BUFFALO, NY – Locally and nationally, the number of COVID-19 cases is dropping and the overwhelming message seems to be that the worst of the pandemic may be behind us.
Yet as those vaccinated enjoy the return to many normal activities, scientists at the University of Buffalo doing genomic sequencing of COVID-19 samples note that the actual picture is locally more nuanced.
âThe virus is still here and it’s different from what we started with,â said Jennifer A. Surtees, PhD, co-director of the Genome, Environment and Microbiome Community of Excellence at UB and Associate Professor of Biochemistry at the Jacobs School. of Medicine and Biomedical Sciences at UB, who leads the sequencing team. “If you were in close contact with someone who tested positive for COVID-19, you should get tested and quarantined as recommended by the Department of Health.”
She noted that all of the variants identified as variants of concern by the Centers for Disease Control and Prevention are now present in Erie County.
âMore than 90% of the cases sequenced in April in western New York City were variants of concern,â she said. Variants of concern are mutations in the virus that are more easily transmitted, cause more severe disease, and are less able to be neutralized by antibody treatments.
âThe good news is that all of the vaccines available in the United States – the Pfizer vaccine, the Moderna vaccine, and the Johnson & Johnson vaccine – they all protect against all of the variants of concern,â Surtees said. âThe best way to protect yourself, your loved ones and your community, is therefore to get vaccinated. If you are not vaccinated you are at a significantly higher risk and should wear a mask and avoid travel to places with high disease rates.
“We want this information to be made public because even though the number of cases is going down, especially with the ‘unmasking’ which is now allowed, it is really becoming essential that people are aware of what is out there and to encourage more vaccination. , “she added.
âNew strains of novel variant coronavirus are circulating in our community,â said Gale Burstein, MD, MPH, Erie County Health Commissioner and Clinical Professor of Pediatrics at the Jacobs School. âIt is absolutely essential for those who are not yet fully vaccinated to continue to wear a mask in public places to protect themselves and to protect others who cannot yet be vaccinated, such as children, and those who are immunocompromised.
The worrying variant B.1.1.7, originally identified in the UK, is now dominant in County Erie, accounting for around half of cases in April. “About half of them were B.1.1.7, originally called the UK variant, which is more transmissible, may make antibody treatments less effective and may make you sicker than the original virus,” she declared.
Other variants of concern detected here are B.1.351 (South Africa), B.1.427 (California) and P.1 (Brazil). Five other variants of so-called New York interest have also been detected, which so far have not demonstrated more transmissibility or severity of the disease.
The incidence of worrisome variants in Erie County jumped dramatically to 62.9% in March from 12.2% in February, a trend that has continued. âBy April, the variants, and in particular B.1.1.7, had taken over in Erie County,â Surtees said.
While increases in both variants of concern and variants of interest have been observed nationally, the Surtees noted that there are clearly regional differences in the types of variants seen.
âFor example, in western New York, B.1.1.7 and B.1.427 are the variants that have been mostly seen,â she said. âThis is in direct contrast to the situation in upstate New York, where cases were dominated by lines B.1.526 (a New York variant) in addition to B.1.1.7. Smaller numbers of B.1.351 (originally detected in South Africa) were seen in both the north and the lower part of the state.
âThis underscores the importance of regional surveillance to provide the most relevant data to clinicians in a region,â Surtees said. She added that increased genomic surveillance locally has allowed more sequence information to be generated from western New York, thus increasing confidence in the ability to detect variants of concern and variants of interest locally.
John Tomaszewski, MD, SUNY Emeritus Professor and Chair of the Department of Pathology and Anatomical Sciences, highlighted the importance of whole genome sequencing data for COVID-19 in the greater Buffalo area.
âWithout this robust UB pipeline to identify the worrisome variants circulating in our community, we cannot anticipate new directions this disease may take in western New York. The UB Sequencing Resource for COVID-19 is one of the few laboratories in New York State that can perform both the sequencing and bioinformatics necessary to effectively identify COVID variants.
Since the start of the pandemic, genomic sequencing of COVID-19 samples in western New York has been carried out by Surtees and colleagues fromthe Jacobs School Department of Biochemistry; and the Genomics and Bioinformatics Core of the New York State Center of Excellence in Bioinformatics and Life Sciences (CBLS) at UB.
The team has significantly increased its sequencing capacity, from around 150 initially to around 700 since January. The Erie County Public Health Laboratory is providing samples and the UB team recently started receiving samples from Kaleida Health and the Erie County Medical Center.
âIt’s really hard to predict anything about what’s to come next,â Surtees said. âWith these worrisome variants, the coronavirus is operating in a different genomic landscape than the one we started with – different combinations of mutations may end up being really important in terms of transmission of the virus in the future.
âThe first thing to do is to reduce the ability of the virus to continue to evolve, and the best way to do this is to limit the infection,â she continued. âThe mutations we see occur when the virus replicates its genome. Less infection means less replication and fewer possibilities for mutations. “