Merge pull request #1047 from rando2/minor-fixes

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manuscript.md

@@ -6,7 +6,7 @@ keywords:
 - pandemic
 - viral infection
 lang: en-US
-date-meta: '2021-09-24'
+date-meta: '2021-09-27'
 author-meta:
 - Halie M. Rando
 - Casey S. Greene
@@ -70,8 +70,8 @@ header-includes: |-
   <meta name="citation_title" content="SARS-CoV-2 and COVID-19: An Evolving Review of Diagnostics and Therapeutics" />
   <meta property="og:title" content="SARS-CoV-2 and COVID-19: An Evolving Review of Diagnostics and Therapeutics" />
   <meta property="twitter:title" content="SARS-CoV-2 and COVID-19: An Evolving Review of Diagnostics and Therapeutics" />
-  <meta name="dc.date" content="2021-09-24" />
-  <meta name="citation_publication_date" content="2021-09-24" />
+  <meta name="dc.date" content="2021-09-27" />
+  <meta name="citation_publication_date" content="2021-09-27" />
   <meta name="dc.language" content="en-US" />
   <meta name="citation_language" content="en-US" />
   <meta name="dc.relation.ispartof" content="Manubot" />
@@ -279,13 +279,13 @@ header-includes: |-
   <meta name="citation_fulltext_html_url" content="https://greenelab.github.io/covid19-review/" />
   <meta name="citation_pdf_url" content="https://greenelab.github.io/covid19-review/manuscript.pdf" />
   <link rel="alternate" type="application/pdf" href="https://greenelab.github.io/covid19-review/manuscript.pdf" />
-  <link rel="alternate" type="text/html" href="https://greenelab.github.io/covid19-review/v/b7903328cf10901239332f76bdb5bf2c52e97356/" />
-  <meta name="manubot_html_url_versioned" content="https://greenelab.github.io/covid19-review/v/b7903328cf10901239332f76bdb5bf2c52e97356/" />
-  <meta name="manubot_pdf_url_versioned" content="https://greenelab.github.io/covid19-review/v/b7903328cf10901239332f76bdb5bf2c52e97356/manuscript.pdf" />
+  <link rel="alternate" type="text/html" href="https://greenelab.github.io/covid19-review/v/caa4d5ac0458eb37498ef0e7d86c1a3e1e39b228/" />
+  <meta name="manubot_html_url_versioned" content="https://greenelab.github.io/covid19-review/v/caa4d5ac0458eb37498ef0e7d86c1a3e1e39b228/" />
+  <meta name="manubot_pdf_url_versioned" content="https://greenelab.github.io/covid19-review/v/caa4d5ac0458eb37498ef0e7d86c1a3e1e39b228/manuscript.pdf" />
   <meta property="og:type" content="article" />
   <meta property="twitter:card" content="summary_large_image" />
-  <meta property="og:image" content="https://github.com/greenelab/covid19-review/raw/b7903328cf10901239332f76bdb5bf2c52e97356/content/images/thumbnail.png" />
-  <meta property="twitter:image" content="https://github.com/greenelab/covid19-review/raw/b7903328cf10901239332f76bdb5bf2c52e97356/content/images/thumbnail.png" />
+  <meta property="og:image" content="https://github.com/greenelab/covid19-review/raw/caa4d5ac0458eb37498ef0e7d86c1a3e1e39b228/content/images/thumbnail.png" />
+  <meta property="twitter:image" content="https://github.com/greenelab/covid19-review/raw/caa4d5ac0458eb37498ef0e7d86c1a3e1e39b228/content/images/thumbnail.png" />
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@@ -307,11 +307,11 @@ manubot-clear-requests-cache: false
 
