Rice Coronavirus Research

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https://hdl.handle.net/1911/108371

Works related to coronaviruses that are authored by members of the Rice community.

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Enacting national social distancing policies corresponds with dramatic reduction in COVID19 infection rates
(Public Library of Science, 2020) McGrail, Daniel J.; Dai, Jianli; McAndrews, Kathleen M.; Kalluri, Raghu
The outbreak the SARS-CoV-2 (CoV-2) virus has resulted in over 6.5 million cases of COVID19, greatly stressing global healthcare infrastructure. Lacking medical prophylactic measures to combat disease spread, many nations have adopted social distancing policies in order to mitigate transmission of CoV-2. While mathematical models have suggested the efficacy of social distancing to curb the spread of CoV-2, there is a lack of systematic studies to quantify the real-world efficacy of these approaches. Here, we first demonstrate that implementation of social distancing policies in US states corresponded with a reduction in COVID19 spread rates, and that the reduction in spread rate is proportional to the average change in mobility. We validate this observation on a worldwide scale by analyzing COVID19 spread rate in 134 nations with varying social distancing policies. Globally, we find that social distancing policies significantly reduced the COVID19 spread rate, with resulting in an estimated 65% reduction (95% CI = 39–80%) in new COVID19 cases over a two week time period. These data suggest that social distancing policies may be a powerful tool to prevent spread of COVID19 in real-world scenarios.
How Do We See COVID-19? Visual Iconographies of Racial Contagion
(Duke University Press, 2020) Ostherr, Kirsten
Contagion media have historically performed the dual functions of scientific and ideological persuasion, often deploying an iconography of racial contagion that combines these two functions. In efforts to halt the spread of the virus, health, science, and media organizations create visual imagery to teach the public to imagine we can see and therefore avoid contaminants that are invisible to the naked eye. Comparison of COVID-19 with other global disease outbreaks shows how a core set of contagion media visualizations are repeatedly deployed with subtle adaptations for unique diseases and display interfaces. The variations among different corpora of contagion media point to the interplay among persistent, transhistorical tropes, particular sites of meaning production, and novel technical affordances. This article will examine a subset of these representational techniques, including microscopic images of the virus, close-ups of disease vectors, global and local maps of contagion, health workers in biohazard suits, and visibly ill patients. The essay argues that techniques for visualizing the invisible produce a narrative logic of causality in COVID-19 that reinforces racist and xenophobic discourses of containment and control with direct and deadly consequences. Mitigation of this pandemic and future pandemics will require not only medical but also representational interventions.
Association of anticoagulation dose and survival in hospitalized COVID‐19 patients: A retrospective propensity score‐weighted analysis
(Wiley, 2020) Ionescu, Filip; Jaiyesimi, Ishmael; Petrescu, Ioana; Lawler, Patrick R.; Castillo, Edward; Munoz‐Maldonado, Yolanda; Imam, Zaid; Narasimhan, Mangala; Abbas, Amr E.; Konde, Anish; Nair, Girish B.
Background: Hypercoagulability may contribute to COVID‐19 pathogenicity. The role of anticoagulation (AC) at therapeutic (tAC) or prophylactic doses (pAC) is unclear. Objectives: We evaluated the impact on survival of different AC doses in COVID‐19 patients. Methods: Retrospective, multi‐center cohort study of consecutive COVID‐19 patients hospitalized between March 13 and May 5, 2020. Results: A total of 3480 patients were included (mean age, 64.5 years [17.0]; 51.5% female; 52.1% black and 40.6% white). 18.5% (n = 642) required intensive care unit (ICU) stay. 60.9% received pAC (n = 2121), 28.7% received ≥3 days of tAC (n = 998), and 10.4% (n = 361) received no AC. Propensity score (PS) weighted Kaplan‐Meier plot demonstrated different 25‐day survival probability in the tAC and pAC groups (57.5% vs 50.7%). In a PS–weighted multivariate proportional hazards model, AC was associated with reduced risk of death at prophylactic (hazard ratio [HR] 0.35 [95% confidence interval {CI} 0.22‐0.54]) and therapeutic doses (HR 0.14 [95% CI 0.05‐0.23]) compared to no AC. Major bleeding occurred more frequently in tAC patients (81 [8.1%]) compared to no AC (20 [5.5%]) or pAC (46 [2.2%]) subjects. Conclusions: Higher doses of AC were associated with lower mortality in hospitalized COVID‐19 patients. Prospective evaluation of efficacy and risk of AC in COVID‐19 is warranted.
