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1.
Acta Veterinaria et Zootechnica Sinica ; 53(9):2819-2832, 2022.
Article in Chinese | EMBASE | ID: covidwho-2080952

ABSTRACT

The 13th Five-Year National Key Research and Development Program has established a key project of "Prevention and Control of Major Animal Diseases, Efficient and Safe Husbandry Technology Research and Development" (Animal Project), which supported scientific and technological innovation research in the field of animal epidemic prevention and control, efficient and safe breeding and breeding environment treatment. This project carried out the design of "whole chain design and integrated implementation" according to basic research, key technology research and development and integrated demonstration to solve the important basic theory and technical bottleneck of animal breeding in China. Based on the method of bibliometric, a statistical analysis was conducted of the papers supported mainly by the project to master the research progress and hot spots of the special project in basic research and frontier theory. Moreover, the future key research direction and development trend in the field of animal husbandry and veterinary medicine was discussed in combination with the layout of animal husbandry and veterinary related projects in the 14th Five-Year Plan. The results showed that this special funded papers had achieved breakthrough research in the basic research fields of major animal diseases and zoonotic diseases such as the COVID-19, Zika virus and African Swine Fever Achievements: Agriculture-related universities and scientific research institutes cooperate closely and have made great contributions;International cooperation is not only with the United States and other developed countries, but also closely cooperated with developing countries such as Pakistan and Egypt related to the "Belt and Road" initiative. The probability of publishing high-quality papers which cooperated with scientific research teams in developed countries has increased significantly;Research hotspots mainly focus on epidemiology, pathogen replication and evolution, drug resistance, pathogen and host interaction and network regulation, immune and pathogenic mechanisms, cross-species transmission, etc. The livestock and poultry special project focuses on the research direction of the prevention and control of major livestock and poultry diseases and efficient and safe breeding, and has made important research progress in major basic theories, supporting the research and application demonstration of key core technologies. The 14th Five-Year National Key Research and Development Program will make a comprehensive layout in the field of animal seed industry innovation, prevention and control of animal diseases, purification and eradication, nutrition regulation and efficient breeding, waste resource utilization and green breeding, breeding equipment and intelligent breeding. Copyright © 2022 Editorial Board, Institute of Animal Science of the Chinese Academy of Agricultural Sciences.

2.
Sustainability ; 14(14):18, 2022.
Article in English | Web of Science | ID: covidwho-1979361

ABSTRACT

Vaccine hesitancy plays a key role in vaccine delay and refusal, but its measurement is still a challenge due to multiple intricacies and uncertainties in factors. This paper attempts to tackle this problem through fuzzy cognitive inference techniques. Firstly, we formulate a vaccine hesitancy determinants matrix containing multi-level factors. Relations between factors are formulated through group decision-making of domain experts, which results in a fuzzy cognitive map. The subjective uncertainty of linguistic variables is expressed by fuzzy numbers. A double-weighted method is designed to integrate the distinguished decisions, in which the subjective hesitancy is considered for each decision. Next, three typical scenarios are constructed to identify key and sensitive factors under different experimental conditions. The experimental results are further discussed, which enrich the approaches of vaccine hesitancy estimation for the post-pandemic global recovery.

