[OHDSI Covid19] Literature review on Covid19 characterization

Patrick_Ryan · March 18, 2020, 2:36pm

I’m opening up this thread to be a place for the ‘lit review on Covid19 baseline characterization’ sub-team, led by @MDGeist and @Denys_Kaduk , can have team discussions and share progress. Thanks for all your efforts!

Patrick_Ryan · March 19, 2020, 1:31am

Today’s cdc report is a good source to include here: https://www.cdc.gov/mmwr/volumes/69/wr/mm6912e2.htm?s_cid=mm6912e2_w

estone96 · March 19, 2020, 2:04am

Thanks Parick

Best, Yeesuk

Denys_Kaduk · March 19, 2020, 2:18pm

Hi all, I found article with characterization and outcomes with critically ill patients with SARS-CoV-2 pneumonia. Can we add it to our literature review?

ncbi.nlm.nih.gov

Clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia in Wuhan, China: a single-centered, retrospective, observational study.

X Yang, Y Yu, J Xu, H Shu, J Xia, H Liu, Y Wu, L Zhang, Z Yu, M Fang, T Yu, Y Wang, S Pan, X Zou, S Yuan and Y Shang, The Lancet. Respiratory medicine, Feb 24 2020

An ongoing outbreak of pneumonia associated with the severe acute respiratory coronavirus 2 (SARS-CoV-2) started in December, 2019, in Wuhan, China. Information about critically ill patients with SARS-CoV-2 infection is scarce. We aimed to describe the clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia.In this single-centered, retrospective, observational study, we enrolled 52 critically ill adult patients with SARS-CoV-2 pneumonia who were admitted to the intensive care unit (ICU) of Wuhan Jin Yin-tan hospital (Wuhan, China) between late December, 2019, and Jan 26, 2020. Demographic data, symptoms, laboratory values, comorbidities, treatments, and clinical outcomes were all collected. Data were compared between survivors and non-survivors. The primary outcome was 28-day mortality, as of Feb 9, 2020. Secondary outcomes included incidence of SARS-CoV-2-related acute respiratory distress syndrome (ARDS) and the proportion of patients requiring mechanical ventilation.Of 710 patients with SARS-CoV-2 pneumonia, 52 critically ill adult patients were included. The mean age of the 52 patients was 59·7 (SD 13·3) years, 35 (67%) were men, 21 (40%) had chronic illness, 51 (98%) had fever. 32 (61·5%) patients had died at 28 days, and the median duration from admission to the intensive care unit (ICU) to death was 7 (IQR 3-11) days for non-survivors. Compared with survivors, non-survivors were older (64·6 years [11·2] vs 51·9 years [12·9]), more likely to develop ARDS (26 [81%] patients vs 9 [45%] patients), and more likely to receive mechanical ventilation (30 [94%] patients vs 7 [35%] patients), either invasively or non-invasively. Most patients had organ function damage, including 35 (67%) with ARDS, 15 (29%) with acute kidney injury, 12 (23%) with cardiac injury, 15 (29%) with liver dysfunction, and one (2%) with pneumothorax. 37 (71%) patients required mechanical ventilation. Hospital-acquired infection occurred in seven (13·5%) patients.The mortality of critically ill patients with SARS-CoV-2 pneumonia is considerable. The survival time of the non-survivors is likely to be within 1-2 weeks after ICU admission. Older patients (>65 years) with comorbidities and ARDS are at increased risk of death. The severity of SARS-CoV-2 pneumonia poses great strain on critical care resources in hospitals, especially if they are not adequately staffed or resourced.None.

julie_kohler · March 19, 2020, 2:40pm

Question–how are we collecting the literature? Are we posting everything here? Do we want to have a google sheet or other shared resource for collecting the metadata? I’m afraid I don’t have to cite my research as a general rule, so I don’t know the best ways for collecting metadata.

Also, do we need to have any rules for what literature we’re collecting? Are we just looking for anything that explains symptoms? Only symptoms used for diagnosis? Are we looking for natural history of disease? How will we consolidate all of the information?

