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1.
Microb Genom ; 7(11)2021 11.
Article in English | MEDLINE | ID: covidwho-1541625

ABSTRACT

Understanding the evolution of the SARS-CoV-2 virus in various regions of the world during the Covid-19 pandemic is essential to help mitigate the effects of this devastating disease. We describe the phylogenomic and population genetic patterns of the virus in Mexico during the pre-vaccination stage, including asymptomatic carriers. A real-time quantitative PCR screening and phylogenomic reconstructions directed at sequence/structure analysis of the spike glycoprotein revealed mutation of concern E484K in genomes from central Mexico, in addition to the nationwide prevalence of the imported variant 20C/S:452R (B.1.427/9). Overall, the detected variants in Mexico show spike protein mutations in the N-terminal domain (i.e. R190M), in the receptor-binding motif (i.e. T478K, E484K), within the S1-S2 subdomains (i.e. P681R/H, T732A), and at the basis of the protein, V1176F, raising concerns about the lack of phenotypic and clinical data available for the variants of interest we postulate: 20B/478K.V1 (B.1.1.222 or B.1.1.519) and 20B/P.4 (B.1.1.28.4). Moreover, the population patterns of single nucleotide variants from symptomatic and asymptomatic carriers obtained with a self-sampling scheme confirmed the presence of several fixed variants, and differences in allelic frequencies among localities. We identified the mutation N:S194L of the nucleocapsid protein associated with symptomatic patients. Phylogenetically, this mutation is frequent in Mexican sub-clades. Our results highlight the dual and complementary role of spike and nucleocapsid proteins in adaptive evolution of SARS-CoV-2 to their hosts and provide a baseline for specific follow-up of mutations of concern during the vaccination stage.


Subject(s)
COVID-19/virology , Coronavirus Nucleocapsid Proteins/genetics , Phylogeny , SARS-CoV-2/genetics , COVID-19/epidemiology , COVID-19/immunology , COVID-19/prevention & control , COVID-19 Vaccines/administration & dosage , Carrier State/prevention & control , Carrier State/virology , Genome, Viral , Humans , Mexico , Mutation , Phosphoproteins/genetics , SARS-CoV-2/classification , SARS-CoV-2/immunology , SARS-CoV-2/isolation & purification , Vaccination
3.
Nature ; 599(7883): 108-113, 2021 11.
Article in English | MEDLINE | ID: covidwho-1434121

ABSTRACT

Throughout the coronavirus disease 2019 (COVID-19) pandemic, countries have relied on a variety of ad hoc border control protocols to allow for non-essential travel while safeguarding public health, from quarantining all travellers to restricting entry from select nations on the basis of population-level epidemiological metrics such as cases, deaths or testing positivity rates1,2. Here we report the design and performance of a reinforcement learning system, nicknamed Eva. In the summer of 2020, Eva was deployed across all Greek borders to limit the influx of asymptomatic travellers infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and to inform border policies through real-time estimates of COVID-19 prevalence. In contrast to country-wide protocols, Eva allocated Greece's limited testing resources on the basis of incoming travellers' demographic information and testing results from previous travellers. By comparing Eva's performance against modelled counterfactual scenarios, we show that Eva identified 1.85 times as many asymptomatic, infected travellers as random surveillance testing, with up to 2-4 times as many during peak travel, and 1.25-1.45 times as many asymptomatic, infected travellers as testing policies that utilize only epidemiological metrics. We demonstrate that this latter benefit arises, at least partially, because population-level epidemiological metrics had limited predictive value for the actual prevalence of SARS-CoV-2 among asymptomatic travellers and exhibited strong country-specific idiosyncrasies in the summer of 2020. Our results raise serious concerns on the effectiveness of country-agnostic internationally proposed border control policies3 that are based on population-level epidemiological metrics. Instead, our work represents a successful example of the potential of reinforcement learning and real-time data for safeguarding public health.


