Initial viral load and decay kinetics of SARS-CoV-2 lineage B.1.1.7 in the upper respiratory tract of adults and children.
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ABSTRACT:
SUBMITTER: Costa R
PROVIDER: S-EPMC8356795 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:The role of human metapneumovirus (hMPV) in acute otitis media complicating upper respiratory tract infection (URI) was studied. Nasopharyngeal specimens from 700 URI episodes in 200 children were evaluated; 47 (7%) were positive for hMPV, 25 (3.6%) with hMPV as the only virus. Overall, 24% of URI episodes with hMPV only were complicated by acute otitis media, which was the lowest rate compared with other respiratory viruses. hMPV viral load was significantly higher in children with fever, but there was no difference in viral load in children with hMPV-positive URI with or without acute otitis media complication.
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Project description:New lineages of SARS-CoV-2 are of potential concern due to higher transmissibility, risk of severe outcomes, and/or escape from neutralizing antibodies. Lineage B.1.1.7 (the Alpha variant) became dominant in early 2021, but the association between transmissibility and risk factors, such as age of primary case and viral load remains poorly understood. Here, we used comprehensive administrative data from Denmark, comprising the full population (January 11 to February 7, 2021), to estimate household transmissibility. This study included 5,241 households with primary cases; 808 were infected with lineage B.1.1.7 and 4,433 with other lineages. Here, we report an attack rate of 38% in households with a primary case infected with B.1.1.7 and 27% in households with other lineages. Primary cases infected with B.1.1.7 had an increased transmissibility of 1.5-1.7 times that of primary cases infected with other lineages. The increased transmissibility of B.1.1.7 was multiplicative across age and viral load.
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Project description:Background.The etiologic inference of identifying a pathogen in the upper respiratory tract (URT) of children with pneumonia is unclear. To determine if viral load could provide evidence of causality of pneumonia, we compared viral load in the URT of children with World Health Organization-defined severe and very severe pneumonia and age-matched community controls.Methods.In the 9 developing country sites, nasopharyngeal/oropharyngeal swabs from children with and without pneumonia were tested using quantitative real-time polymerase chain reaction for 17 viruses. The association of viral load with case status was evaluated using logistic regression. Receiver operating characteristic (ROC) curves were constructed to determine optimal discriminatory viral load cutoffs. Viral load density distributions were plotted.Results.The mean viral load was higher in cases than controls for 7 viruses. However, there was substantial overlap in viral load distribution of cases and controls for all viruses. ROC curves to determine the optimal viral load cutoff produced an area under the curve of <0.80 for all viruses, suggesting poor to fair discrimination between cases and controls. Fatal and very severe pneumonia cases did not have higher viral load than less severe cases for most viruses.Conclusions.Although we found higher viral loads among pneumonia cases than controls for some viruses, the utility in using viral load of URT specimens to define viral pneumonia was equivocal. Our analysis was limited by lack of a gold standard for viral pneumonia.
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Project description:BackgroundThe outbreak of coronavirus disease 2019 (COVID-19) has aroused global public health concerns. Multiple clinical features relating to host profile but not for virus have been identified as the risk factors for illness severity and/or the outcomes in COVID-19.MethodsThe clinical features obtained from a cohort of 195 laboratory-confirmed, nasopharynx-sampled patients with COVID-19 in Guangdong, China from January 13 to February 29, 2020 were enrolled to this study. The differences in clinical features among 4 groups (mild, moderate, severe, and critical) and between 2 groups (severe vs nonsevere) were compared using one-way analysis of variance and Student's t test, respectively. Principal component analysis and correlation analysis were performed to identify the major factors that account for illness severity.ResultsIn addition to the previously described clinical illness severity-related factors, including older age, underlying diseases, higher level of C-reactive protein, D-dimer and aspartate aminotransferase, longer fever days and higher maximum body temperature, larger number of white blood cells and neutrophils but relative less lymphocytes, and higher ratio of neutrophil to lymphocytes, we found that the initial viral load is an independent factor that accounts for illness severity in COVID-19 patients.ConclusionsThe initial viral load of severe acute respiratory syndrome coronavirus 2 is a novel virological predictor for illness severity of COVID-19.
