , Dyspnea , Early Diagnosis , Fever , Humans , India , Male , Middle Aged , Multiple Organ Failure/complications , Respiratory Distress Syndrome/complications , Scrub Typhus/blood
11.
Viruses ; 14(1)2022 01 13.
Article in English | MEDLINE | ID: covidwho-1632083

ABSTRACT

Rhinoviruses (RVs) have been reported as one of the main viral causes for severe respiratory illnesses that may require hospitalization, competing with the burden of other respiratory viruses such as influenza and RSV in terms of severity, economic cost, and resource utilization. With three species and 169 subtypes, RV presents the greatest diversity within the Enterovirus genus, and despite the efforts of the research community to identify clinically relevant subtypes to target therapeutic strategies, the role of species and subtype in the clinical outcomes of RV infection remains unclear. This review aims to collect and organize data relevant to RV illness in order to find patterns and links with species and/or subtype, with a specific focus on species and subtype diversity in clinical studies typing of respiratory samples.


Subject(s)
Picornaviridae Infections/virology , Rhinovirus/classification , Rhinovirus/genetics , Asthma/etiology , Coinfection/virology , Enterovirus , Enterovirus Infections/virology , Genotyping Techniques , Hospitalization , Humans , Respiratory Tract Infections/virology , Serotyping
12.
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
13.
Emerg Microbes Infect ; 11(1): 412-423, 2022 Dec.
Article in English | MEDLINE | ID: covidwho-1585244

ABSTRACT

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


Subject(s)
Coinfection/virology , Influenza A virus/physiology , Influenza B virus/physiology , Respiratory System/virology , Rhinovirus/physiology , SARS-CoV-2/physiology , Virus Replication/physiology , Coinfection/immunology , Humans , Immunity, Innate , Interferons/physiology
14.
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
15.
PLoS Negl Trop Dis ; 15(11): e0009997, 2021 11.
Article in English | MEDLINE | ID: covidwho-1542166

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mimics the influenza A (H1N1) virus in terms of clinical presentation, transmission mechanism, and seasonal coincidence. Comprehensive data for the clinical severity of adult patients co-infected by both H1N1 and SARS-CoV-2, and, particularly, the relationship with PCR cycle threshold (Ct) values are not yet available. All participants in this study were tested for H1N1 and SARS-CoV-2 simultaneously at admission. Demographic, clinical, treatment, and laboratory data were extracted from electronic medical records and compared among adults hospitalized for H1N1 infection, SARS-CoV-2 infection and co-infection with both viruses. Ct values for viral RNA detection were further compared within SARS-CoV-2 and co-infection groups. Score on seven-category ordinal scale of clinical status at day 7 and day 14 were assessed. Among patients with monoinfection, H1N1 infection had higher frequency of onset symptoms but lower incidence of adverse events during hospitalization than SAR-CoV-2 infection (P < 0.05). Co-infection had an increased odds of acute kidney injury, acute heart failure, secondary bacterial infections, multilobar infiltrates and admittance to ICU than monoinfection. Score on seven-category scale at day 7 and day 14 was higher in patients with coinfection than patients with SAR-CoV-2 monoinfection (P<0.05). Co-infected patients had lower initial Ct values (referring to higher viral load) (median 32) than patients with SAR-CoV-2 monoinfection (median 36). Among co-infected patients, low Ct values were significantly and positively correlated with acute kidney injury and ARDS (P = 0.03 and 0.02, respectively). Co-infection by SARS-CoV-2 and H1N1 caused more severe disease than monoinfection by either virus in adult inpatients. Early Ct value could provide clues for the later trajectory of the co-infection. Multiplex molecular diagnostics for both viruses and early assessment of SAR-CoV-2 Ct values are recommended to achieve optimal treatment for improved clinical outcome.


