Rapid genomic surveillance of healthcare-associated SARS-CoV-2

By Dr. Ananya Mandal, MDJul 16 2020

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that causes COVID-19 disease has infected over 13.7 million individuals and taken more than 589,000 lives around the world. The novel virus was first detected in late December last year in Wuhan China and since then has become one of the greatest public health challenges in recent memory. One of the most significant impacts of this pandemic is to healthcare systems. The highly infectious nature of the virus has caused the rapid spread of the infection among communities in almost all countries, and with thousands getting severely ill requiring hospitalization, intensive care, and ventilation, the healthcare systems are overwhelmed in developed as well as developing nations. Now, researchers have come up with a rapid genomic sequencing test to identify and stratify healthcare-associated infections.

The researchers from the University of Cambridge, Cambridge United Kingdom have published their findings in a study titled, “Rapid implementation of SARS-CoV-2 sequencing to investigate cases of healthcare-associated COVID-19: a prospective genomic surveillance study,” in the latest issue of The Lancet Infectious Diseases. This study on COVID-19 Genomics in the UK was funded by the Department of Health and Social Care, UK Research and Innovation, and the Wellcome Sanger Institute.

Novel Coronavirus SARS-CoV-2 Colorized scanning electron micrograph of a cell heavily infected with SARS-CoV-2 virus particles (yellow), isolated from a patient sample. The black area in the image is extracellular space between the cells. Image captured at the NIAID Integrated Research Facility (IRF) in Fort Detrick, Maryland. Credit: NIAID

Sequencing the viral strains – Why is it needed?

SARS-CoV-2 is an RNA virus and rapidly replicates when it infects a host. As it replicates in humans, it mutates, and the strains become diverse as time passes. At present, wrote the researchers, the rate of mutation of the SARS-CoV-2 virus is “approximately 2·5 nucleotides per month”.

The researchers explained that the genomes of these viral strains need to be sequenced to obtain information about infectivity and biology in order to develop drugs and vaccines against it. Genomic sequencing can also reveal the strains of lineages of the viruses that are circulating in the human populations around the world and their impact on the outcome of the patients. Changes in the SARS-CoV-2  genome also show the success of the control measures and how the virus is responding to the interventions and control measures.

Healthcare-associated infections

Healthcare-associated infections are those that can affect the healthcare personnel as well as patients. Among patients, it can affect the morbidity or sickness and also the rate of deaths, and among the health care workers also, it can also affect “staff sickness and morale.” Either way, the healthcare-acquired infections can be detrimental to patient care write the researchers. Thus detection of health care acquire infections at the earliest is vital, they wrote. To date, over 22,000 health care workers have been infected by healthcare-acquired infectious strains, and the World Health Organization (WHO) believes these numbers to be a gross underestimate.

What was done?

Studies on genome surveillance of SARS-COV-2 were collated up until 11^th May 2020. The purpose of this study was to use rapid SARS-CoV-2 sequencing in the epidemiology of these healthcare-associated infections and define necessary infection control measures.

This was a prospective study where the team used “rapid SARS-CoV-2 nanopore sequencing” of the virus samples obtained from those who were positive on reverse transcription-polymerase chain reaction (RT-PCR). The samples were from hospitals in the East of England. Sequencing was completed within 24 hours of receiving the samples. Every week a review of the reports was established, and the epidemiological, as well as the genomic data, was shared to look into the healthcare-associated COVID-19 cases and the strains associated with them.

What was found?

The study was conducted between 13^th March and 24^th April 2020, and a total of 5,613 patient samples were obtained during this time. Of these, 1,000 samples were sequenced, and high-quality genomic data were obtained from 747 samples. Epidemiological and genomic data was combined in 299 patients from the host hospital.

The team found that there were 35 clusters of viruses that were identical. These were obtained from 159 patients. They further noted that 58 percent or 92 of the 159 patients had strong correlating epidemiological evidence, while 20 percent or 32 patients had possible epidemiological links.

As the next step, the researchers provided their data to the clinical infection control authorities and hospital management teams. Policies on infection control were thus modified, and patient safety reporting was also amended accordingly.

Conclusions and implications

The authors have successfully established real-time genomic surveillance of the virus and have also correlated it with the epidemiological findings. This could help understand the healthcare-associated infections they wrote and also “identify opportunities to target infection-control interventions to reduce healthcare-associated infections further.” The team signed off, “Our findings have important implications for national public health policy as they enable rapid tracking and investigation of infections in hospital and community settings.”