Employing drug delivery strategies to create safe and effective pharmaceuticals for COVID ‐19
(Wiley, 2020) McHugh, Kevin J.
Will COVID-19 become the next neglected tropical disease?
(Public Library of Science, 2020) Hotez, Peter J.; Bottazzi, Maria E.; Singh, Sunit K.; Brindley, Paul J.; Kamhawi, Shaden
Heterogeneous antibodies against SARS-CoV-2 spike receptor binding domain and nucleocapsid with implications for COVID-19 immunity
(American Society for Clinical Investigation, 2020) McAndrews, Kathleen M.; Dowlatshahi, Dara P.; Dai, Jianli; Becker, Lisa M.; Hensel, Janine; Snowden, Laura M.; Leveille, Jennifer M.; Brunner, Michael R.; Holden, Kylie W.; Hopkins, Nikolas S.; Harris, Alexandria M.; Kumpati, Jerusha; Whitt, Michael A.; Lee, J. Jack; Ostrosky-Zeichner, Luis L.; Papanna, Ramesha; LeBleu, Valerie S.; Allison, James P.; Kalluri, Raghu
Evaluation of potential immunity against the novel severe acute respiratory syndrome (SARS) coronavirus that emerged in 2019 (SARS-CoV-2) is essential for health, as well as social and economic recovery. Generation of antibody response to SARS-CoV-2 (seroconversion) may inform on acquired immunity from prior exposure, and antibodies against the SARS-CoV-2 spike protein receptor binding domain (S-RBD) are speculated to neutralize virus infection. Some serology assays rely solely on SARS-CoV-2 nucleocapsid protein (N-protein) as the antibody detection antigen; however, whether such immune responses correlate with S-RBD response and COVID-19 immunity remains unknown. Here, we generated a quantitative serological ELISA using recombinant S-RBD and N-protein for the detection of circulating antibodies in 138 serial serum samples from 30 reverse transcription PCR–confirmed, SARS-CoV-2–hospitalized patients, as well as 464 healthy and non–COVID-19 serum samples that were collected between June 2017 and June 2020. Quantitative detection of IgG antibodies against the 2 different viral proteins showed a moderate correlation. Antibodies against N-protein were detected at a rate of 3.6% in healthy and non–COVID-19 sera collected during the pandemic in 2020, whereas 1.9% of these sera were positive for S-RBD. Approximately 86% of individuals positive for S-RBD–binding antibodies exhibited neutralizing capacity, but only 74% of N-protein–positive individuals exhibited neutralizing capacity. Collectively, our studies show that detection of N-protein–binding antibodies does not always correlate with presence of S-RBD–neutralizing antibodies and caution against the extensive use of N-protein–based serology testing for determination of potential COVID-19 immunity.
Dying in the Face of the COVID-19 Pandemic: Contextual Considerations and Clinical Recommendations
(American Psychological Association, 2020) LeRoy, Angie S.; Robles, Barbara; Kilpela, Lisa S.; Garcini, Luz M.
Dying is a natural part of life; however, death is often a fearful, frightening event. Dying in the midst of the COVID-19 pandemic presents challenges that magnify normative fears and may interfere with a healthy grieving process. To maintain a resilient spirit among those who are at risk of losing a loved one or who have lost a family member to COVID-19, it is important that they be provided with the necessary contextually and culturally appropriate skills and resources to facilitate healing in the face of hardship and uncertainty.
Potential fecal transmission of SARS-CoV-2: Current evidence and implications for public health
(Elsevier, 2020) Amirian, E. Susan
Coronavirus disease 2019 (COVID-19) emerged in Hubei Province, China in December 2019 and has since become a global pandemic, with hundreds of thousands of cases and over 165 countries affected. Primary routes of transmission of the causative virus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), are through respiratory droplets and close person-to-person contact. While information about other potential modes of transmission are relatively sparse, evidence supporting the possibility of a fecally mediated mode of transmission has been accumulating. Here, current knowledge on the potential for fecal transmission is briefly reviewed and the possible implications are discussed from a public health perspective.