Subject(s)
COVID-19/virology , Coinfection/virology , Influenza A Virus, H1N1 Subtype/physiology , Influenza, Human/virology , SARS-CoV-2/physiology , Adolescent , Adult , COVID-19/epidemiology , China/epidemiology , Female , Hospitalization , Humans , Influenza A Virus, H1N1 Subtype/genetics , Influenza, Human/epidemiology , Male , Middle Aged , Retrospective Studies , SARS-CoV-2/genetics , Viral Load , Young Adult
16.
Jpn J Infect Dis ; 74(6): 570-572, 2021 Nov 22.
Article in English | MEDLINE | ID: covidwho-1534553

ABSTRACT

An individual may contract coronavirus disease 2019 (COVID-19) and influenza simultaneously; hence, adequate measures must be undertaken for the next winter in Japan. In preparation for the future, this study aimed to clarify the incidence of influenza coinfection in patients with COVID-19 during the previous winter. We conducted a retrospective study of the medical records of 193 patients diagnosed with COVID-19 between January 31, 2020, and April 23, 2020, in a single hospital. We evaluated the incidence of COVID-19 and influenza coinfection. Using rapid diagnostic testing, we found that no patient with COVID-19 was coinfected with influenza. Coinfection with influenza and COVID-19 was rare during the past winter in Japan.


Subject(s)
COVID-19 , Coinfection , Influenza, Human , COVID-19/epidemiology , Coinfection/epidemiology , Coinfection/virology , Hospitals , Humans , Influenza, Human/epidemiology , Japan/epidemiology , Retrospective Studies
17.
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
18.
Cells ; 10(11)2021 11 16.
Article in English | MEDLINE | ID: covidwho-1523883

ABSTRACT

While the risk of SARS-CoV-2 infection and/or COVID-19 disease progression in the general population has been largely assessed, its impact on HIV-positive individuals remains unclear. We present clinical and immunological data collected in a cohort of HIV-infected young individuals during the first wave of COVID-19 pandemic. SARS-CoV-2 RNA, virus-specific antibodies, as well as the expression of factors involved in the anti-viral immune response were analyzed. Moreover, we set up an in vitro coinfection assay to study the mechanisms correlated to the coinfection process. Our results did not show any increased risk of severe COVID-19 in HIV-positive young individuals. In those subjects who contracted SARS-CoV-2 infection, an increase in IL-10 expression and production was observed. Furthermore, in the in vitro coinfection assay, we revealed a reduction in SARS-CoV-2 replication associated to an upregulation of IL-10. We speculate that IL-10 could play a crucial role in the course of SARS-CoV-2 infection in HIV-positive individuals. These results might help defining clinical management of HIV/SARS-CoV-2 co-infected young individuals, or putative indications for vaccination schedules in this population.


Subject(s)
COVID-19/immunology , Coinfection/immunology , HIV Infections/immunology , Adolescent , Adult , COVID-19/virology , Child , Child, Preschool , Coinfection/virology , HIV Infections/virology , Humans , Infant , Inflammation , Interleukin-10/blood , Interleukin-10/genetics , Male , RNA, Messenger/blood , SARS-CoV-2/immunology , Young Adult
19.
Viruses ; 12(8)2020 08 18.
Article in English | MEDLINE | ID: covidwho-1453290

ABSTRACT

Enteric viral co-infections, infections involving more than one virus, have been reported for a diverse group of etiological agents, including rotavirus, norovirus, astrovirus, adenovirus, and enteroviruses. These pathogens are causative agents for acute gastroenteritis and diarrheal disease in immunocompetent and immunocompromised individuals of all ages globally. Despite virus-virus co-infection events in the intestine being increasingly detected, little is known about their impact on disease outcomes or human health. Here, we review what is currently known about the clinical prevalence of virus-virus co-infections and how co-infections may influence vaccine responses. While experimental investigations into enteric virus co-infections have been limited, we highlight in vivo and in vitro models with exciting potential to investigate viral co-infections. Many features of virus-virus co-infection mechanisms in the intestine remain unclear, and further research will be critical.


Subject(s)
Coinfection/virology , Gastroenteritis/virology , Virus Diseases/physiopathology , Viruses/classification , Viruses/pathogenicity , Animals , Asymptomatic Infections , Disease Models, Animal , Feces/virology , Humans , Intestines/virology , Mice , Primates
20.
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
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