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1.
Preprint in English | medRxiv | ID: ppmedrxiv-22268729

ABSTRACT

BackgroundThere is ongoing uncertainty regarding transmission chains and the respective roles of healthcare workers (HCWs) and elderly patients in nosocomial outbreaks of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in geriatric settings. MethodsWe performed a retrospective cohort study including patients with nosocomial coronavirus disease 2019 (COVID-19) in four outbreak-affected wards, and all SARS-CoV-2 RT-PCR positive HCWs from a Swiss university-affiliated geriatric acute-care hospital that admitted both Covid-19 and non-Covid-19 patients during the first pandemic wave in Spring 2020. We combined epidemiological and genetic sequencing data using a Bayesian modelling framework, and reconstructed transmission dynamics of SARS-CoV-2 involving patients and HCWs, in order to determine who infected whom. We evaluated general transmission patterns according to type of case (HCWs working in dedicated Covid-19 cohorting wards: HCWcovid; HCWs working in non-Covid-19 wards where outbreaks occurred: HCWoutbreak; patients with nosocomial Covid-19: patientnoso) by deriving the proportion of infections attributed to each type of case across all posterior trees and comparing them to random expectations. ResultsDuring the study period (March 1 to May 7, 2020) we included 180 SARS-CoV-2 positive cases: 127 HCWs (91 HCWcovid, 36 HCWoutbreak) and 53 patients. The attack rates ranged from 10-19% for patients, and 21% for HCWs. We estimated that there were 16 importation events (3 patients, 13 HCWs) that jointly led to 16 secondary cases. Most patient-to-patient transmission events involved patients having shared a ward (97.6%, 95% credible interval [CrI] 90.4-100%), in contrast to those having shared a room (44.4%, 95%CrI 27.8-62.5%). Transmission events tended to cluster by type of case: patientnoso were almost twice as likely to be infected by other patientnoso than expected (observed:expected ratio 1.91, 95%CrI 1.08 - 4.00, p = 0.02); similarly, HCWoutbreak were more than twice as likely to be infected by other HCWoutbreak than expected (2.25, 95%CrI 1.00-8.00, p = 0.04). The proportion of infectors of HCWcovid were as expected as random. The proportions of high transmitters ([≥]2 secondary cases) were significantly higher among HCWoutbreak than patientnoso in the late phases (26.2% vs. 13.4%, p<2.2e-16) of the outbreak. ConclusionsMost importation events were linked to HCW. Unexpectedly, transmission between HCWcovid was more limited than transmission between patients and HCWoutbreak. This highlights gaps in infection control and suggests possible areas of improvements to limit the extent of nosocomial transmission.

2.
Preprint in English | medRxiv | ID: ppmedrxiv-21266598

ABSTRACT

1Forecasts based on epidemiological modelling have played an important role in shaping public policy throughout the COVID-19 pandemic. This modelling combines knowledge about infectious disease dynamics with the subjective opinion of the researcher who develops and refines the model and often also adjusts model outputs. Developing a forecast model is difficult, resource- and time-consuming. It is therefore worth asking what modelling is able to add beyond the subjective opinion of the researcher alone. To investigate this, we analysed different real-time forecasts of cases of and deaths from COVID-19 in Germany and Poland over a 1-4 week horizon submitted to the German and Polish Forecast Hub. We compared crowd forecasts elicited from researchers and volunteers, against a) forecasts from two semi-mechanistic models based on common epidemiological assumptions and b) the ensemble of all other models submitted to the Forecast Hub. We found crowd forecasts, despite being overconfident, to outperform all other methods across all forecast horizons when forecasting cases (weighted interval score relative to the Hub ensemble 2 weeks ahead: 0.89). Forecasts based on computational models performed comparably better when predicting deaths (rel. WIS 1.26), suggesting that epidemiological modelling and human judgement can complement each other in important ways.