Current knowledge about the antivirals remdesivir (GS-5734) and GS-441524 as therapeutic options for coronaviruses
(2020) Amirian, E. Susan; Levy, Julie K.; Texas Policy Lab; Elsevier
Recent international epidemics of coronavirus-associated illnesses underscore the urgent medical and public health need for vaccine development and regulatory body approved therapies. In particular, the current coronavirus disease 2019 (COVID-19) pandemic has quickly intensified interest in developing treatment options to mitigate impact on human life. Remdesivir (GS-5734™) is a broad-spectrum antiviral drug that is now being tested as a potential treatment for COVID-19 in international, multi-site clinical trials. Currently available evidence about the antiviral effects of remdesivir against coronaviruses is primarily based on in vitro and in vivo studies (including some on a chemically related compound, GS-441524™), which have demonstrated largely favorable findings. As the pandemic progresses, information from human compassionate use cases will continue to accumulate before the clinical trials are concluded. It is imperative for public health practitioners and the One Health community to stay up to date on the most promising potential therapeutic options that are under investigation. Thus, the purpose of this review is to synthesize the knowledge to date about remdesivir as a therapeutic option for coronaviruses, with a special focus on information relevant to the One Health community.
Protection against SARS-CoV-2 by BCG vaccination is not supported by epidemiological analyses
(Springer Nature, 2020) Hensel, Janine; McAndrews, Kathleen M.; McGrail, Daniel J.; Dowlatshahi, Dara P.; LeBleu, Valerie S.; Kalluri, Raghu
The Bacillus Calmette-Guerin (BCG) vaccine provides protection against tuberculosis (TB), and is thought to provide protection against non-TB infectious diseases. BCG vaccination has recently been proposed as a strategy to prevent infection with SARS-CoV-2 (CoV-2) to combat the COVID-19 outbreak, supported by its potential to boost innate immunity and initial epidemiological analyses which observed reduced severity of COVID-19 in countries with universal BCG vaccination policies. Seventeen clinical trials are currently registered to inform on the benefits of BCG vaccinations upon exposure to CoV-2. Numerous epidemiological analyses showed a correlation between incidence of COVID-19 and BCG vaccination policies. These studies were not systematically corrected for confounding variables. We observed that after correction for confounding variables, most notably testing rates, there was no association between BCG vaccination policy and COVD-19 spread rate or percent mortality. Moreover, we found variables describing co-morbidities, including cardiovascular death rate and smoking prevalence, were significantly associated COVID-19 spread rate and percent mortality, respectively. While reporting biases may confound our observations, our epidemiological findings do not provide evidence to correlate overall BCG vaccination policy with the spread of CoV-2 and its associated mortality.
COVID-19 in the Americas and the erosion of human rights for the poor
(Public Library of Science, 2020) Hotez, Peter J.; Huete-Perez, Jorge A.; Bottazzi, Maria Elena; James A Baker III Institute for Public Policy
A predictive model of the temperature-dependent inactivation of coronaviruses
(AIP, 2020) Yap, Te Faye; Liu, Zhen; Shveda, Rachel A.; Preston, Daniel J.
The COVID-19 pandemic has stressed healthcare systems and supply lines, forcing medical doctors to risk infection by decontaminating and reusing single-use personal protective equipment. The uncertain future of the pandemic is compounded by limited data on the ability of the responsible virus, SARS-CoV-2, to survive across various climates, preventing epidemiologists from accurately modeling its spread. However, a detailed thermodynamic analysis of experimental data on the inactivation of SARS-CoV-2 and related coronaviruses can enable a fundamental understanding of their thermal degradation that will help model the COVID-19 pandemic and mitigate future outbreaks. This work introduces a thermodynamic model that synthesizes existing data into an analytical framework built on first principles, including the rate law for a first-order reaction and the Arrhenius equation, to accurately predict the temperature-dependent inactivation of coronaviruses. The model provides much-needed thermal decontamination guidelines for personal protective equipment, including masks. For example, at 70 °C, a 3-log (99.9%) reduction in virus concentration can be achieved, on average, in 3 min (under the same conditions, a more conservative decontamination time of 39 min represents the upper limit of a 95% interval) and can be performed in most home ovens without reducing the efficacy of typical N95 masks as shown in recent experimental reports. This model will also allow for epidemiologists to incorporate the lifetime of SARS-CoV-2 as a continuous function of environmental temperature into models forecasting the spread of the pandemic across different climates and seasons.
