Merge branch 'master' into master

build/assets/custom-dictionary.txt

@@ -875,6 +875,7 @@ Nutraceuticals
 O’Meara
 obesogenic
 OC
+ODSP
 olfaction
 omics
 oncolytic

content/02.introduction.md

@@ -8,8 +8,6 @@ Most of these cases were in China, but one to two exported cases had also been i
 One week later, 4,593 confirmed cases had been identified, spanning not only Asia, but also Australia, North America, and Europe [@url:https://www.who.int/docs/default-source/coronaviruse/situation-reports/20200128-sitrep-8-ncov-cleared.pdf].
 On March 11, 2020, the WHO formally classified the situation as a pandemic [@url:https://www.who.int/docs/default-source/coronaviruse/situation-reports/20200311-sitrep-51-covid-19.pdf].
 On April 4, 2020, the WHO reported that the global number of confirmed cases had surpassed one million [@url:https://www.who.int/docs/default-source/coronaviruse/situation-reports/20200404-sitrep-75-covid-19.pdf].
-
-**Global COVID-19 deaths since January 22, 2020.**
 {{csse_deaths}} COVID-19 deaths had been reported worldwide as of {{csse_date_pretty}} (Figure @fig:csse-deaths).
 
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@@ -43,7 +41,7 @@ Public health addresses social and human factors influencing individuals' exposu
 Strategies from public health and epidemiology for managing the current epidemic have included the promotion of hand hygiene, social distancing, and personal protective equipment such as masks to mitigate spread, as well as containment approaches such as test, trace, and isolate, which depends on widespread testing, contact tracing, and quarantining.
 An effective public health management strategy involves response coordination, disease surveillance, intervention monitoring, risk communication, and health education (including the containment of “infodemics” of false information) [@isbn:978-92-4-156553-0].
 Epidemiology and public health intersect with the topics addressed in this manuscript because they both inform and benefit from relevant biotechnological developments.
-For example, the development of accurate and fast diagnostic testing is relevant to test, trace, and isolate strategies for containment, and public education will be critical to deploying vaccines once they become available..
+For example, the development of accurate and fast diagnostic testing is relevant to test, trace, and isolate strategies for containment, and public education will be critical to deploying vaccines once they become available.
 The present analysis focuses less on human and social factors and more on the basic biology of infection, diagnosis, and recovery, but these areas are inextricable in understanding and responding to the COVID-19 pandemic.
 
 ### Initial Characterization of SARS-CoV-2
@@ -127,7 +125,7 @@ The variability of both which symptoms present and their severity makes it diffi
 
 Several review articles on aspects of COVID-19 have already been published.
 These have included reviews on the disease epidemiology [@doi:10.1016/j.molmed.2020.02.008], immunological response [@doi:10.1016/j.immuni.2020.05.002], diagnostics [@doi:10.1126/scitranslmed.abc1931], and pharmacological treatments [@doi:10.1016/j.immuni.2020.05.002; @doi:10.1001/jama.2020.6019].
-Others [@doi:10.1038/d41591-020-00026-w] and [@doi:10.1001/jama.2020.12839] provide narrative reviews of progress on some important ongoing COVID-19 research questions.
+Others [@doi:10.1038/d41591-020-00026-w; @doi:10.1001/jama.2020.12839] provide narrative reviews of progress on some important ongoing COVID-19 research questions.
 With the worldwide scientific community uniting during 2020 to investigate SARS-CoV-2 and COVID-19 from a wide range of perspectives, findings from many disciplines are relevant on a rapid timescale to a broad scientific audience.
 Additionally, many findings are published as preprints, which are available prior to going through the peer review process.
 As a result, centralizing, summarizing, and critiquing new literature broadly relevant to COVID-19 can help to expedite the interdisciplinary scientific process that is currently happening at an advanced pace.
@@ -140,7 +138,7 @@ Some possible approaches include the identification of existing pharmaceuticals
 Due to the long timeline for the development of novel pharmaceuticals, in most cases, research surrounding possible pharmaceutical interventions focuses on the identification and investigation of existing compounds whose mechanisms may be relevant to COVID-19.
 Other foci of current research include the identification of antibodies produced by survivors of COVID-19 and the development of vaccines.
 Understanding the mechanisms describing host-virus interactions between humans and SARS-CoV-2 is thus critical to identifying candidate therapeutics.
-An overview of the topics covered is visualized in Figure (Figure @fig:overview).
+An overview of the topics covered is visualized in Figure @fig:overview.
 Thus, in this review, we seek to consolidate information about efforts to develop strategies for diagnosis and therapeutics as new information is released by the scientific community.
 We include information from both traditional peer-reviewed scientific literature and from preprints, which typically have not undergone peer review but have been critically evaluated by the scientists involved in this effort.
 The goal of this manuscript is to present preliminary findings within the broader context of COVID-19 research and to identify the broad interpretations of new research, as well as limitations to interpretability.