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Project description:Respiratory infectious diseases are mainly caused by viruses or bacteria that often interact with one another. Although their presence is a prerequisite for subsequent infections, viruses and bacteria may be present in the nasopharynx without causing any respiratory symptoms. The upper respiratory tract hosts a vast range of commensals and potential pathogenic bacteria, which form a complex microbial community. This community is assumed to be constantly subject to synergistic and competitive interspecies interactions. Disturbances in the equilibrium, for instance due to the acquisition of new bacteria or viruses, may lead to overgrowth and invasion. A better understanding of the dynamics between commensals and pathogens in the upper respiratory tract may provide better insight into the pathogenesis of respiratory diseases. Here we review the current knowledge regarding specific bacterial-bacterial and viral-bacterial interactions that occur in the upper respiratory niche, and discuss mechanisms by which these interactions might be mediated. Finally, we propose a theoretical model to summarize and illustrate these mechanisms.
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Project description:The amount of SARS-CoV-2 detected in the upper respiratory tract (URT viral load) is a key driver of transmission of infection. Current evidence suggests that mechanisms constraining URT viral load are different from those controlling lower respiratory tract viral load and disease severity. Understanding such mechanisms may help to develop treatments and vaccine strategies to reduce transmission. Combining mathematical modelling of URT viral load dynamics with transcriptome analyses we aimed to identify mechanisms controlling URT viral load. COVID-19 patients were recruited in Spain during the first wave of the pandemic. RNA sequencing of peripheral blood and targeted NanoString nCounter transcriptome analysis of nasal epithelium were performed and gene expression analysed in relation to paired URT viral load samples collected within 15 days of symptom onset. Proportions of major immune cells in blood were estimated from transcriptional data using computational differential estimation. Weighted correlation network analysis (adjusted for cell proportions) and fixed transcriptional repertoire analysis were used to identify associations with URT viral load, quantified as standard deviations (z-scores) from an expected trajectory over time.
2023-04-01 | E-MTAB-12791 | biostudies-arrayexpress
Project description:Relationships between viral load, severity of illness, and transmissibility of virus are fundamental to understanding pathogenesis and devising better therapeutic and prevention strategies for COVID-19. Here we present within-host modelling of viral load dynamics observed in the upper respiratory tract (URT), drawing upon 2172 serial measurements from 605 subjects, collected from 17 different studies. We developed a mechanistic model to describe viral load dynamics and host response and contrast this with simpler mixed-effects regression analysis of peak viral load and its subsequent decline. We observed wide variation in URT viral load between individuals, over 5 orders of magnitude, at any given point in time since symptom onset. This variation was not explained by age, sex, or severity of illness, and these variables were not associated with the modelled early or late phases of immune-mediated control of viral load. We explored the application of the mechanistic model to identify measured immune responses associated with the control of the viral load. Neutralising antibodies correlated strongly with modelled immune-mediated control of viral load amongst subjects who produced neutralising antibodies. Our models can be used to identify host and viral factors which control URT viral load dynamics, informing future treatment and transmission blocking interventions.
| S-EPMC8755404 | biostudies-literature
Project description:BackgroundRespiratory pathogens including Streptococcus pneumoniae and Haemophilus influenzae, are implicated in the pathogenicity of acute lower respiratory infection (ALRI). These are also commonly found in both healthy and sick children. In this study, we describe the first data on the most frequent bacteria and viruses detected in the nasopharynx of children from the general population in the Eastern DR Congo.MethodsFrom January 2014 to June 2015, nasopharyngeal samples from 375 children aged from 2 to 60 months attending health centres for immunisation or growth monitoring were included in the study. Multiplex real-time PCR assays were used for detection of 15 different viruses and 5 bacterial species and for determination of pneumococcal serotypes/serogroups in the nasopharyngeal secretions.ResultsHigh levels of S. pneumoniae were detected in 77% of cases, and H. influenzae in 51%. Rhinovirus and enterovirus were the most commonly found viruses, while respiratory syncytial virus (RSV) was rare (1%). Co-occurrence of both bacteria and viruses at high levels was detected in 33% of the children. The pneumococcal load was higher in those children who lived in a dwelling with an indoor kitchen area with an open fire, i.e. a kitchen with an open fire for cooking located inside the dwelling with the resultant smoke passing to the living room and/or bedrooms; this was also higher in children from rural areas as compared to children from urban areas or children not living in a dwelling with an indoor kitchen area with an open fire/not living in this type of dwelling. Immunization with 2-3 doses of PCV13 was associated with lower rates of pneumococcal detection. Half of the identified serotypes were non-PCV13 serotypes. The most common non-PCV13 serotypes/serogroups were 15BC, 10A, and 12F, while 5, 6, and 19F were the most prevalent PCV13 serotypes/serogroups.ConclusionsThe burden of respiratory pathogens including S. pneumoniae in Congolese children was high but relatively few children had RSV. Non-PCV13 serotypes/serogroups became predominant soon after PCV13 was introduced in DR Congo.
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