The 2020 State of Housing in Harris County and Houston
(Kinder Institute for Urban Research, 2020) Shelton, Kyle; Park, John; Villegas, Carlos; Guajardo, Luis; Servidio, Chris; Zhang, Zhiyan
The Kinder Institute's inaugural State of Housing in Harris County and Houston report provides a consistent and accessible baseline of information about housing-related issues to all Houstonians. This report will be updated annually to track shifts in how the housing system in our region is changing. The Kinder Institute will provide an updated report annually and make housing indicators available for all stakeholders to access. This first report establishes a baseline by comparing how dozens of key housing indicators have shifted between 2010 and 2018. Subsequent annual reports will add the latest year of data to the analysis and track trends over time.
Already vulnerable neighborhoods are hardest hit by COVID-19 job losses
(Kinder Institute for Urban Research, 2020)
An interactive dashboard created by the Kinder Institute’s Houston Community Data Connections shows job-loss estimates in each Harris County community. The numbers can be further broken down by industry and neighborhood. Many of the areas impacted most by the economic downturn are home to low-income renters, the working poor and single-parent households.
Staying at home may have saved 4,533 lives in Harris County so far
(Kinder Institute for Urban Research, 2020) Wu, Jie; Zhang, Mingming; Wang, Katie
Based on epidemiologists’ COVID-19 models, the Kinder Institute's Houston Community Data Connections Team estimated the number of hospitalizations and deaths that can be prevented in Harris County between March 24 and June by collective adherence to the city of Houston's and Harris County's stay-at-home orders.
Impact of COVID-19 on residency choice: A survey of New York City medical students
(Public Library of Science, 2021) Lee, Kate E.; Lim, Francesca; Silver, Elisabeth R.; Faye, Adam S.; Hur, Chin
Objectives: The Coronavirus disease 2019 (COVID-19) pandemic disrupted medical student education, particularly in New York City (NYC). We aimed to assess the impact of the COVID-19 pandemic on medical students’ residency choices. Methods: The authors conducted a cross-sectional survey of medical students in all years of study at four NYC medical schools (Columbia, Cornell, NYU, and SUNY Downstate). The survey was fielded from 19 Aug 2020 to 21 Sep 2020. Survey questions included items assessing COVID-19 impact on residency choices, personal impact of COVID-19, residency/specialty choices, and factors influencing these choices. Results: A total of 2310 students received the survey, with 547 (23.7%) providing partial responses and 212 (9.2%) providing valid responses for our primary analysis. 59.0% of participants thought that COVID-19 influenced their choice of residency/specialty, with 0.9% saying the influence was to a great extent, 22.2% to some extent, and 35.8% very little. On multivariable analysis, factors that were independently associated with COVID-19 impacting residency choice included low debt ($1 to $99,999: adjOR 2.23, 95%CI 1.02–5.03) compared with no debt and Other race/ethnicity (adjOR 0.26, 95%CI 0.10–0.63) compared with White race/ethnicity. On secondary analysis of all participants answering survey items for logistic regression regardless of survey completion, direct personal impact of COVID-19 was significantly associated with COVID-19 impacting specialty choice (adjOR 1.90, 95%CI 1.04–3.52). Moreover, 24 students (11.6%) reported a change in their top residency choice from before to during/after COVID-19, citing concerns about frontline work, work-life balance, and risk of harm. Conclusions: Our study found that 3 in 5 (59.0%) participants felt that COVID-19 impacted their residency choice, with 11.6% of respondents explicitly changing their top specialty choice. Investigating the impact of the pandemic on medical student residency considerations is crucial to understand how medical career outlooks may change in the future.
Texas Public Agencies’ Tweets and Public Engagement During the COVID-19 Pandemic: Natural Language Processing Approach
(JMIR, 2021) Tang, Lu; Liu, Wenlin; Thomas, Benjamin; Tran, Hong Thoai Nga; Zou, Wenxue; Zhang, Xueying; Zhi, Degui
Background: The ongoing COVID-19 pandemic is characterized by different morbidity and mortality rates across different states, cities, rural areas, and diverse neighborhoods. The absence of a national strategy for battling the pandemic also leaves state and local governments responsible for creating their own response strategies and policies. Objective: This study examines the content of COVID-19–related tweets posted by public health agencies in Texas and how content characteristics can predict the level of public engagement. Methods: All COVID-19–related tweets (N=7269) posted by Texas public agencies during the first 6 months of 2020 were classified in terms of each tweet’s functions (whether the tweet provides information, promotes action, or builds community), the preventative measures mentioned, and the health beliefs discussed, by using natural language processing. Hierarchical linear regressions were conducted to explore how tweet content predicted public engagement. Results: The information function was the most prominent function, followed by the action or community functions. Beliefs regarding susceptibility, severity, and benefits were the most frequently covered health beliefs. Tweets that served the information or action functions were more likely to be retweeted, while tweets that served the action and community functions were more likely to be liked. Tweets that provided susceptibility information resulted in the most public engagement in terms of the number of retweets and likes. Conclusions: Public health agencies should continue to use Twitter to disseminate information, promote action, and build communities. They need to improve their strategies for designing social media messages about the benefits of disease prevention behaviors and audiences’ self-efficacy.