3.
PubMed; 2022.
Preprint in English | PubMed | ID: ppcovidwho-338328

ABSTRACT

BACKGROUND: Mechanisms underlying persistent cardiopulmonary symptoms following SARS-CoV-2 infection (post-acute sequelae of COVID-19 "PASC" or "Long COVID") remain unclear. The purpose of this study was to elucidate the pathophysiology of cardiopulmonary PASC using multimodality cardiovascular imaging including cardiopulmonary exercise testing (CPET), cardiac magnetic resonance imaging (CMR) and ambulatory rhythm monitoring. METHODS: We performed CMR, CPET, and ambulatory rhythm monitoring among adults > 1 year after PCR-confirmed SARS-CoV-2 infection in the UCSF Long-Term Impact of Infection with Novel Coronavirus cohort (LIINC;NCT04362150 ) and correlated findings with previously measured biomarkers. We used logistic regression to estimate associations with PASC symptoms (dyspnea, chest pain, palpitations, and fatigue) adjusted for confounders and linear regression to estimate differences between those with and without symptoms adjusted for confounders. RESULTS: Out of 120 participants in the cohort, 46 participants (unselected for symptom status) had at least one advanced cardiac test performed at median 17 months following initial SARS-CoV-2 infection. Median age was 52 (IQR 42-61), 18 (39%) were female, and 6 (13%) were hospitalized for severe acute infection. On CMR (n=39), higher extracellular volume was associated with symptoms, but no evidence of late-gadolinium enhancement or differences in T1 or T2 mapping were demonstrated. We did not find arrhythmias on ambulatory monitoring. In contrast, on CPET (n=39), 13/23 (57%) with cardiopulmonary symptoms or fatigue had reduced exercise capacity (peak VO 2 <85% predicted) compared to 2/16 (13%) without symptoms (p=0.008). The adjusted difference in peak VO 2 was 5.9 ml/kg/min lower (-9.6 to -2.3;p=0.002) or -21% predicted (-35 to -7;p=0.006) among those with symptoms. Chronotropic incompetence was the primary abnormality among 9/15 (60%) with reduced peak VO 2 . Adjusted heart rate reserve <80% was associated with reduced exercise capacity (OR 15.6, 95%CI 1.30-187;p=0.03). Inflammatory markers (hsCRP, IL-6, TNF-alpha) and SARS-CoV-2 antibody levels measured early in PASC were negatively correlated with peak VO 2 more than 1 year later. CONCLUSIONS: Cardiopulmonary symptoms and elevated inflammatory markers present early in PASC are associated with objectively reduced exercise capacity measured on cardiopulmonary exercise testing more than 1 year following COVID-19. Chronotropic incompetence may explain reduced exercise capacity among some individuals with PASC. Clinical Perspective: What is New?Elevated inflammatory markers in early post-acute COVID-19 are associated with reduced exercise capacity more than 1 year later.Impaired chronotropic response to exercise is associated with reduced exercise capacity and cardiopulmonary symptoms more than 1 year after SARS-CoV-2 infection.Findings on ambulatory rhythm monitoring point to perturbed autonomic function, while cardiac MRI findings argue against myocardial dysfunction and myocarditis. Clinical Implications: Cardiopulmonary testing to identify etiologies of persistent symptoms in post-acute sequalae of COVID-19 or "Long COVID" should be performed in a manner that allows for assessment of heart rate response to exercise. Therapeutic trials of anti-inflammatory and exercise strategies in PASC are urgently needed and should include assessment of symptoms and objective testing with cardiopulmonary exercise testing.

4.
PubMed; 2022.
Preprint in English | PubMed | ID: ppcovidwho-338321

ABSTRACT

We developed a spatially structured, fully stochastic, individual-based SARS-CoV-2 transmission model to evaluate the feasibility of sustaining SARS-CoV-2 local containment in mainland China considering currently dominant Omicron variants, China's current immunization level, and non-pharmaceutical interventions (NPIs). We also built a statistical model to estimate the overall disease burden under various hypothetical mitigation scenarios. We found that due to high transmissibility, neither Omicron BA.1 or BA.2 could be contained by China's pre-Omicron NPI strategies which were successful prior to the emergence of the Omicron variants. However, increased intervention intensity, such as enhanced population mobility restrictions and multi-round mass testing, could lead to containment success. We estimated that an acute Omicron epidemic wave in mainland China would result in significant number of deaths if China were to reopen under current vaccine coverage with no antiviral uptake, while increasing vaccination coverage and antiviral uptake could substantially reduce the disease burden. As China's current vaccination has yet to reach high coverage in older populations, NPIs remain essential tools to maintain low levels of infection while building up protective population immunity, ensuring a smooth transition out of the pandemic phase while minimizing the overall disease burden.

5.
Ksii Transactions on Internet and Information Systems ; 16(4):1128-1145, 2022.
Article in English | Web of Science | ID: covidwho-1869887

ABSTRACT

Owing to the rapid development of information science, data analysis based on machine learning has become an interdisciplinary and strategic area. Marine predators algorithm (MPA) is a novel metaheuristic algorithm inspired by the foraging strategies of marine organisms. Considering the randomness of these strategies, an improved algorithm called co-evolutionary cultural mechanism-based marine predators algorithm (CECMPA) is proposed. Through this mechanism, search agents in different spaces can share knowledge and experience to improve the performance of the native algorithm. More specifically, CECMPA has a higher probability of avoiding local optimum and can search the global optimum quickly. In this paper, it is the first to use CECMPA to perform feature subset selection and optimize hyperparameters in support vector machine (SVM) simultaneously. For performance evaluation the proposed method, it is tested on twelve datasets from the university of California Irvine (UCI) repository. Moreover, the coronavirus disease 2019 (COVID-19) can be a real-world application and is spreading in many countries. CECMPA is also applied to a COVID-19 dataset. The experimental results and statistical analysis demonstrate that CECMPA is superior to other compared methods in the literature in terms of several evaluation metrics. The proposed method has strong competitive abilities and promising prospects.