 <small><em>
 This manuscript
-([permalink](https://greenelab.github.io/covid19-review/v/b7903328cf10901239332f76bdb5bf2c52e97356/))
+([permalink](https://greenelab.github.io/covid19-review/v/caa4d5ac0458eb37498ef0e7d86c1a3e1e39b228/))
 was automatically generated
-from [greenelab/covid19-review@b790332](https://github.com/greenelab/covid19-review/tree/b7903328cf10901239332f76bdb5bf2c52e97356)
-on September 24, 2021.
-It is also available as a [PDF](https://greenelab.github.io/covid19-review/v/b7903328cf10901239332f76bdb5bf2c52e97356/manuscript.pdf).
+from [greenelab/covid19-review@caa4d5a](https://github.com/greenelab/covid19-review/tree/caa4d5ac0458eb37498ef0e7d86c1a3e1e39b228)
+on September 27, 2021.
+It is also available as a [PDF](https://greenelab.github.io/covid19-review/v/caa4d5ac0458eb37498ef0e7d86c1a3e1e39b228/manuscript.pdf).
 Snapshots of individual sections have been published [@individual-pathogenesis; @individual-nutraceuticals; @individual-pharmaceuticals; @individual-methods].
 </em></small>
 
@@ -1322,7 +1322,7 @@ These are valuable resources, yet it is also important to note that the estimate
 The novel coronavirus SARS-CoV-2 is the third HCoV to emerge in the 21st century, and research into previous HCoVs has provided a strong foundation for characterizing the pathogenesis and transmission of SARS-CoV-2.
 Critical insights into how the virus interacts with human cells have been gained from previous research into HCoVs and other viral infections.
 With the emergence of three devastating HCoV over the past twenty years, emergent viruses are likely to represent an ongoing threat.
-Contextualizing SARS-CoV-2 alongside other viruses serves not only to provide insights that can be immediately useful for combating this virus itself, but may also prove valuable in the face of future viral threats.
+Contextualizing SARS-CoV-2 alongside other viruses serves not only to provide insights that can be immediately useful for combating this virus itself but may also prove valuable in the face of future viral threats.
 
 Host-pathogen interactions provide a basis not only for understanding COVID-19, but also for developing a response.
 As with other HCoVs, the immune response to SARS-CoV-2 is likely driven by detection of its spike protein, which allows it to enter cells through ACE2.
@@ -1920,14 +1920,14 @@ The scale of the COVID-19 pandemic has made the repurposing and development of p
 
 ![
 **Cumulative global incidence of COVID-19 and SARS.**
-As of September 22, 2021, 230,087,742 COVID-19 cases and 4,719,178 COVID-19 deaths had been reported worldwide since January 22, 2020.
+As of September 25, 2021, 231,515,976 COVID-19 cases and 4,743,196 COVID-19 deaths had been reported worldwide since January 22, 2020.
 A total of 8,432 cases and 813 deaths were reported for SARS from March 17 to July 11, 2003.
 SARS-CoV-1 was officially contained on July 5, 2003, within 9 months of its appearance [@doi:10.3390/ijerph17113973].
 In contrast, SARS-CoV-2 remains a significant global threat nearly two years after its emergence.
 COVID-19 data are from the COVID-19 Data Repository by the Center for Systems Science and Engineering at Johns Hopkins University [@https://github.com/CSSEGISandData/COVID-19/tree/master/csse_covid_19_data/csse_covid_19_time_series; @doi:10/ggnsjk].
 SARS data are from the WHO [@url:https://www.who.int/csr/sars/country/en] and were obtained from a dataset on GitHub [@url:https://github.com/imdevskp/sars-2003-outbreak-data-webscraping-code].
 See https://greenelab.github.io/covid19-review/ for the most recent version of this figure, which is updated daily.
-](https://github.com/greenelab/covid19-review/raw/e7a34481bf2a1a3431ecac4983573fb473d1eb56/csse/csse-deaths.png "Global incidence of COVID-19 and SARS"){#fig:csse-deaths secno=1}
+](https://github.com/greenelab/covid19-review/raw/0e36a517bc88e54459c2b6ed3a4803e621267045/csse/csse-deaths.png "Global incidence of COVID-19 and SARS"){#fig:csse-deaths secno=1}
 