I’ve seen a lot of similar studies (including this one, I think) on the WHO database: https://www.who.int/emergencies/diseases/novel-coronavirus-2019/global-research-on-novel-coronavirus-2019-ncov

julie_kohler · March 19, 2020, 2:43pm

Also, I’m not sure where this goes, so I’m going to post it in a couple of different fora:

From the Global Digital Health Forum (this wasn’t written by me):
I was on the AeHIN COIL webinar today and the presenter mentioned that OpenEHR has a COVID-19 project that has archetypes and templates for COVID19 data in clinical settings. Here is the link: https://www.openehr.org/ckm/projects/1013.30.81

estone96 · March 19, 2020, 10:52pm

Hi. All
I found a new article about our issues. Can it be useful?
Thanks

Yeesuk

Denys_Kaduk · March 20, 2020, 11:08am

Hello all, we create google sheet for collecting all metadata which can help in research!

julie_kohler · March 20, 2020, 12:21pm

I’m going to start going through the WHO database and adding those articles. I’m going to add a field in the google sheet for the WHO reference number so that we don’t duplicate any articles.

julie_kohler · March 20, 2020, 12:22pm

Also, can we give the actual date of the article? if all we put is year, that’s not helpful–everything is 2020.

Denys_Kaduk · March 20, 2020, 12:42pm

The goal of this characterization literature review is to synthesize the population characteristics of Covid19 studies. This means we are looking to extract population (e.g. sample size, geography), which baseline features are assessed, including symptoms and diagnostics (% overall and within strata (death/recovery) and what statistical analysis was conducted, e.g. statistical modeling for ‘risk factors’. We will also summarize treatments used, when that information is available.

Ben & Denys

MDGeist · March 20, 2020, 12:43pm

For our review, we will use Covidence , which is one of Cochrane’s recommended tools for standard reviews. Covidence supports key steps in the Review process, such as citation screening and Risk of Bias assessment. You will be able to upload search results, screen abstracts and full text, complete data collection, conduct risk of bias assessment, resolve disagreements, and export data into RevMan or Excel.

We will invite you to our Covidence account and provide some guidance shortly.

Thank you for being part of this group and thank you your assistance,

Ben & Denys

lhester · March 21, 2020, 11:12pm

Hi All - I wanted to make you aware of this site where the US NIH/NLM is compiling literature on COVID-19/SARS-COV-2. This may help in your literature review on the characterization of the disease. https://www.ncbi.nlm.nih.gov/research/coronavirus/?fbclid=IwAR3VFuE3ENFkCi1t3Ri4PK6C3D_lJVhuFvRFoofxvHDaZW7COZrLwwwaFYs

julie_kohler · March 22, 2020, 1:30am

So, just to clarify, should I exclude any systematic reviews or meta-analyses from the list?

estone96 · March 22, 2020, 10:12am

Hi. All

I have just added baseline characteristics of several literatures in the google sheet . All are case series with patient characteristics.

Yeesuk

MDGeist · March 23, 2020, 11:12am

Dear Julianne,
If you can find additional papers through those, please include them in Covidence.
Thank you,
Ben

julie_kohler · March 23, 2020, 1:52pm

I’ve been going through several articles, and I want to make sure I’m on the same page so that I’m doing this right. And my apologies if these questions have been answered in other fora.

What is the expected output of the review? Are we looking for useful articles that can inform the data studies that are being done? Or is this expected to become a systematic review/meta-analysis in its own right?
Do we have inclusion/exclusion criteria for studies to be included? If we’re just doing a review for researchers’ use, presumably this question is less important, but I’ve been including more narrative case reports that only follow a couple of people and have no statistics involved. Is that useful?
How careful do we want to be with fields like “Data type used for characterization”? If I’m doing a systematic review, I would infer nothing; should I be inferring things like a hospital report if it’s case reports from a given hospital?
How general do we want to be with the baseline characterization? For example, if patients were characterized on the basis of their symptoms, do I want the list of all symptoms they were characterized for?
Does stratification variables refer to outcomes? Normally, I would think of stratification variables to be any variable included in a regression analysis (as an example), but you listed survivor/non-survivor as your example, which I would think of as the outcome variable. Does it assume a statistical analysis of some sort? If this is a retrospective analysis that talks about how many people died, does that outcome belong here? Or is it in the baseline characteristics because they looked at it at the same time as everything else?
Does statistical modeling count the statistics used for Table 1 or only a final model?

Thank you for all your help!

MDGeist · March 23, 2020, 1:59pm

Dear Julie,

these are great points.
I sent you and the other collborators on this channel an e-mail with explanations, an invite to Covidence and a request for a meeting Tuesday 24, where we can best discuss this and then post our summary here in the forum as well.

Thank you,

Ben

julie_kohler · March 23, 2020, 2:18pm

Thank you! I will wait for your invite.

julie_kohler · April 2, 2020, 3:00pm

Hi Ben,

Are we still working on the literature review? I saw it marked as complete on the Sunday call but am happy to do more. Also, would it be more useful for me to fill out the google sheet or the covidence?

many thanks,
Julianna