6.
PubMed; 2022.
Preprint in English | PubMed | ID: ppcovidwho-336850

ABSTRACT

We developed a spatially structured, fully stochastic, individual-based SARS-CoV-2 transmission model to evaluate the feasibility of sustaining a "Zero-COVID" policy in mainland China in light of currently dominant Omicron variants, China's current immunization level, and non-pharmaceutical intervention (NPI) strategies. We found that due to high transmissibility, neither Omicron BA.1 or BA.2 sublineages could be contained by China's Pre-Omicron non-pharmaceutical intervention strategies which were successful at sustaining the "Zero-COVID" policy until March 2022. However, increased intervention intensity, such as enhanced population mobility restrictions and multi-round mass testing, could lead to containment success without the necessity of population-wide lockdown. As China's current vaccination has yet to reach high coverage in older populations, non-pharmaceutical interventions remain essential tools to maintain low levels of infection while building protective population immunity, ensuring a smooth transition out of the pandemic phase, and minimizing the overall disease burden and societal costs.

7.
IEEE International Conference on Recent Advances in Systems Science and Engineering (RASSE) ; 2021.
Article in English | Web of Science | ID: covidwho-1822040

ABSTRACT

As Corona Virus Disease (COVID-19) emerged at the end of 2019, traditional detection is mainly carried out using four methods: coronavirus screening detection strips, COVID-19 antibody detection kits, COVID-19 nucleic acid detection and CT detection, and the problem of low efficiency exists. In order to solve the problem of using neural network to detection a large number of data, slow speed, low efficiency, high cost, complex algorithm structure and low accuracy of detection of large data sets at present. In this paper, by collecting known public COVID-19 CT image data sets, a convolutional neural network algorithm based on residual network is proposed to reduce parameter complexity, modify weights and biases associated with neurons, and simplify the overall network structure. This algorithm is used to improve the accuracy of COVID-19 case classification detection and the convergence speed of the model. Through model verification, the accuracy of the proposed algorithm model is 0.985, the precision is 0.805, the area under the curve (AUC) of the ROC curve is found to be 0.852, and the recall rate is 0.897. The results show that the classification detection algorithm model proposed in this paper has higher accuracy than the general image classification model, is more concise in the network model, reduces the complexity, and can be more effectively applied to the detection of COVID-19. The combination of traditional medical imaging diagnosis and deep learning technology helps medical personnel to make more rapid, accurate and effective diagnosis.

8.
PubMed; 2020.
Preprint in English | PubMed | ID: ppcovidwho-333498

ABSTRACT

OBJECTIVE: The outbreak of novel coronavirus disease 2019 (COVID-19) imposed a substanal health burden in mainland China and remains a global epidemic threat. Our objectives are to assess the case fatality risk (CFR) among CO VID-19 patients detected in mainland China, stratified by clinical category and age group. METHODS: We collected individual information on laboratory-confirmed COVID-19 cases from publicly available official sources from December 29, 2019 to February 23, 2020. We explored the risk factors associated with mortality. We used methods accounting for right-censoring and survival analyses to estimatethe CFR among detected cases. RESULTS: Of 12,863 cases reported outside Hubei, we obtained individual records for 9,651 cases, including 62 deaths and 1,449 discharged cases. The deceased were significantly older than discharged cases (median age: 77 vs 39 years, p<0.001). 58% (36/62) were male. Older age (OR 1.18 per year;95% CI: 1.14 to 1.22), being male (OR 2.02;95% CI: 1.02 to 4.03), and being treated in less developed economic regions (e.g., West and Northeast vs. East, OR 3.93;95 %Cl:1.74 to 8.85) were mortality risk factors. The estimated CFR was 0.89-1.24% among all cases. The fatality risk among critical patients was 2-fold higher than that among severe and critical patients, and 24-fold higher than that among moderate, severe and critical patients. CONCLUSIONS: Our estimates of CFR based on laboratory-confirmed cases ascertained outside of Hubei suggest that COVID-19 is not as severe as severe acute respiratory syndrome and Middle East respiratory syndrome, but more similar to the mortality risk of 2009 H1N1 influenza pandemic in hospitalized patients. The fatality risk of COVID-19 is higher in males and increases with age. Our study improves the severity assessment of the ongoing epidemic and can inform the COVID-19 outbreak response in China and beyond.