 At first, SARS-CoV-2's rapid shift from an unknown virus to a significant worldwide threat closely paralleled the emergence of _Severe acute respiratory syndrome-related coronavirus_ (SARS-CoV-1), which was responsible for the 2002-03 SARS epidemic.
 The first documented case of COVID-19 was reported in Wuhan, China in November 2019, and the disease quickly spread worldwide in the early months of 2020.
@@ -1984,7 +1984,7 @@ Recruitment status and trial phase are shown only for interventional trials in w
 Common interventions refers to interventions used in at least ten trials.
 Combinations of interventions, such as hydroxychloroquine with azithromycin, are tallied separately from the individual interventions.
 See https://greenelab.github.io/covid19-review/ for the most recent version of this figure, which is updated daily.
-](https://github.com/greenelab/covid19-review/raw/e7a34481bf2a1a3431ecac4983573fb473d1eb56/ebmdatalab/ebmdatalab-trials.png "COVID-19 clinical trials"){#fig:ebm-trials secno=1}
+](https://github.com/greenelab/covid19-review/raw/0e36a517bc88e54459c2b6ed3a4803e621267045/ebmdatalab/ebmdatalab-trials.png "COVID-19 clinical trials"){#fig:ebm-trials secno=1}
 
 The purpose of this review is to provide an evolving resource tracking the status of efforts to repurpose and develop drugs for the treatment of COVID-19.
 We highlight four strategies that provide different paradigms for the identification of potential pharmaceutical treatments.
@@ -3052,7 +3052,7 @@ Vaccine development began almost five centuries ago, but the SARS-CoV-2 pandemic
 ### Importance
 
 The SARS-CoV-2 pandemic has caused untold damage to the global population, but it also presented some unique opportunities for vaccine development.
-As of September 22, 2021, SARS-CoV-2 has infected over 230,087,742 and cost the lives of 4,719,178 people globally.
+As of September 25, 2021, SARS-CoV-2 has infected over 231,515,976 and cost the lives of 4,743,196 people globally.
 The development, production, and distribution of vaccines is imperative to saving lives, preventing illness, and reducing the economic and social burdens caused by the COVID-19 pandemic.
 Now that promising candidates exist, effective deployment will provide an opportunity to move into a new phase of the pandemic where the susceptibility of worldwide populations is significantly reduced.
 This review provides a historical context for vaccine devleopment and highlights the main strategies utilized for the development of the COVID-19 vaccines, their clinical appraisal, and their distribution.
@@ -4705,7 +4705,7 @@ Trials that recruit across multiple countries do appear to broaden geographic re
 The density of clinical trials is reported at the country level.
 As of December 31, 2020, there are 6,987 trials in the University of Oxford Evidence-Based Medicine Data Lab's COVID-19 TrialsTracker [@doi:10.5281/zenodo.3732709], of which 3,962 are interventional.
 The top figure demonstrates the density of interventional trials recruiting only from a singular country, while the bottom shows the distribution of recruitment for interventional trials that involve more than one country.
-](https://github.com/greenelab/covid19-review/raw/e7a34481bf2a1a3431ecac4983573fb473d1eb56/ebmdatalab/ebmdatalab-map.png "COVID-19 clinical trials"){#fig:ebm-map secno=1}
+](https://github.com/greenelab/covid19-review/raw/0e36a517bc88e54459c2b6ed3a4803e621267045/ebmdatalab/ebmdatalab-map.png "COVID-19 clinical trials"){#fig:ebm-map secno=1}
 
 A few different concerns arise from this skewed geographic representation in clinical trial recruitment.
 First, treatments such as remdesivir that are promising but primarily available to clinical trial participants are unlikely to be accessible by people in many countries.