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Research reveals how the SARS-CoV-2B.1.1.7 variant invaded the United States

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Team led by researchers Graduate School of Public Health Discovered how the B.1.1.7 mutant of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), first discovered in the United States, penetrated several states in the United States. did. The coronavirus pandemic affects almost every country in the world, but the United States currently has more than 27.8 million reported infections and the world’s highest death toll of more than 2.4 million. ..

Kirsten St. George, Nathan D. Grubaugh and colleagues have sequenced potential new mutants from confirmed positive COVID-19 cases in the United States, despite increased travel restrictions and increased coronavirus testing. It states that it underreports. Since the United States sequenced only about 0.13% of COVID-19 cases, it was difficult to first detect when the B.1.1.7 variant first appeared in the United States.

“Sequencing capabilities vary widely across countries. Our travel data disproportionately underreport B.1.1.7 cases, and it is wise to prioritize variant surveillance immediately. Helps identify, “the author writes.

The study of “Early introduction of SARS-CoV-2 variant B.1.1.7 and community infection in the United States” medRxiv* Servers and articles have been peer reviewed.

Virus tracking

Researchers used a combination of October 2020 flight records from the UK to all US airports and SARS-CoV-2 genomic sequencing to detect the origin of the US B.1.1.7 variant. did. Not only was this the latest data available, but it also overlapped with the time when the B.1.1.7 variant was initially thought to be widespread throughout the UK.

The CDC reported in early February that 33 states identified 541 B.1.1.7 cases in the United States. However, the authors believe that low-genome surveillance may not represent the true extent of mutant spread. Instead, they analyzed the number of cases reported between December 2020 and January 2021 in proportion to the SARS-CoV-2 clinical sample.

Identify areas at risk of imports of B.1.1.7 and at risk of underreporting of B.1.1.7.  A. The number of inbound passengers from the UK at the top 15 airports in October 2020 (dot labels, size and color scaling according to population, see legend) will be displayed on a map of the continental United States (gray).  B. Bar charts are sequenced on GISAID.org (accessed February 4) in the December 2020 and January 2021 states (x-axis below, provided from https://covidtracking.com/data). Represents the percentage of uploaded cases.  2021). The bars are color coded according to region (legend, top right). The number of B.1.1.7 sequences for each state (top x-axis, black dot) was determined by the Pangolin lineage assignment in the GSIAID.org metadata.  CD.  The total number of passengers arriving from the United Kingdom to each state of the Americas in October 2020 is the number of SARS-CoV-2 (C) or B.1.1.7 SARS-CoV-2 (D) sequences available in GISAID. It is plotted against.  .org. The points are color coded according to region (Panel B legend). The data used to create this figure is listed in Data S1.

Identify areas at risk of imports of B.1.1.7 and at risk of underreporting of B.1.1.7. A. The number of inbound passengers from the UK at the top 15 airports in October 2020 (dot labels, size and color scaling according to population, see legend) will be displayed on a map of the continental United States (gray). B. The bar chart shows the percentage of cases in each state in December 2020 and January 2021 (x-axis below. https://covidtracking.com/data) There is a sequence uploaded to GISAID.org (accessed February 4, 2021). The bars are color coded according to region (legend, top right). The number of B.1.1.7 sequences for each state (top x-axis, black dot) was determined by the Pangolin lineage assignment in the GSIAID.org metadata. CD. The total number of passengers arriving from the United Kingdom to each state of the Americas in October 2020 is the number of SARS-CoV-2 (C) or B.1.1.7 SARS-CoV-2 (D) sequences available in GISAID. It is plotted against. .org. The points are color coded according to region (Panel B legend). The data used to create this figure is listed in Data S1.

Strong evidence of the first variant spread in New York

Low-genome surveillance was reported from December to January, and only 0.1% of COVID-19 cases were sequenced and made available to researchers. A total of 26 states had less than 0.1% of case sequences, and at the time the preprint was issued, 14 states had not submitted a genomic sequence associated with B.1.1.7.

Numerous B.1.1.7 strains have been found in New York, California and Florida. The ordering coincides with the arrival of numerous international flights from the United Kingdom to airports in these states.

Multiple introductions, domestic dissemination, and community infections of B.1.1.7 SARS-CoV-2 in the United States.  A. Maximum likelihood phylogeny of B.1.1.7, including representative genomes from the United States, Europe and other global locations.  B. Singleton and clade highlights representing the direct introduction of B.1.1.7 from Europe to different regions of the United States, based on the same phylogenetic tree shown in (A). A list of migrations from Europe to the United States can be found in Data S1.  CE. Time information for separate B.1.1.7 clades showing cases of domestic spread (C, E) and / or community infections within New York (C), Connecticut (C), Michigan (C, D), and Illinois. Maximum likelihood phylogeny based on (E). A list of SARS-CoV-2 sequences used in this study and the author's acknowledgments can be found in data S2.

Multiple introductions, domestic dissemination, and community infections of B.1.1.7 SARS-CoV-2 in the United States. A. Maximum likelihood phylogeny of B.1.1.7, including representative genomes from the United States, Europe and other global locations. B. Singleton and clade highlights representing the direct introduction of B.1.1.7 from Europe to different regions of the United States, based on the same phylogenetic tree shown in (A). A list of migrations from Europe to the United States can be found in Data S1. CE. Time information for separate B.1.1.7 clades showing cases of domestic spread (C, E) and / or community infections within New York (C), Connecticut (C), Michigan (C, D), and Illinois. Most likely phylogeny based on (E). A list of SARS-CoV-2 sequences used in this study and the author’s acknowledgments can be found in data S2.

Of all three, researchers concluded that New York was likely to be the central hub for the B.1.1.7 variant, which would later spread to other states. The New York-New Jersey region has a record of 14,317 passengers to and from the United Kingdom. These results correspond to the first COVID-19 cases of a new subspecies detected in Saratoga County, New York on December 24, 2020.

The B.1.1.7 variant remained undetected, suggesting that researchers are likely to have had persistent community infections in New York, New Jersey, Connecticut, and Illinois since January 2021. I will.

“Therefore, increased monitoring of B.1.1.7 and other variants by sequencing and more general methods needs to be a high priority,” the researchers write.

Most likely B.1.17 variant in other states

Researchers have sequenced most B.1.1.7 variants in New York, but researchers say underreporting may have contributed to cases where they were not detected in other states. Their results show that more than 2,500 people are flying from the United Kingdom to Texas, Illinois and New Jersey. Still, in all three states, it was less than 0.05% of the sequenced cases. The authors suggest that the epidemic of new strains is likely to be increasing in other states.

“But in places like New Jersey, Illinois, and Texas, if SARS-CoV-2 genomic surveillance could be increased, would B.1.1.7 cases be disproportionately underreported compared to New York and California? You may be able to judge whether or not. ” researcher.

More Genome Surveillance Needed for Future Research

Given the limited travel data and low genomic surveillance, researchers say the samples are too small to represent the entire spread of this variant in the United States. In addition, they were unable to assess infection rates between different regions and assumed that the community was highly expansive. “In fact, local conditions and behaviors play an important role in establishing B.1.1.7 and can explain why there are so few cases in some states.”

With the spread of new variants, the researchers suggest that strengthening genomic surveillance is a high-priority task needed to mitigate the spread of the virus.

*Important Notices

medRxiv Publish preliminary scientific reports that should not be considered definitive as they are not peer-reviewed, guide clinical practice / health-related behaviors, and should not be treated as established information.

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