9.
PubMed; 2020.
Preprint in English | PubMed | ID: ppcovidwho-333495

ABSTRACT

BACKGROUND: The COVID-19 epidemic originated in Wuhan City of Hubei Province in December 2019 and has spread throughout China. Understanding the fast evolving epidemiology and transmission dynamics of the outbreak beyond Hubei would provide timely information to guide intervention policy. METHODS: We collected individual information on 8,579 laboratory-confirmed cases from official publically sources reported outside Hubei in mainland China, as of February 17, 2020. We estimated the temporal variation of the demographic characteristics of cases and key time-to-event intervals. We used a Bayesian approach to estimate the dynamics of the net reproduction number (Rt) at the provincial level. RESULTS: The median age of the cases was 44 years, with an increasing of cases in younger age groups and the elderly as the epidemic progressed. The delay from symptom onset to hospital admission decreased from 4.4 days (95%CI: 0.0-14.0) until January 27 to 2.6 days (0.0-9.0) from January 28 to February 17. The mean incubation period was estimated at 5.2 days (1.8-12.4) and the mean serial interval at 5.1 days (1.3-11.6). The epidemic dynamics in provinces outside Hubei was highly variable, but consistently included a mix of case importations and local transmission. We estimate that the epidemic was self-sustained for less than three weeks with Rt reaching peaks between 1.40 (1.04-1.85) in Shenzhen City of Guangdong Province and 2.17 (1.69-2.76) in Shandong Province. In all the analyzed locations (n=10) Rt was estimated to be below the epidemic threshold since the end of January. CONCLUSION: Our findings suggest that the strict containment measures and movement restrictions in place may contribute to the interruption of local COVID-19 transmission outside Hubei Province. The shorter serial interval estimated here implies that transmissibility is not as high as initial estimates suggested.

10.
Journal of Humanistic Mathematics ; 12(1):187-209, 2022.
Article in English | Web of Science | ID: covidwho-1728495

ABSTRACT

As we begin to transition from online instruction to in-person, we (four mathematics teacher educators) reflect on how COVID-19 impacted our instruction and address the question: what will we take back to in-person instruction? This article includes our individual reflections and an analytical synthesis of them. Findings reveal that there were unanticipated ways that human connection and consideration arose from teaching online, much of which we want to maintain in some form when returning to brick and mortar classrooms. We conclude by highlighting the value and importance of reflection for our own well-being.

11.
Arthritis & Rheumatology ; 73:3354-3356, 2021.
Article in English | Web of Science | ID: covidwho-1728442
12.
Arthritis & Rheumatology ; 73:3314-3316, 2021.
Article in English | Web of Science | ID: covidwho-1728441
13.
Circulation ; 144:2, 2021.
Article in English | Web of Science | ID: covidwho-1711006
14.
MEDLINE;
Preprint in English | MEDLINE | ID: ppcovidwho-326640