Contact Tracing Apps: Lessons Learned on Privacy, Autonomy, and the Need for Detailed and Thoughtful Implementation
(JMIR, 2021) Hogan, Katie; Macedo, Briana; Macha, Venkata; Barman, Arko; Jiang, Xiaoqian; Data to Knowledge Lab
The global and national response to the COVID-19 pandemic has been inadequate due to a collective lack of preparation and a shortage of available tools for responding to a large-scale pandemic. By applying lessons learned to create better preventative methods and speedier interventions, the harm of a future pandemic may be dramatically reduced. One potential measure is the widespread use of contact tracing apps. While such apps were designed to combat the COVID-19 pandemic, the time scale in which these apps were deployed proved a significant barrier to efficacy. Many companies and governments sprinted to deploy contact tracing apps that were not properly vetted for performance, privacy, or security issues. The hasty development of incomplete contact tracing apps undermined public trust and negatively influenced perceptions of app efficacy. As a result, many of these apps had poor voluntary public uptake, which greatly decreased the apps’ efficacy. Now, with lessons learned from this pandemic, groups can better design and test apps in preparation for the future. In this viewpoint, we outline common strategies employed for contact tracing apps, detail the successes and shortcomings of several prominent apps, and describe lessons learned that may be used to shape effective contact tracing apps for the present and future. Future app designers can keep these lessons in mind to create a version that is suitable for their local culture, especially with regard to local attitudes toward privacy-utility tradeoffs during public health crises.
The new COVID-19 poor and the neglected tropical diseases resurgence
(BioMed Central, 2021) Hotez, Peter J.; Fenwick, Alan; Molyneux, David; James A Baker III Institute of Public Policy
More than 100 million people are facing a return to extreme poverty because of coronavirus disease 2019 (COVID-19), while new estimates suggest that three nations—India, Nigeria, and the Democratic Republic of the Congo—may suffer the greatest economic contractions. Such findings will have profound consequences in terms of our ability to control or eliminate the most widely prevalent neglected tropical diseases
Birthing Between the “Traditional” and the “Modern”: DāĪ Practices and Childbearing Women’s Choices During COVID-19 in Pakistan
(Frontiers Media S.A., 2021) Ali, Inayat; Sadique, Salma; Ali, Shahbaz; Davis-Floyd, Robbie
Pregnancy and birth are biological phenomena that carry heavy cultural overlays, and pregnant and birthing women need care and attention during both ordinary and extraordinary times. Most Pakistani pregnant women now go to doctors and hospitals for their perinatal care. Yet traditional community midwives, called DāĪ in the singular and Dāyūn in the plural, still attend 24% of all Pakistani births, primarily in rural areas. In this article, via data collected from 16 interviews—5 with Dāyūn and 11 with mothers, we explore a maternity care system in tension between the past and the present, the DāĪ and the doctor. We ask, what does the maternity care provided by the Dāyūn look like during times of normalcy, and how does it differ during COVID-19? We look at the roles the DāĪ has traditionally performed and how these roles have been changing, both in ordinary and in Covidian circumstances. Presenting the words of the Dāyūn we interviewed, all from Pakistan’s Sindh Province, we demonstrate their practices and show that these have not changed during this present pandemic, as these Dāyūn, like many others in Sindh Province, do not believe that COVID-19 is real—or are at least suspect that it is not. To contextualize the Dāyūn, we also briefly present local mother’s perceptions of the Dāyūn in their regions, which vary between extremely positive and extremely negative. Employing the theoretical frameworks of “authoritative knowledge” and of critical medical anthropology, we highlight the dominance of “modern” biomedicine over “traditional” healthcare systems and its effects on the Dāyūn and their roles within their communities. Positioning this article within Pakistan’s national profile, we propose formally training and institutionalizing the Dāyūn in order to alleviate the overwhelming burdens that pandemics—present and future—place on this country’s fragile maternity care system, to give mothers more—and more viable—options at all times, and to counterbalance the rising tide of biomedical hegemony over pregnancy and birth.

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