Subject(s)
COVID-19/diagnosis , COVID-19/prevention & control , Carrier State/diagnosis , Carrier State/prevention & control , Machine Learning , Travel Medicine , Travel , COVID-19/epidemiology , COVID-19/transmission , Carrier State/epidemiology , Carrier State/transmission , Greece , Humans , Prevalence , Public Health
6.
Sci Rep ; 11(1): 14488, 2021 07 14.
Article in English | MEDLINE | ID: covidwho-1310812

ABSTRACT

Since its emergence, the phenomenon of SARS-CoV-2 transmission by seemingly healthy individuals has become a major challenge in the effort to achieve control of the pandemic. Identifying the modes of transmission that drive this phenomenon is a perquisite in devising effective control measures, but to date it is still under debate. To address this problem, we have formulated a detailed mathematical model of discrete human actions (such as coughs, sneezes, and touching) and the continuous decay of the virus in the environment. To take into account those discrete and continuous events we have extended the common modelling approach and employed a hybrid stochastic mathematical framework. This allowed us to calculate higher order statistics which are crucial for the reconstruction of the observed distributions. We focused on transmission within a household, the venue with the highest risk of infection and validated the model results against the observed secondary attack rate and the serial interval distribution. Detailed analysis of the model results identified the dominant driver of pre-symptomatic transmission as the contact route via hand-face transfer and showed that wearing masks and avoiding physical contact are an effective prevention strategy. These results provide a sound scientific basis to the present recommendations of the WHO and the CDC.


Subject(s)
COVID-19/prevention & control , COVID-19/transmission , Carrier State/prevention & control , Carrier State/transmission , Contact Tracing , Family Characteristics , Humans , Hygiene , Incidence , Masks , Models, Theoretical , Pandemics/prevention & control , Quarantine , Risk Factors , SARS-CoV-2
8.
Med Sci Monit ; 27: e929701, 2021 Jun 14.
Article in English | MEDLINE | ID: covidwho-1292186

ABSTRACT

BACKGROUND At the beginning of the COVID-19 pandemic, a cluster outbreak caused by an imported case from Hubei Province was reported in Xi'an City, Shaanxi Province, China. Ten patients from 2 families and 1 hospital were involved in the transmission. MATERIAL AND METHODS We conducted an epidemiological investigation to identify the cluster transmission of COVID-19. The demographic, epidemiological, clinical, laboratory, and cluster characteristics were described and analyzed. RESULTS From January 27 to February 13, 2020, a total of 10 individuals were confirmed to be infected with SARS-CoV-2 by the nucleic acid testing of nasopharyngeal swabs from 2 families and 1 hospital. Among the confirmed cases, 7 had atypical clinical symptoms and 3 were asymptomatic. The median times from onset to diagnosis and to discharge were 3.5 days (range, 1-5 days) and 19.5 days (range, 16-38 days), respectively. There were 4 patients whose exposure dates were 1, 3, 3, and 2 days earlier than the onset dates of their previous-generation cases, respectively. Four prevention and control measures were effectively used to interrupt the disease transmission. CONCLUSIONS SARS-CoV-2 can be easily transmitted within families and in hospitals, and asymptomatic patients could act as a source of disease transmission. The results of this outbreak at the early epidemic stage support the recommendation that individuals with confirmed COVID-19 and all their close contacts should be subjected to medical quarantined observation and nucleic acid screening as early as possible, even if they do not have any symptoms. Meanwhile, people in high-risk areas should improve their protective measures.


Subject(s)
Asymptomatic Infections/epidemiology , COVID-19/epidemiology , COVID-19/transmission , Carrier State/prevention & control , Carrier State/transmission , Pandemics/prevention & control , SARS-CoV-2/genetics , Adolescent , Adult , Aged , Aged, 80 and over , COVID-19/prevention & control , COVID-19/virology , COVID-19 Nucleic Acid Testing/methods , China/epidemiology , Female , Humans , Male , Mass Screening/methods , Middle Aged , Quarantine/methods , Real-Time Polymerase Chain Reaction , Reverse Transcriptase Polymerase Chain Reaction , Young Adult
9.
N Engl J Med ; 385(4): 320-329, 2021 07 22.
Article in English | MEDLINE | ID: covidwho-1287848