ABSTRACT

Background: Whether HIV infection is associated with differences in clinical outcomes among people hospitalized with COVID-19 is uncertain. Objective: To evaluate the impact of HIV infection on COVID-19 outcomes among hospitalized patients. Methods: Using the American Heart Association's COVID-19 Cardiovascular Disease registry, we used hierarchical mixed effects models to assess the association of HIV with in-hospital mortality accounting for patient demographics and comorbidities and clustering by hospital. Secondary outcomes included major adverse cardiac events (MACE), severity of illness, and length of stay (LOS). Results: The registry included 21,528 hospitalization records of people with confirmed COVID-19 from 107 hospitals in 2020, including 220 people living with HIV (PLWH). PLWH were younger (56.0+/-13.0 versus 61.3+/-17.9 years old) and more likely to be male (72.3% vs 52.7%), Non-Hispanic Black (51.4% vs 25.4%), on Medicaid (44.5% vs 24.5), and active tobacco users (12.7% versus 6.5%). Of the study population, 36 PLWH (16.4%) had in-hospital mortality compared with 3,290 (15.4%) without HIV (Risk ratio 1.06, 95%CI 0.79-1.43;risk difference 0.9%, 95%CI -4.2 to 6.1%;p=0.71). After adjustment for age, sex, race, and insurance, HIV was not associated with in-hospital mortality (aOR 1.13;95%CI 0.77-1.6;p 0.54) even after adding body mass index and comorbidities (aOR 1.15;95%CI 0.78-1.70;p=0.48). HIV was not associated with MACE (aOR 0.99, 95%CI 0.69-1.44, p=0.91), severity of illness (aOR 0.96, 95%CI 0.62-1.50, p=0.86), or LOS (aOR 1.03;95% CI 0.76-1.66, p=0.21). Conclusion: HIV was not associated with adverse outcomes of COVID-19 including in-hospital mortality, MACE, or severity of illness. Condensed Abstract: We studied 21,528 patients hospitalized with COVID-19 at 107 hospitals in AHA's COVID-19 registry to examine the association between HIV and COVID-19 outcomes. More patients with HIV were younger, male, non-Hispanic Black, on Medicaid and current smokers. HIV was not associated with worse COVID-19 in-hospital mortality (Risk ratio 1.06, 95%CI 0.79-1.43;p=0.71) even after adjustment (aOR 1.15;95%CI 0.78-1.70;p=0.48). HIV was also not associated with MACE (aOR 0.99, 95%CI 0.69-1.44, p=0.91) or severity of illness (aOR 0.96, 95%CI 0.62-1.50, p=0.86. Our findings do not support that HIV is a major risk factor for adverse COVID-19 outcomes.

15.
Environmental Science & Technology Letters ; 9(1):3-9, 2022.
Article in English | Web of Science | ID: covidwho-1655414

ABSTRACT

In situ measurements have suggested vehicle emissions may dominate agricultural sources of NH3 in many cities, which is alarming given the potential for urban NH3 to significantly increase human exposure to ambient particulate matter. However, confirmation of the prevalence of vehicle NH3 throughout a city has been challenging because of mixing with agricultural sources, and the latter are thus routinely assumed to dominate. Here we report vehicle NH3 emissions based on TROPOMI NO2 and CrIS NH3 (0.152 kg s(-1)) that are consistent with a model-based estimate (0.178 kg s(-1)) and show that COVID-19 lockdowns provide a unique opportunity for making the first satellite-based constraints on vehicle NH3 emissions for an entire urban region (western Los Angeles), which we find make up 60-95% of total NH3 emissions, substantially higher than the values of 13-22% in state and national inventories. This provides a new means of constraining a component of transportation emissions whose impacts may rival those of NOx yet which has been largely under-recognized and uncontrolled.

16.
Circulation ; 144(SUPPL 1), 2021.
Article in English | EMBASE | ID: covidwho-1638116

ABSTRACT

Introduction: Myocardial injury is associated with COVID-19 mortality, but the prognostic value of adverse right ventricular (RV) remodeling on transthoracic echocardiogram (TTE) is uncertain. Therefore we studied the association between RV dilation and in-hospital mortality in acute COVID19. Methods: We included all adults hospitalized with COVID-19 between March 2020 and February 2021 who had a clinical TTE performed during hospitalization at UCSF Health (Parnassus, Mission Bay, or Mount Zion) or Zuckerberg San Francisco General. Clinical and echo data were extracted from the electronic medical record. Biomarkers (BNP & troponin) were log transformed. The primary exposure was qualitative assessment of RV dilation on TTE and the primary outcome was inhospital mortality. We conducted analysis with STATA MP 16.1 using logistic regression models with adjustment for age and sex (Model 1) and age, sex, log(BNP), log(troponin), and mechanical ventilation (Model 2) and compared models with and without RV size with the likelihood ratio test. Results: There were 225 people hospitalized with COVID-19 who had a clinical TTE performed. The mean age was 62.9 years old, 77 (34%) were female, and 48 (21%) died. The majority of patients identified as Latinx (40%), and most patients received Medicaid (58%). Of 212 TTEs adequate to assess RV size, 47 (22%) had RV dilation of whom 16 (34%) died compared to 31 (19%) with normal RV size (RR 1.81, 95%CI 1.09-3.01, p=0.03). Of 185 TTEs adequate to assess RV function, 18 (10%) had RV dysfunction of whom 6 (33%) died compared to 12 (18%) with normal RV function (RR 1.86, 95%CI 0.89-3.84, p=0.12). There were no differences in tricuspid annulus plane systolic excursion or RV systolic excursion velocity. Adjusted for age and sex, RV dilation was associated with mortality (OR 2.16, 95%CI 1.02-4.58;p=0.045), with a larger effect among those with RV dilation and dysfunction (OR 3.40, 95% CI 0.93-12.4, p=0.063). This effect was attenuated after adjusting for BNP, troponin and mechanical ventilation at the time of TTE (OR 1.61, 95%CI 0.52-4.98, p=0.41). Conclusions: RV dilation on TTE is associated with mortality in acute COVID-19, although the effect is attenuated after accounting for mechanical ventilation and biomarkers.

