Research explores speedy SARS-CoV-2 genome sequencing to assist cut back hospital-acquired COVID-19 infections

In a latest examine posted to the medRxiv* pre-print server, researchers examined whether or not extreme acute respiratory syndrome coronavirus 2 (SARS-CoV-2) whole-genome sequencing (WGS) could possibly be routinely used for an infection prevention and management (IPC) in hospitals.

Study: Evaluating the effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control teams: the COG-UK hospital-onset COVID-19 infection study. Image Credit: Evaluating the effectiveness of speedy SARS-CoV-2 genome sequencing in supporting an infection management groups: the COG-UK hospital-onset COVID-19 an infection examine. Picture Credit score:

Amid the continuing coronavirus illness 2019 (COVID-19) pandemic, the mitigation of the nosocomial transmission of SARS-CoV-2, notably hospital-acquired infections (HAIs), is a serious space of concern for public well being officers globally.

Within the UK, HAIs accounted for over 5% of confirmed SARS-CoV-2 circumstances between August and March 2020 and represented 11% of COVID-19 circumstances inside hospitals throughout this time interval. The necessity to develop intervention measures to manage or reduce the prevalence of nosocomial transmission is certainly pressing.

In regards to the examine

Within the current examine, researchers carried out a potential non-randomized trial at 14 UK hospitals to judge the impression of the WGS-based interventions on IPC actions and the incidence of possible and particular HAIs.

The researchers recorded knowledge for all these sufferers who didn’t have COVID-19 on the time of hospital admission however examined COVID-19-positive inside or throughout 48 hours of hospital admission, i.e. exhibited hospital-onset COVID-19 an infection (HOCI), utilizing a custom-made sequence reporting device (SRT). 

The examine included the baseline knowledge, collected all through 4 weeks, adopted by knowledge collected over two intervention durations, outlined because the time taken from diagnostic sampling to the return of WGS knowledge to IPC groups. The intervention durations comprised of first eight weeks of ‘speedy’ sequencing and 4 weeks of ‘longer’ turnaround sequencing for every website. The focused turnaround occasions of ‘speedy’ and ‘longer-turnaround’ sequencing phases had been 48 hours and 5 to 10 days, respectively.

All of the taking part hospitals aimed to sequence all SARS-CoV-2 circumstances, together with HOCI and non-HOCI circumstances throughout the intervention section. The WGS and affected person meta-data had been built-in to provide a one-page report for IPC groups utilizing SRT, which additionally helped researchers standardize knowledge assortment throughout websites. The researchers used a central study-specific database to check affected person knowledge within the gentle of data impacting the IPC implementation.      

There have been two major outcomes of the study- i) incidence of IPC-defined SARS-CoV-2 HAIs per week per 100 admitted non-COVID-19 inpatients and ii) for every HOCI, SRT recognized linkage to people inside an outbreak of SARS-CoV-2 nosocomial transmission utilizing sequencing knowledge. Notably, these linkages weren’t recognized by pre-sequencing IPC analysis throughout intervention phases. 

The examine additionally reported any change to IPC actions following receipt of the SRT report for every HOCI throughout intervention phases and any beneficial change to IPC actions as secondary outcomes. 


For the examine interval between 15 October 2020 and 26 April 2021, authors famous a complete of two,170 HOCIs of which 80% had not less than one clinically important comorbidity. All of the 14 websites accomplished baseline and speedy sequencing intervention phases, with the typical turnaround time within the speedy and the longer-turnaround section being 5 and 13 days, respectively.

Though SRT reviews for HOCIs returned within the intervention phases, solely 9.3% of these returned inside the goal timeframes, of which 4.6% had been within the speedy section, and 21.2% had been within the longer-turnaround intervention section.

In the course of the examine interval, whereas eight hospitals applied ‘speedy’ adopted by ‘longer-turnaround’ sequencing phases, the opposite 5 did the alternative; nonetheless, one hospital utterly omitted the longer-turnaround sequencing as a result of they thought of it a discount of their normal apply. Apparently, whereas HOCIs recognized three to seven days after hospital admission had been usually excluded from assessments of nosocomial SARS-CoV-2 infections, the SRT reviews confirmed that 78.9% of those indeterminate HAIs had been hospital-acquired. 

A secondary final result of the examine, IPC-defined SARS-CoV-2 hospital outbreaks are outlined at the least of two HOCI circumstances in the identical ward, with not less than one having greater than eight days from admission to symptom onset. The authors noticed that the typical variety of HOCI incidence per IPC-defined SARS-CoV-2 hospital outbreaks was 4 per week per 100 non-COVID-19 inpatients, and the biggest outbreak included 43 HOCIs.


In keeping with the authors of the examine, to this point, no different evaluation has carried out WGS for acute IPC investigation of nosocomial transmission. This trial was run as a part of routine apply with the UK Nationwide Well being Service (NHS); due to this fact, the challenges confronted in implementation mirrored the true obstacles current within the UK.

Outbreak investigations are inherently advanced, therefore interventions centered on IPC practices evaluated on the hospital stage are required to generate high-quality proof. IPC groups, notably within the per-protocol evaluation, had a optimistic notion about utilizing WGS for outbreak investigation. 

The SRT quickly mixed sequence and affected person meta-data to differentiate hospital and community-acquired infections inside a clinically related time scale. Concerning price, the distinction in the price of ‘speedy’ in contrast with ‘longer-turnaround’ hospital pattern sequencing incurred low price in comparison with the general price of such interventions used at current. Furthermore, if frequently used for public well being functions, the aggregated advantages would offset the added price of speedy sequencing for IPC functions.

Though this examine didn’t straight present the impression of sequencing on the numbers of HAIs or outbreaks, the information proof that these correlated with the excessive group SARS-CoV-2 charges urged that even elements past the management of IPC had a serious affect. 

To conclude, with quicker turnaround occasions, WSG can inform ongoing IPC actions in managing nosocomial SARS-CoV-2 transmissions; subsequently, in shut to twenty% of COVID-19 circumstances, outcomes returned inside 5 days from sampling to tell IPC actions. For future analysis, the present examine generated a wealth of information to beat the challenges to understand the total potential of WGS for IPC apply at a bigger scale.

*Vital discover

medRxiv publishes preliminary scientific reviews that aren’t peer-reviewed and, due to this fact, shouldn’t be thought to be conclusive, information medical apply/health-related habits, or handled as established info.

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