Abstract Some social settings such as households and workplaces, have been identified as high risk for SARS-CoV-2 transmission. Identifying and quantifying the importance of these settings is critical for designing interventions. A tightly-knit religious community in the UK experienced a very large COVID-19 epidemic in 2020, reaching 64.3% seroprevalence within 10 months, and we surveyed this community both for serological status and individual-level attendance at particular settings. Using these data, and a network model of people and places represented as a stochastic graph rewriting system, we estimated the relative contribution of transmission in households, schools and religious institutions to the epidemic, and the relative risk of infection in each of these settings. All congregate settings were important for transmission, with some such as primary schools and places of worship having a higher share of transmission than others. We found that the model needed a higher general-community transmission rate for women (3.3-fold), and lower susceptibility to infection in children to recreate the observed serological data. The precise share of transmission in each place was related to assumptions about the internal structure of those places. Identification of key settings of transmission can allow public health interventions to be targeted at these locations.
Abstract Conjunctival pneumococcal serotypes among members of a community have not been investigated well. We determined the prevalence and association of Streptococcus pneumoniae in the nasopharynx and conjunctiva among children in a community before pneumococcal conjugate vaccine introduction. In October 2016, conjunctival and nasopharyngeal swabs were collected from children (< 24 months old) and nasopharyngeal swabs from mothers in Nha Trang, Vietnam. Quantitative lytA PCR and DNA microarray were performed to detect and serotype S. pneumoniae . The association between S. pneumoniae in the nasopharynx and conjunctiva was evaluated using multivariable logistic regression model. Among 698 children, 62 (8.9%, 95% CI 6.9–11.2%) were positive for S. pneumoniae in the conjunctiva. Non-encapsulated S. pneumoniae were most commonly identified, followed by serotypes 6A, 6B, and 14. Nasopharyngeal and conjunctival detection were positively associated (aOR 47.30, 95% CI 24.07–92.97). Low birth-weight, day-care attendance, and recent eye symptoms were independently associated with S. pneumoniae detection in the conjunctiva (aOR 11.14, 95% CI 3.76–32.98, aOR 2.19, 95% CI 1.45–3.31, and aOR 3.59, 95% CI 2.21–5.84, respectively). Serotypes and genotypes in the conjunctiva and nasopharynx matched in 87% of the children. Three mothers’ nasopharyngeal pneumococcal samples had matched serotype and genotype with their child’s in the conjunctiva and nasopharynx. S. pneumoniae presence in nasopharynx and conjunctiva were strongly associated. The high concordance of serotypes suggests nasopharyngeal carriage may be a source of transmission to the conjunctiva.
Coronavirus disease 2019 (COVID-19) has been declared a pandemic by WHO, owing to its rapid global spread and alarming ability to quickly overwhelm health-care services as a result of patients requiring critical care. A pertinent question for COVID-19 mitigation strategies is whether the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus is less transmissible in hot and humid climates. Sajadi and colleagues1Sajadi MM Habibzadeh P Vintzileos A Shokouhi S Miralles-Wilhelm F Amoroso A Temperature, humidity and latitude analysis to predict potential spread and seasonality for COVID-19. SSRN, 2020https://ssrn.com/abstract=3550308Google Scholar found that regions with established community outbreaks had a lower mean temperature and specific humidity compared with areas that did not report substantial community transmission. Similar findings have been observed using ecological niche modelling2Wang J Tang K Feng K Lv W High temperature and high humidity reduce the transmission of COVID-19.SSRN. 2020; (published online March 9.) (preprint).https://ssrn.com/abstract=3551767Google Scholar and in comparisons of climate and transmission intensity.3Araujo MB Naimi B Spread of SARS-CoV-2 Coronavirus likely to be constrained by climate.medRxiv. 2020; (published online March 16.) (preprint).DOI: 10.1101/2020.03.12.20034728Google Scholar These studies, in addition to the observation that SARS-CoV-1 has a lower survival rate at higher temperatures and humidity, have been interpreted by some as sufficient evidence to assume that rising temperatures in the boreal summer are likely to facilitate COVID-19 control. However, these findings are prone to confounding, including the delay in spread to warmer regions of the world due to travel patterns.4Lai S Bogoch I Ruktanonchai N et al.Assessing spread risk of Wuhan novel coronavirus within and beyond China, January–April 2020: a travel network-based modelling study.medRxiv. 