17.
2021 International Conference on Construction and Real Estate Management: Challenges of the Construction Industry under the Pandemic, ICCREM 2021 ; : 10-29, 2021.
Article in English | Scopus | ID: covidwho-1598452

ABSTRACT

COVID-19 has become a major public health emergency in the world. At the beginning of the outbreak of the COVID-19 epidemic, a series of medical squeezes appeared in Wuhan, which exposed the problems existing in the implementation of the hierarchical diagnosis and treatment system. Based on GIS platform, this paper analyzes the spatial layout of medical facilities at all levels in Wuhan and compares and analyzes the usage of daily and epidemic periods. It is found that the interlevel gap in the development of daily medical resources leads to spatial differences in the reserved development flexibility, showing the characteristics of weak elastic coping ability and low reserved development flexibility in the surrounding urban areas, strong elastic coping ability and high-reserved development flexibility in the central old urban area. Therefore, to improve the resilience of medical institutions at all levels, we should promote the balanced layout of primary medical institutions and the "decentralization"of high-level medical institutions in spatial layout, coordinate the number and organizational structure of medical resources at different levels, and implement differentiated allocation strategies. © ASCE.

18.
PubMed; 2021.
Preprint in English | PubMed | ID: ppcovidwho-296601

ABSTRACT

Background: By August 2021, South Africa experienced three SARS-CoV-2 waves;the second and third associated with emergence of Beta and Delta variants respectively. Methods: We conducted a prospective cohort study during July 2020-August 2021 in one rural and one urban community. Mid-turbinate nasal swabs were collected twice-weekly from household members irrespective of symptoms and tested for SARS-CoV-2 using real-time reverse transcription polymerase chain reaction (rRT-PCR). Serum was collected every two months and tested for anti-SARS-CoV-2 antibodies. Results: Among 115,759 nasal specimens from 1,200 members (follow-up rate 93%), 1976 (2%) were SARS-CoV-2-positive. By rRT-PCR and serology combined, 62% (749/1200) of individuals experienced >=1 SARS-CoV-2 infection episode, and 12% (87/749) experienced reinfection. Of 662 PCR-confirmed episodes with available data, 15% (n=97) were associated with >=1 symptom. Among 222 households, 200 (90%) had >=1 SARS-CoV-2-positive individual. Household cumulative infection risk (HCIR) was 25% (213/856). On multivariable analysis, accounting for age and sex, index case lower cycle threshold value (OR 3.9, 95%CI 1.7-8.8), urban community (OR 2.0,95%CI 1.1-3.9), Beta (OR 4.2, 95%CI 1.7-10.1) and Delta (OR 14.6, 95%CI 5.7-37.5) variant infection were associated with increased HCIR. HCIR was similar for symptomatic (21/110, 19%) and asymptomatic (195/775, 25%) index cases (p=0.165). Attack rates were highest in individuals aged 13-18 years and individuals in this age group were more likely to experience repeat infections and to acquire SARS-CoV-2 infection. People living with HIV who were not virally supressed were more likely to develop symptomatic illness, and shed SARS-CoV-2 for longer compared to HIV-uninfected individuals. Conclusions: In this study, 85% of SARS-CoV-2 infections were asymptomatic and index case symptom status did not affect HCIR, suggesting a limited role for control measures targeting symptomatic individuals. Increased household transmission of Beta and Delta variants, likely contributed to successive waves, with >60% of individuals infected by the end of follow-up. Research in context: Evidence before this study: Previous studies have generated wide-ranging estimates of the proportion of SARS-CoV-2 infections which are asymptomatic. A recent systematic review found that 20% (95% CI 3%-67%) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections remained asymptomatic throughout infection and that transmission from asymptomatic individuals was reduced. A systematic review and meta-analysis of 87 household transmission studies of SARS-CoV-2 found an estimated secondary attack rate of 19% (95% CI 16-22). The review also found that household secondary attack rates were increased from symptomatic index cases and that adults were more likely to acquire infection. As of December 2021, South Africa experienced three waves of SARS-CoV-2 infections;the second and third waves were associated with circulation of Beta and Delta variants respectively. SARS-CoV-2 vaccines became available in February 2021, but uptake was low in study sites reaching 5% fully