3.
Preprint in English | medRxiv | ID: ppmedrxiv-21266899

ABSTRACT

Recent months have demonstrated that emerging variants may set back the global COVID-19 response. The ability to rapidly assess the threat of new variants in real-time is critical for timely optimisation of control strategies. We extend the EpiEstim R package, designed to estimate the time-varying reproduction number (Rt), to estimate in real-time the effective transmission advantage of a new variant compared to a reference variant. Our method can combine information across multiple locations and over time and was validated using an extensive simulation study, designed to mimic a variety of real-time epidemic contexts. We estimate that the SARS-CoV-2 Alpha variant is 1.46 (95% Credible Interval 1.44-1.47) and 1.29, (95% CrI 1.29-1.30) times more transmissible than the wild type, using data from England and France respectively. We further estimate that Beta and Gamma combined are 1.25 (95% CrI 1.24-1.27) times more transmissible than the wildtype (France data). All results are in line with previous estimates from literature, but could have been obtained earlier and more easily with our off-the-shelf open-source tool. Our tool can be used as an important first step towards quantifying the threat of new variants in real-time. Given the popularity of EpiEstim, this extension will likely be used widely to monitor the co-circulation and/or emergence of multiple variants of infectious pathogens. Significance StatementEarly assessment of the transmissibility of new variants of an infectious pathogen is critical for anticipating their impact and designing appropriate interventions. However, this often requires complex and bespoke analyses relying on multiple data streams, including genomic data. Here we present a novel method and software to rapidly quantify the transmission advantage of new variants. Our method is fast and requires only routinely collected disease surveillance data, making it easy to use in real-time. The ongoing high level of SARS-CoV-2 circulation in a number of countries makes the emergence of new variants highly likely. Our work offers a powerful tool to help public health bodies monitor such emerging variants and rapidly detect those with increased transmissibility.

4.
Preprint in English | medRxiv | ID: ppmedrxiv-21265309

ABSTRACT

ObjectivesWe investigated the relative contribution of occupational (vs. community) exposure for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection among employees of a university-affiliated long-term care facility (LTCF), during the 1st pandemic wave in Switzerland (March to June 2020). MethodsWe performed a nested analysis of a seroprevalence study among all volunteering LTCF staff to determine community and nosocomial risk factors for SARS-CoV-2 seropositivity using modified Poison regression. We also combined epidemiological and genetic sequencing data from a coronavirus disease 2019 (COVID-19) outbreak investigation in a LTCF ward to infer transmission dynamics and acquisition routes of SARS-CoV-2, and evaluated strain relatedness using a maximum likelihood phylogenetic tree. ResultsAmong 285 LTCF employees, 176 participated in the seroprevalence study, of whom 30 (17%) were seropositive for SARS-CoV-2. Most (141/176, 80%) were healthcare workers (HCWs). Risk factors for seropositivity included exposure to a COVID-19 inpatient (adjusted prevalence ratio [aPR] 2.6; 95%CI 0.9-8.1) and community contact with a COVID-19 case (aPR 1.7; 95%CI 0.8-3.5). Among 18 employees included in the outbreak investigation, the outbreak reconstruction suggests 4 likely importation events by HCWs with secondary transmissions to other HCWs and patients. ConclusionsThese two complementary epidemiologic and molecular approaches suggest a substantial contribution of both occupational and community exposures to COVID-19 risk among HCWs in LTCFs. These data may help to better assess the importance of occupational health hazards and related legal implications during the COVID-19 pandemic.

5.
Preprint in English | medRxiv | ID: ppmedrxiv-21262164

ABSTRACT

BackgroundEnglands COVID-19 "roadmap out of lockdown" set out the timeline and conditions for the stepwise lifting of non-pharmaceutical interventions (NPIs) as vaccination roll-out continued. Here we assess the roadmap, the impact of the Delta variant, and potential future epidemic trajectories. MethodsWe extended a model of SARS-CoV-2 transmission to incorporate vaccination and multi-strain dynamics to explicitly capture the emergence of the Delta variant. We calibrated the model to English surveillance data using a Bayesian evidence synthesis framework, then modelled the potential trajectory of the epidemic for a range of different schedules for relaxing NPIs. FindingsThe roadmap was successful in offsetting the increased transmission resulting from lifting NPIs with increasing population immunity through vaccination. However due to the emergence of Delta, with an estimated transmission advantage of 73% (95%CrI: 68-79) over Alpha, fully lifting NPIs on 21 June 2021 as originally planned may have led to 3,400 (95%CrI: 1,300-4,400) peak daily hospital admissions under our central parameter scenario. Delaying until 19 July reduced peak hospitalisations by three-fold to 1,400 (95%CrI: 700-1,500) per day. There was substantial uncertainty in the epidemic trajectory, with particular sensitivity to estimates of vaccine effectiveness and the intrinsic transmissibility of Delta. InterpretationOur findings show that the risk of a large wave of COVID hospitalisations resulting from lifting NPIs can be substantially mitigated if the timing of NPI relaxation is carefully balanced against vaccination coverage. However, with Delta, it may not be possible to fully lift NPIs without a third wave of hospitalisations and deaths, even if vaccination coverage is high. Variants of concern, their transmissibility, vaccine uptake, and vaccine effectiveness must be carefully monitored as countries relax pandemic control measures. FundingNational Institute for Health Research, UK Medical Research Council, Wellcome Trust, UK Foreign, Commonwealth & Development Office. Research in contextO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed up to 23 July 2021 with no language restrictions using the search terms: (COVID-19 or SARS-CoV-2 or 2019-nCoV or "novel coronavirus") AND (vaccine or vaccination) AND ("non pharmaceutical interventions" OR "non-pharmaceutical interventions) AND (model*). We found nine studies that analysed the relaxation of controls with vaccination roll-out. However, none explicitly analysed real-world evidence balancing lifting of interventions, vaccination, and emergence of the Delta variant. Added value of this studyOur data synthesis approach combines real-world evidence from multiple data sources to retrospectively evaluate how relaxation of COVID-19 measures have been balanced with vaccination roll-out. We explicitly capture the emergence of the Delta variant, its transmissibility over Alpha, and quantify its impact on the roadmap. We show the benefits of maintaining NPIs whilst vaccine coverage continues to increase and capture key uncertainties in the epidemic trajectory after NPIs are lifted. Implications of all the available evidenceOur study shows that lifting interventions must be balanced carefully and cautiously with vaccine roll-out. In the presence of a new, highly transmissible variant, vaccination alone may not be enough to control COVID-19. Careful monitoring of vaccine uptake, effectiveness, variants, and changes in contact patterns as restrictions are lifted will be critical in any exit strategy.