2020; (published March 9.) (preprint).DOI: 10.1101/2020.02.04.20020479Google Scholar Thus, it is essential to contextualise these findings considering the current global spread of COVID-19. As of April 8, 2020, 180 countries and territories across the globe had reported local SARS-CoV-2 transmission, 23 of which had reported imported cases only (appendix).5WHOCoronavirus disease 2019 (COVID-19). Situation report—79.https://www.who.int/docs/default-source/coronaviruse/situation-reports/20200408-sitrep-79-covid-19.pdf?sfvrsn=4796b143_6Date: April 8, 2020Date accessed: April 27, 2020Google Scholar At least ten countries in all WHO Regions have confirmed local transmission, spanning all climatic zones, from cold and dry to hot and humid regions. Notably, countries reporting local transmission include Malaysia, the Philippines, Indonesia, and Thailand, which represent popular travel destinations from China. Other countries outside of Asia including Burkina Faso, the Democratic Republic of the Congo, Panama, and Paraguay, with mean ambient temperatures greater than 25°C recorded between Jan 1, 2020, and March 31, 2020 (appendix), also report local transmission. The ability of SARS-CoV-2 to effectively spread globally, suggests that seasonality cannot be considered a key modulating factor of SARS-CoV-2 transmissibility. Although warmer weather might slightly reduce transmission of SARS-CoV-2, no evidence has suggested that warmer conditions will reduce the effectiveness of SARS-CoV-2 transmission to an extent that few additional interventions are needed to curb its spread. Further studies on the impact of climate variability, air pollution, and other extrinsic factors on COVID-19 transmission will need to consider population movement from locations with a high incidence, population susceptibility, and surveillance for respiratory infections. At present, policy makers must focus on reducing physical contact within communities and any COVID-19 risk predictions based on climate information alone should be interpreted with caution. We declare no competing interests. SF and RL contributed equally. Download .pdf (.24 MB) Help with pdf files Supplementary appendix
Significance Cross-protection from seasonal epidemics of human coronaviruses (HCoVs) has been hypothesized to contribute to the relative sparing of children during the early phase of the pandemic. Testing this relies on understanding the prepandemic age distribution of recent HCoV infections, but little is known about their dynamics. Using England and Wales as a case study, we use a transmission model to estimate the duration of immunity to seasonal coronaviruses, and show how cross-protection could have affected the age distribution of susceptibility during the first wave, and could alter SARS-CoV-2 transmission patterns over the coming decade.
BACKGROUND: In December, 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a novel coronavirus, emerged in Wuhan, China. Since then, the city of Wuhan has taken unprecedented measures in response to the outbreak, including extended school and workplace closures. We aimed to estimate the effects of physical distancing measures on the progression of the COVID-19 epidemic, hoping to provide some insights for the rest of the world. METHODS: To examine how changes in population mixing have affected outbreak progression in Wuhan, we used synthetic location-specific contact patterns in Wuhan and adapted these in the presence of school closures, extended workplace closures, and a reduction in mixing in the general community. Using these matrices and the latest estimates of the epidemiological parameters of the Wuhan outbreak, we simulated the ongoing trajectory of an outbreak in Wuhan using an age-structured susceptible-exposed-infected-removed (SEIR) model for several physical distancing measures. We fitted the latest estimates of epidemic parameters from a transmission model to data on local and internationally exported cases from Wuhan in an age-structured epidemic framework and investigated the age distribution of cases. We also simulated lifting of the control measures by allowing people to return to work in a phased-in way and looked at the effects of returning to work at different stages of the underlying outbreak (at the beginning of March or April). FINDINGS: Our projections show that physical distancing measures were most effective if the staggered return to work was at the beginning of April; this reduced the median number of infections by more than 92% (IQR 66-97) and 24% (13-90) in mid-2020 and end-2020, respectively. There are benefits to sustaining these measures until April in terms of delaying and reducing the height of the peak, median epidemic size at end-2020, and affording health-care systems more time to expand and respond. However, the modelled effects of physical distancing measures vary by the duration of infectiousness and the role school children have in the epidemic. INTERPRETATION: Restrictions on activities in Wuhan, if maintained until April, would probably help to delay the epidemic peak. Our projections suggest that premature and sudden lifting of interventions could lead to an earlier secondary peak, which could be flattened by relaxing the interventions gradually. However, there are limitations to our analysis, including large uncertainties around estimates of R0 and the duration of infectiousness. FUNDING: Bill & Melinda Gates Foundation, National Institute for Health Research, Wellcome Trust, and Health Data Research UK.