ABSTRACT

BACKGROUND: Information is limited regarding the effectiveness of the two-dose messenger RNA (mRNA) vaccines BNT162b2 (Pfizer-BioNTech) and mRNA-1273 (Moderna) in preventing infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and in attenuating coronavirus disease 2019 (Covid-19) when administered in real-world conditions. METHODS: We conducted a prospective cohort study involving 3975 health care personnel, first responders, and other essential and frontline workers. From December 14, 2020, to April 10, 2021, the participants completed weekly SARS-CoV-2 testing by providing mid-turbinate nasal swabs for qualitative and quantitative reverse-transcriptase-polymerase-chain-reaction (RT-PCR) analysis. The formula for calculating vaccine effectiveness was 100% × (1 - hazard ratio for SARS-CoV-2 infection in vaccinated vs. unvaccinated participants), with adjustments for the propensity to be vaccinated, study site, occupation, and local viral circulation. RESULTS: SARS-CoV-2 was detected in 204 participants (5%), of whom 5 were fully vaccinated (≥14 days after dose 2), 11 partially vaccinated (≥14 days after dose 1 and <14 days after dose 2), and 156 unvaccinated; the 32 participants with indeterminate vaccination status (<14 days after dose 1) were excluded. Adjusted vaccine effectiveness was 91% (95% confidence interval [CI], 76 to 97) with full vaccination and 81% (95% CI, 64 to 90) with partial vaccination. Among participants with SARS-CoV-2 infection, the mean viral RNA load was 40% lower (95% CI, 16 to 57) in partially or fully vaccinated participants than in unvaccinated participants. In addition, the risk of febrile symptoms was 58% lower (relative risk, 0.42; 95% CI, 0.18 to 0.98) and the duration of illness was shorter, with 2.3 fewer days spent sick in bed (95% CI, 0.8 to 3.7). CONCLUSIONS: Authorized mRNA vaccines were highly effective among working-age adults in preventing SARS-CoV-2 infection when administered in real-world conditions, and the vaccines attenuated the viral RNA load, risk of febrile symptoms, and duration of illness among those who had breakthrough infection despite vaccination. (Funded by the National Center for Immunization and Respiratory Diseases and the Centers for Disease Control and Prevention.).


Subject(s)
COVID-19 Vaccines , COVID-19/prevention & control , Viral Load , Adolescent , Adult , COVID-19/diagnosis , COVID-19/virology , COVID-19 Nucleic Acid Testing , COVID-19 Vaccines/immunology , Carrier State/diagnosis , Carrier State/prevention & control , Emergency Responders , Female , Health Personnel , Humans , Male , Middle Aged , Patient Acuity , Prospective Studies , SARS-CoV-2/isolation & purification , Treatment Outcome , Young Adult
11.
Epidemiol Infect ; 149: e91, 2021 04 14.
Article in English | MEDLINE | ID: covidwho-1182770

ABSTRACT

An outbreak of SARS-CoV2 infection in a Barcelona prison was studied. One hundred and forty-eight inmates and 36 prison staff were evaluated by rt-PCR, and 24.1% (40 prisoners, two health workers and four non-health workers) tested positive. In all, 94.8% of cases were asymptomatic. The inmates were isolated in prison module 4, which was converted into an emergency COVID unit. There were no deaths. Generalised screening and the isolation and evaluation of the people infected were key measures. Symptom-based surveillance must be supplemented by rapid contact-based monitoring in order to avoid asymptomatic spread among prisoners and the community at large.


Subject(s)
COVID-19/epidemiology , Carrier State/epidemiology , Infection Control , Prisons , Public Health , Quarantine , Adult , Aged , COVID-19/diagnosis , COVID-19/prevention & control , COVID-19 Nucleic Acid Testing , Carrier State/diagnosis , Carrier State/prevention & control , Disease Outbreaks , Health Personnel , Hospitalization , Humans , Male , Middle Aged , Prisoners , SARS-CoV-2 , Severity of Illness Index , Spain/epidemiology , Young Adult
12.
A A Pract ; 15(3): e01419, 2021 Mar 08.
Article in English | MEDLINE | ID: covidwho-1150452

ABSTRACT

The risk of aerosol transmission has been a key factor for the rapid dissemination of the coronavirus pandemic. Transportation of coronavirus disease 2019 (COVID-19)-infected patients with active air leaks could expose unprotected health care personnel and other patients to aerosolized viral particles. We devised a way to avoid aerosolization while the chest tube drain is on water seal. It involves placing an Ultipor100 viral filter on the suction port of the drain system as well as sealing off the safety valve. This mechanism allows positive pressure from an air leak to escape while on water seal while trapping viral particles.