content/07.pathogenesis.md

@@ -238,6 +238,7 @@ Another area of interest is whether SARS-CoV-2 is likely to induce similar chang
 For example, because of the high level of sequence homology between SARS-CoV-2 and SARS-CoV, it has been hypothesized that sera from convalescent SARS-CoV patients might show some efficacy in cross-neutralizing SARS-CoV-2-S-driven entry [@doi:10.1016/j.cell.2020.02.052].
 However, despite the high level of sequence homology, certain protein structures might be immunologically distinct, which would be likely to prohibit effective cross-neutralization across different SARS species [@doi:10.1101/2020.03.21.990770].
 Consequently, proteomic analyses of SARS-CoV might also provide some essential information regarding the new pathogen [@doi:10.1073/pnas.0407992101; @doi:10.1016/j.bbrc.2004.02.074].
+
 Considering the paucity of omics-level big data sets for SARS-CoV-2 currently available, existing data hubs that contain information for other coronaviruses such as UniProt, NCBI Genome Database, The Immune Epitope Database and Analysis Resource (IEDB), and The Virus Pathogen Resource (ViPR) will serve as useful resources for computational and bioinformatics research on SARS-CoV-2.
 Using such databases, the systems-level reconstruction of the protein-protein interaction (PPI) will enable the generation of hypotheses about the mechanism of action of SARS-CoV-2 and suggest potential drug targets.
 In an initial study [@doi:10.1101/2020.03.22.002386], 26 of the 29 SARS-CoV-2 proteins were cloned and expressed in HEK293T kidney cells, allowing for the identification of 332 high-confidence human proteins interacting with them.
@@ -281,7 +282,7 @@ The SARS-CoV-2 mutation rate is moderate compared to other RNA viruses [@doi:10.
 Nevertheless, genomic analyses have yielded statistical evidence of ongoing evolution.
 There are two known variants of the spike protein that differ by a single amino acid at position 614 (G614 and D614), and there is evidence that G614 had become more prevalent than D614 by June 2020 [@doi:10.1016/j.cell.2020.06.043].
 While there is a hypothesis that this genomic change increased the SARS-CoV-2 infectivity and virulence, this hypothesis has not yet been tested due to a lack of data [@doi:10.1016/j.cell.2020.06.040].
-Another study [@doi:10.1016/j.meegid.2020.104351] identified 198 recurrent mutations in a dataset of 7666 curated sequences.
+Another study [@doi:10.1016/j.meegid.2020.104351] identified 198 recurrent mutations in a dataset of 7,666 curated sequences.
 This pattern of convergent evolution at some sites could indicate that certain mutations confer an adaptive advantage.
 While it is evident that SARS-CoV-2 exhibits moderate potential for ongoing and future evolution, the relationship between mutations and pathogenicity is not yet known.
 Additional data is needed in order to understand patterns of evolutionary change and whether they are likely to affect virulence.

content/08.transmission.md

@@ -215,7 +215,7 @@ While several possible hypotheses for the apparent reduced impact of COVID-19 on
 Additionally, ethnic minorities in the United Kingdom also tend to be younger than white British living in the same areas, yet the burden of COVID-19 is still more serious for minorities, especially people of Black Caribbean ancestry, both in absolute numbers and when controlling for age and location [@url:https://www.ifs.org.uk/inequality/chapter/are-some-ethnic-groups-more-vulnerable-to-covid-19-than-others/].
 Furthermore, the groups in the United States and United Kingdom that have been identified as carrying elevated COVID-19 burden, namely Black American, indigenous American, and Black and South Asian British, are quite distinct in their position on the human ancestral tree.
 What is shared across these groups is instead a history of disenfranchisement under colonialism and ongoing systematic racism.
-A large analysis of over 11,000 COVID-19 patients hospitalized in 92 hospitals across U.S. states revealed that Black patients were younger, more often female, more likely to be on Medicaid, more likely to have comorbidities, and came from neighborhoods identified as more economically deprived than white patients [@doi:10.1001/jamanetworkopen.2020.18039].i
+A large analysis of over 11,000 COVID-19 patients hospitalized in 92 hospitals across U.S. states revealed that Black patients were younger, more often female, more likely to be on Medicaid, more likely to have comorbidities, and came from neighborhoods identified as more economically deprived than white patients [@doi:10.1001/jamanetworkopen.2020.18039].
 This study reported that when these factors were accounted for, the differences in mortality between Black and white patients were no longer significant.
 Thus, the current evidence suggests that the apparent correlations between ancestry and health outcomes must be examined in the appropriate social context.
 We explore the role these social factors have played in shaping the COVID-19 pandemic broadly in the Discussion.