Mutation pattern in coronavirus sequence reveals it has been silently SPREADING in the USA for weeks

The coronavirus is sweeping across the United States at an unprecedented rate. Since the first confirmed case in Washington state on January 20, hundreds of new cases have emerged in different states, and the number of coronavirus deaths has risen to nine as of Tuesday.

Following warnings of possible community spread of the coronavirus by the Centers for Disease Control and Prevention (CDC), researchers in the state have uncovered new details about the coronavirus which suggest that it may have spread undetected since the first confirmed case in the United States.

Coronavirus mutation and “cryptic transmission”

Trevor Bedford, an associate professor at the University of Washington, studies viruses, evolution and immunity. He is also part of the Seattle Flu Study, which has recently started screening and sequencing the coronavirus from samples collected in areas with reported cases.

In his blog post published on March 2, Bedford discussed in detail how mutation patterns in the coronavirus genome support the possibility of a viral transmission occurring sometime between January 15 and January 19 in Washington state. The first confirmed case in the U.S. was a returning traveler from Wuhan, China, who arrived in Snohomish County on January 15 and was confirmed to be infected five days later.

On February 28, the Snohomish Health District reported a presumptive positive case involving an adolescent — the second coronavirus case in the county. “Presumptive positive” is the term used for tests that return positive from state labs and are awaiting confirmation from the CDC. The sample from this case was shared with the Seattle Flu Study.

Sequencing results revealed that the virus from the sample has an identical genome to the virus from the first confirmed case. The only difference was that the former had three additional mutations in its genomic sequence.

Viruses, according to Bedford, mutate very quickly. They undergo genetic changes as they are transmitted from person to person. In the case of the new coronavirus, genetic epidemiology studies show that it incurs an average of two mutations per month. This aligns with the mutation pattern found in the virus from the presumptive positive case and increases the possibility that it was a direct descendant of the first case virus.

“If this virus arrived in Snohomish County in mid-January with the WA1 [first case virus] traveler from Wuhan and circulated locally for 5 weeks, we’d expect exactly this pattern, where the WA2 [presumptive positive case virus] genome is a copy of the WA1 genome except it has some mutations that have arisen over the 5 weeks that separate them,” Bedford wrote in his blog. He referred to the scenario as “cryptic” or “undetected transmission.”

The Seattle Flu Study also determined the likelihood of the mutation pattern arising by chance instead of direct transmission to be only 3 percent. This was based on the fact that the genetic variant shared by the two viruses at a specific site can only be found in 2 of the 59 sequenced viruses from China.

According to Bedford, this, together with the location of cases in Washington, is firm evidence of continued cryptic transmission of the virus.

CDC expands testing guidelines

In a series of tweets posted on Sunday, Bedford said that the state of Washington is on the brink of a substantial outbreak due to the narrow case definition set by the CDC. The agency only approved testing for people who had traveled to China and those they had contact with.

The team at the @seattleflustudy have sequenced the genome the #COVID19 community case reported yesterday from Snohomish County, WA, and have posted the sequence publicly to https://t.co/tbVb4MAGpy. There are some enormous implications here. 1/9

— Trevor Bedford (@trvrb) March 1, 2020

At a news conference on Monday, Dr. Kathy Lofy, a Washington State Health Officer, said that the agency is finding more coronavirus cases that appear to be acquired locally. She also said that the virus is actively spreading in some communities. At the time of the briefing, a total of 18 people in Washington had tested positive for the coronavirus, according to officials, and five of them had died. (Related: New York Emergency Room Doctor: There Will Be “Thousands” Of Confirmed Cases In The U.S. “By Next Week”.)

In response to the community spread that has already begun, the CDC has expanded its guidelines to accommodate more people for testing. Once this is implemented, the number of coronavirus cases in the U.S. is expected to increase dramatically. Officials say broader testing will help identify which communities have been experiencing community transmission for a while.

Sources include:

NYTimes.com

Salon.com

Bedford.io

SnoHD.org

Twitter.com