vaccinated at the end of follow up. Studies to quantify the burden of asymptomatic infections, symptomatic fraction, reinfection frequency, duration of shedding and household transmission of SARS-CoV-2 from asymptomatically infected individuals have mostly been conducted as part of outbreak investigations or in specific settings. Comprehensive systematic community studies of SARS-CoV-2 burden and transmission including for the Beta and Delta variants are lacking, especially in low vaccination settings. Added value of this study: We conducted a unique detailed COVID-19 household cohort study over a 13 month period in South Africa, with real time reverse transcriptase polymerase chain reaction (rRT-PCR) testing twice a week irrespective of symptoms and bimonthly serology. By the end of the study in August 2021, 749 (62%) of 1200 individuals from 222 randomly sampled households in a rural and an urban community in South Africa had at least one confirmed SARS-CoV-2 infection, detected on rRT-PCR and/or serology, and 12% (87/749) experienced reinfection. Symptom data were analysed for 662 rRT-PCR-confirmed infection episodes that occurred >14 days after the start of follow-up (of a total of 718 rRT-PCR-confirmed episodes), of these, 15% (n=97) were associated with one or more symptoms. Among symptomatic indvidiausl, 9% (n=9) were hospitalised and 2% (n=2) died. Ninety percent (200/222) of included households, had one or more individual infected with SARS-CoV-2 on rRT-PCR and/or serology within the household. SARS-CoV-2 infected index cases transmitted the infection to 25% (213/856) of susceptible household contacts. Index case ribonucleic acid (RNA) viral load proxied by rRT-PCR cycle threshold value was strongly predictive of household transmission. Presence of symptoms in the index case was not associated with household transmission. Household transmission was four times greater from index cases infected with Beta variant and fifteen times greater from index cases infected with Delta variant compared to wild-type infection. Attack rates were highest in individuals aged 13-18 years and individuals in this age group were more likely to experience repeat infections and to acquire SARS-CoV-2 infection within households. People living with HIV (PLHIV) who were not virally supressed were more likely to develop symptomatic illness when infected with SARS-CoV-2, and shed SARS-CoV-2 for longer when compared to HIV-uninfected individuals. Implications of all the available evidence: We found a high rate of SARS-CoV-2 infection in households in a rural community and an urban community in South Africa, with the majority of infections being asymptomatic in individuals of all ages. Asymptomatic individuals transmitted SARS-CoV-2 at similar levels to symptomatic individuals suggesting that interventions targeting symptomatic individuals such as symptom-based testing and contact tracing of individuals tested because they report symptoms may have a limited impact as control measures. Increased household transmission of

19.
PUBMED; 2021.
Preprint in English | PUBMED | ID: ppcovidwho-293266

ABSTRACT

Given the narrowness of the initial testing criteria, the SARS-CoV-2 virus spread through cryptic transmission in January and February, setting the stage for the epidemic wave experienced in March and April, 2020. We use a global metapopulation epidemic model to provide a mechanistic understanding of the global dynamic underlying the establishment of the COVID-19 pandemic in Europe and the United States (US). The model is calibrated on international case introductions at the early stage of the pandemic. We find that widespread community transmission of SARS-CoV-2 was likely in several areas of Europe and the US by January 2020, and estimate that by early March, only 1 - 3 in 100 SARS-CoV-2 infections were detected by surveillance systems. Modeling results indicate international travel as the key driver of the introduction of SARS-CoV-2 with possible importation and transmission events as early as December, 2019. We characterize the resulting heterogeneous spatio-temporal spread of SARS-CoV-2 and the burden of the first COVID-19 wave (February-July 2020). We estimate infection attack rates ranging from 0.78%-15.2% in the US and 0.19%-13.2% in Europe. The spatial modeling of SARS-CoV-2 introductions and spreading provides insights into the design of innovative, model-driven surveillance systems and preparedness plans that have a broader initial capacity and indication for testing.

20.
Nephrology Dialysis Transplantation ; 36:1, 2021.
Article in English | Web of Science | ID: covidwho-1539468
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