Significance Between June 2014 and February 2015, thousands of Ebola treatment beds were introduced in Sierra Leone, alongside other infection control measures. However, there has been criticism of the timing and focus of this response, and it remains unclear how much it contributed to curbing the 2014–2015 Ebola epidemic. Using a mathematical model, we estimated how many Ebola virus disease cases the response averted in each district of Sierra Leone. We estimated that 56,600 (95% credible interval: 48,300–84,500) Ebola cases were averted in Sierra Leone as a direct result of additional treatment beds. Moreover, the number of cases averted would have been even greater had beds been available 1 month earlier.
Introduction Data on the prevalence of nasopharyngeal carriage of S.pneumoniae in all age groups are important to help predict the impact of introducing pneumococcal conjugate vaccines (PCV) into routine infant immunization, given the important indirect effect of the vaccine. Yet most carriage studies are limited to children under five years of age. We here explore the association between carriage prevalence and serotype distribution in children aged ≥5 years and in adults compared to children. Methods We conducted a systematic review of studies providing carriage estimates across age groups in healthy populations not previously exposed to PCV, using MEDLINE and Embase. We used Bayesian linear meta-regression models to predict the overall carriage prevalence as well as the prevalence and distribution of vaccine and nonvaccine type (VT and NVT) serotypes in older age groups as a function of that in <5 y olds. Results Twenty-nine studies compromising of 20,391 individuals were included in the analysis. In all studies nasopharyngeal carriage decreased with increasing age. We found a strong positive linear association between the carriage prevalence in pre-school childen (<5 y) and both that in school aged children (5–17 y olds) and in adults. The proportion of VT serotypes isolated from carriers was consistently lower in older age groups and on average about 73% that of children <5 y among 5–17 y olds and adults respectively. We provide a prediction model to infer the carriage prevalence and serotype distribution in 5–17 y olds and adults as a function of that in children <5 years of age. Conclusion Such predictions are helpful for assessing the potential population-wide effects of vaccination programmes, e.g. via transmission models, and thus assist in the design of future pneumococcal conjugate vaccination strategies.
Abstract England has experienced a heavy burden of COVID-19, with multiple waves of SARS-CoV-2 transmission since early 2020 and high infection levels following the emergence and spread of Omicron variants since late 2021. In response to rising Omicron cases, booster vaccinations were accelerated and offered to all adults in England. Using a model fitted to more than 2 years of epidemiological data, we project potential dynamics of SARS-CoV-2 infections, hospital admissions and deaths in England to December 2022. We consider key uncertainties including future behavioural change and waning immunity and assess the effectiveness of booster vaccinations in mitigating SARS-CoV-2 disease burden between October 2021 and December 2022. If no new variants emerge, SARS-CoV-2 transmission is expected to decline, with low levels remaining in the coming months. The extent to which projected SARS-CoV-2 transmission resurges later in 2022 depends largely on assumptions around waning immunity and to some extent, behaviour, and seasonality.
Abstract East Asia is as a principal hotspot for emerging zoonotic infections. Understanding the likely pathways for their emergence and spread requires knowledge on human-human and human-animal contacts, but such studies are rare. We used self-completed and interviewer-completed contact diaries to quantify patterns of these contacts for 965 individuals in 2017/2018 in a high-income densely-populated area of China, Shanghai City. Interviewer-completed diaries recorded more social contacts (19.3 vs. 18.0) and longer social contact duration (35.0 vs. 29.1 hours) than self-reporting. Strong age-assortativity was observed in all age groups especially among young participants (aged 7–20) and middle aged participants (25–55 years). 17.7% of participants reported touching animals (15.3% (pets), 0.0% (poultry) and 0.1% (livestock)). Human-human contact was very frequent but contact with animals (especially poultry) was rare although associated with frequent human-human contact. Hence, this densely populated area is more likely to act as an accelerator for human-human spread but less likely to be at the source of a zoonosis outbreak. We also propose that telephone interview at the end of reporting day is a potential improvement of the design of future contact surveys.
Understanding changes in human mobility in the early stages of the COVID-19 pandemic is crucial for assessing the impacts of travel restrictions designed to reduce disease spread. Here, relying on data from mainland China, we investigate the spatio-temporal characteristics of human mobility between 1st January and 1st March 2020, and discuss their public health implications. An outbound travel surge from Wuhan before travel restrictions were implemented was also observed across China due to the Lunar New Year, indicating that holiday travel may have played a larger role in mobility changes compared to impending travel restrictions. Holiday travel also shifted healthcare pressure related to COVID-19 towards locations with lower healthcare capacity. Network analyses showed no sign of major changes in the transportation network after Lunar New Year. Changes observed were temporary and did not lead to structural reorganisation of the transportation network during the study period.
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