6.
Preprint in English | medRxiv | ID: ppmedrxiv-21260746

ABSTRACT

BackgroundAs of July 2021, more than 180,000,000 cases of COVID-19 have been reported across the world, with more than 4 million deaths. Mathematical modelling and forecasting efforts have been widely used to inform policy-making and to create situational awareness. Methods and FindingsFrom 8th March to 29th November 2020, we produced weekly estimates of SARS-CoV-2 transmissibility and forecasts of deaths due to COVID-19 for countries with evidence of sustained transmission. The estimates and forecasts were based on an ensemble model comprising of three models that were calibrated using only the reported number of COVID-19 cases and deaths in each country. We also developed a novel heuristic to combine weekly estimates of transmissibility and potential changes in population immunity due to infection to produce forecasts over a 4-week horizon. We evaluated the robustness of the forecasts using relative error, coverage probability, and comparisons with null models. ConclusionsDuring the 39-week period covered by this study, we produced short- and medium-term forecasts for 81 countries. Both the short- and medium-term forecasts captured well the epidemic trajectory across different waves of COVID-19 infections with small relative errors over the forecast horizon. The model was well calibrated with 56.3% and 45.6% of the observations lying in the 50% Credible Interval in 1-week and 4-week ahead forecasts respectively. We could accurately characterise the overall phase of the epidemic up to 4-weeks ahead in 84.9% of country-days. The medium-term forecasts can be used in conjunction with the short-term forecasts of COVID-19 mortality as a useful planning tool as countries continue to relax stringent public health measures that were implemented to contain the pandemic.

7.
Preprint in English | medRxiv | ID: ppmedrxiv-21260537

ABSTRACT

Structured abstractO_ST_ABSObjectivesC_ST_ABSTo characterise within-hospital SARS-CoV-2 transmission across two waves of the COVID-19 pandemic. DesignA retrospective Bayesian modelling study to reconstruct transmission chains amongst 2181 patients and healthcare workers using combined viral genomic and epidemiological data. SettingA large UK NHS Trust with over 1400 beds and employing approximately 17,000 staff. Participants780 patients and 522 staff testing SARS-CoV-2 positive between 1st March 2020 and 25th July 2020 (Wave 1); and 580 patients and 299 staff testing SARS-CoV-2 positive between 30th November 2020 and 24th January 2021 (Wave 2). Main outcome measuresTransmission pairs including who-infected-whom; location of transmission events in hospital; number of secondary cases from each individual, including differences in onward transmission from community and hospital onset patient cases. ResultsStaff-to-staff transmission was estimated to be the most frequent transmission type during Wave 1 (31.6% of observed hospital-acquired infections; 95% CI 26.9 to 35.8%), decreasing to 12.9% (95% CI 9.5 to 15.9%) in Wave 2. Patient-to-patient transmissions increased from 27.1% in Wave 1 (95% CI 23.3 to 31.4%) to 52.1% (95% CI 48.0 to 57.1%) in Wave 2, to become the predominant transmission type. Over 50% of hospital-acquired infections were concentrated in 8/120 locations in Wave 1 and 10/93 locations in Wave 2. Approximately 40% to 50% of hospital-onset patient cases resulted in onward transmission compared to less than 4% of definite community-acquired cases. ConclusionsPrevention and control measures that evolved during the COVID-19 pandemic may have had a significant impact on reducing infections between healthcare workers, but were insufficient during the second wave to prevent a high number of patient-to-patient transmissions. As hospital-acquired cases appeared to drive most onward transmissions, more frequent and rapid identification and isolation of these cases will be required to break hospital transmission chains in subsequent pandemic waves.

