A team led by researchers from Yale School of Public Health has discovered how variant B.1.1.7 of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), first discovered in the UK, spread to several states in the United States. While the coronavirus pandemic has affected nearly every country around the world, the United States is currently in the lead with more than 27.8 million reported infections and the highest global death toll exceeding 2.4 million.
Kirsten St. George, Nathan D. Grubaugh and colleagues said that despite increased travel restrictions and increased testing for the coronavirus, the United States does not report the genome sequences of potential new variants of confirmed COVID-19 cases. Because the United States only accounts for 0.13% of COVID-19 cases, it was initially difficult to detect when variant B.1.1.7 first appeared in America.
“Sorting capacity varies widely across the country, and our travel data helps to disproportionately identify areas of B.1.1.7 cases that are underreported and where it would be prudent to immediately prioritize variant surveillance,” write the authors.
Study “Early recognition and community transmission of SARS-CoV-2 variant B.1.1.7 in the United States” is available as preprint in medRxiv* server, when articles undergo peer review.
The researchers used a combination of October 2020 flight records from the UK to all United States airports and SARS-CoV-2 genomic sequencing to detect the origin of variant B.1.1.7 in the US. They argued that this time period was chosen because not only was it the most recent data available, but it also overlapped with the timing of variant B.1.1.7 originally thought to have spread throughout Great Britain.
According to the CDC’s February preliminary report, 33 states have confirmed 541 cases of B.1.1.7 in the United States. However, the authors argue that low genomic surveillance may not represent the true extent of variance. They instead analyzed the number of cases reported from December 2020 to January 2021 by the percentage of SARS-CoV-2 clinical samples taken.
Strong evidence for the spread of the variant first came from New York
Low genomic surveillance was reported from December to January, with only 0.1% of COVID-19 cases sequenced and available to researchers. Twenty-six states had less than 0.1% of case sequences, and at the time of preprint publication, 14 states had yet to submit the genome sequences associated with B.1.1.7.
A large number of the B.1.1.7 strain was found in New York, California, and Florida. The ordering coincides with a large number of international flights coming from Great Britain to the state’s airports.
Multiple introductions, domestic spread, and community transmission B.1.1.7 SARS-CoV-2 in the United States. A. Phylogeny maximum likelihood of B.1.1.7, including genome representatives from US, Europe, other global locations. B. Highlights of the singletons and clades representing the direct introduction of B.1.1.7 from Europe, to different regions of the US, based on the same phylogenetic tree shown in (A). A list of European to US transitions can be found in Data S1. CE. Time-based maximum likelihood phylogeny from different clades B.1.1.7 showing examples of domestic (C, E) and / or community transmission in New York (C), Connecticut (C), Michigan (C, D), and Illinois ( E). A list of the SARS-CoV-2 sequences used in this study and the authors’ thanks can be found in Data S2.
From the three, the researchers concluded that New York was most likely the central hub for the incoming B.1.1.7 variant, which then spread to other states. The New York-New Jersey area has a record of 14,317 passengers to and from the UK. These results are consistent with the first case of COVID-19 with a new variant detected in Saratoga County, New York on December 24, 2020.
Since variant B.1.1.7 remains undetected, the researchers suggest continued community transmission is likely in New York, New Jersey, Connecticut, and Illinois from January 2021.
“So, increasing surveillance for B.1.1.7 and other variants through more conventional ordering and methods should be a high priority,” write the researchers.
Strong possibility of variant B.1.17 in other states
While the researchers sequenced most of the B.1.1.7 variant in New York, the investigators say that under-reporting may have contributed to undetected cases in other states. Their results showed Texas, Illinois and New Jersey had more than 2,500 people flying from England. However, all three states had 0.05% or less of cases sorted. The authors suggest a strong possibility that the spread of the new strain is increasing in other states.
“In places like New Jersey, Illinois, and Texas, however, if SARS-CoV-2 genomic surveillance could be improved, it might determine if B.1.1.7 cases were not reported disproportionately compared to New York and California,” wrote the researcher.
More genomic surveillance is needed for future research
Given limited travel data and low genomic surveillance, the researchers said the samples were too small to represent the full spread of this variant in the United States. In addition, they were unable to evaluate the level of transmission in the various areas and considered community distribution high. “In fact, local conditions and behavior played an important role in the formation of B.1.1.7, and may explain why cases are low in some states.”
As the spread of the new variant increases, the research team suggests increasing genome surveillance is a high priority task needed to reduce the spread of the virus.
* Important Notice
medRxiv publishes preliminary scientific reports that are not peer reviewed and, therefore, should not be construed as conclusions, guidelines for health-related clinical / behavioral practice, or are treated as defined information.