Subject(s)
COVID-19/therapy , Carrier State/prevention & control , Chest Tubes/adverse effects , Disease Management , Inventions/trends , Postoperative Care/trends , COVID-19/epidemiology , Carrier State/epidemiology , Humans , Postoperative Care/methods
13.
Nature ; 590(7844): 134-139, 2021 02.
Article in English | MEDLINE | ID: covidwho-1065896

ABSTRACT

As countries in Europe gradually relaxed lockdown restrictions after the first wave, test-trace-isolate strategies became critical to maintain the incidence of coronavirus disease 2019 (COVID-19) at low levels1,2. Reviewing their shortcomings can provide elements to consider in light of the second wave that is currently underway in Europe. Here we estimate the rate of detection of symptomatic cases of COVID-19 in France after lockdown through the use of virological3 and participatory syndromic4 surveillance data coupled with mathematical transmission models calibrated to regional hospitalizations2. Our findings indicate that around 90,000 symptomatic infections, corresponding to 9 out 10 cases, were not ascertained by the surveillance system in the first 7 weeks after lockdown from 11 May to 28 June 2020, although the test positivity rate did not exceed the 5% recommendation of the World Health Organization (WHO)5. The median detection rate increased from 7% (95% confidence interval, 6-8%) to 38% (35-44%) over time, with large regional variations, owing to a strengthening of the system as well as a decrease in epidemic activity. According to participatory surveillance data, only 31% of individuals with COVID-19-like symptoms consulted a doctor in the study period. This suggests that large numbers of symptomatic cases of COVID-19 did not seek medical advice despite recommendations, as confirmed by serological studies6,7. Encouraging awareness and same-day healthcare-seeking behaviour of suspected cases of COVID-19 is critical to improve detection. However, the capacity of the system remained insufficient even at the low epidemic activity achieved after lockdown, and was predicted to deteriorate rapidly with increasing incidence of COVID-19 cases. Substantially more aggressive, targeted and efficient testing with easier access is required to act as a tool to control the COVID-19 pandemic. The testing strategy will be critical to enable partial lifting of the current restrictive measures in Europe and to avoid a third wave.


Subject(s)
COVID-19 Testing/statistics & numerical data , COVID-19/diagnosis , COVID-19/prevention & control , Carrier State/epidemiology , Models, Biological , Age Distribution , COVID-19/epidemiology , COVID-19/transmission , Carrier State/prevention & control , Carrier State/transmission , Female , France/epidemiology , Health Behavior , Hospitalization/statistics & numerical data , Humans , Incidence , Male , Pandemics/statistics & numerical data , Patient Acceptance of Health Care/statistics & numerical data , Physical Distancing , SARS-CoV-2/isolation & purification , Time Factors , Treatment Refusal/statistics & numerical data , World Health Organization
15.
Am J Infect Control ; 49(1): 120-122, 2021 Jan.
Article in English | MEDLINE | ID: covidwho-726382

ABSTRACT

Several countries have undertaken social distancing measures to stop SARS-CoV-2 spread. Asymptomatic carriers' prevalence is unknown and would provide essential information on hidden viral circulation. In our cross-sectional study, 1.82% of 330 asymptomatic confined individuals living in the community carried SARS-CoV-2 despite no contact with declared cases, raising concerns about unnoticed transmission.


Subject(s)
COVID-19/epidemiology , Carrier State/epidemiology , Physical Distancing , Adult , Aged , Attitude to Health , COVID-19/prevention & control , COVID-19/transmission , Carrier State/prevention & control , Carrier State/transmission , Communicable Disease Control , Female , Humans , Male , Middle Aged , Prevalence , Quebec/epidemiology , SARS-CoV-2 , Young Adult
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