8.
Preprint in English | medRxiv | ID: ppmedrxiv-21249564

ABSTRACT

We fitted a model of SARS-CoV-2 transmission in care homes and the community to regional surveillance data for England. Among control measures implemented, only national lockdown brought the reproduction number below 1 consistently; introduced one week earlier it could have reduced first wave deaths from 36,700 to 15,700 (95%CrI: 8,900-26,800). Improved clinical care reduced the infection fatality ratio from 1.25% (95%CrI: 1.18%-1.33%) to 0.77% (95%CrI: 0.71%-0.84%). The infection fatality ratio was higher in the elderly residing in care homes (35.9%, 95%CrI: 29.1%-43.4%) than those residing in the community (10.4%, 95%CrI: 9.1%-11.5%). England is still far from herd immunity, with regional cumulative infection incidence to 1st December 2020 between 4.8% (95%CrI: 4.4%-5.1%) and 15.4% (95%CrI: 14.9%-15.9%) of the population. One-sentence summaryWe fit a mathematical model of SARS-CoV-2 transmission to surveillance data from England, to estimate transmissibility, severity, and the impact of interventions

9.
Preprint in English | medRxiv | ID: ppmedrxiv-20101121

ABSTRACT

As the SARS-CoV-2 pandemic continues its rapid global spread, quantification of local transmission patterns has been, and will continue to be, critical for guiding pandemic response. Understanding the accuracy and limitations of statistical methods to estimate the reproduction number, R0, in the context of emerging epidemics is therefore vital to ensure appropriate interpretation of results and the subsequent implications for control efforts. Using simulated epidemic data we assess the performance of 6 commonly-used statistical methods to estimate R0 as they would be applied in a real-time outbreak analysis scenario - fitting to an increasing number of data points over time and with varying levels of random noise in the data. Method comparison was also conducted on empirical outbreak data, using Zika surveillance data from the 2015-2016 epidemic in Latin America and the Caribbean. We find that all methods considered here frequently over-estimate R0 in the early stages of epidemic growth on simulated data, the magnitude of which decreases when fitted to an increasing number of time points. This trend of decreasing bias over time can easily lead to incorrect conclusions about the course of the epidemic or the need for control efforts. We show that true changes in pathogen transmissibility can be difficult to disentangle from changes in methodological accuracy and precision, particularly for data with significant over-dispersion. As localised epidemics of SARS-CoV-2 take hold around the globe, awareness of this trend will be important for appropriately cautious interpretation of results and subsequent guidance for control efforts. Significance StatementIn line with a real-time outbreak analysis we use simulated epidemic data to assess the performance of 6 commonly-used statistical methods to estimate the reproduction number, R0, at different time points during the epidemic growth phase. We find that estimates of R0 are frequently overestimated by these methods in the early stages of epidemic growth, with decreasing bias when fitting to an increasing number of time points. Reductions in R0 estimates obtained at sequential time points during early epidemic growth may reflect increased methodological accuracy rather than reductions in pathogen transmissibility or effectiveness of interventions. As SARS-CoV-2 continues its geographic spread, awareness of this bias will be important for appropriate interpretation of results and subsequent guidance for control efforts.

10.
Preprint in English | medRxiv | ID: ppmedrxiv-20033357

ABSTRACT

BackgroundA range of case fatality ratio (CFR) estimates for COVID-19 have been produced that differ substantially in magnitude. MethodsWe used individual-case data from mainland China and cases detected outside mainland China to estimate the time between onset of symptoms and outcome (death or discharge from hospital). We next obtained age-stratified estimates of the CFR by relating the aggregate distribution of cases by dates of onset to the observed cumulative deaths in China, assuming a constant attack rate by age and adjusting for the demography of the population, and age- and location-based under-ascertainment. We additionally estimated the CFR from individual line-list data on 1,334 cases identified outside mainland China. We used data on the PCR prevalence in international residents repatriated from China at the end of January 2020 to obtain age-stratified estimates of the infection fatality ratio (IFR). Using data on age-stratified severity in a subset of 3,665 cases from China, we estimated the proportion of infections that will likely require hospitalisation. FindingsWe estimate the mean duration from onset-of-symptoms to death to be 17.8 days (95% credible interval, crI 16.9-19.2 days) and from onset-of-symptoms to hospital discharge to be 22.6 days (95% crI 21.1-24.4 days). We estimate a crude CFR of 3.67% (95% crI 3.56%-3.80%) in cases from mainland China. Adjusting for demography and under-ascertainment of milder cases in Wuhan relative to the rest of China, we obtain a best estimate of the CFR in China of 1.38% (95% crI 1.23%-1.53%) with substantially higher values in older ages. Our estimate of the CFR from international cases stratified by age (under 60 / 60 and above) are consistent with these estimates from China. We obtain an overall IFR estimate for China of 0.66% (0.39%-1.33%), again with an increasing profile with age. InterpretationThese early estimates give an indication of the fatality ratio across the spectrum of COVID-19 disease and demonstrate a strong age-gradient in risk.

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