We report a SARS-CoV-2 lineage that shares N501Y, P681H, and other mutations with known variants of concern, such as B.1.1.7. This lineage, which we refer to as B.1.x (COG-UK sometimes references similar samples as B.1.324.1), is present in at least 20 states across the USA and in at least six countries. However, a large deletion causes the sequence to be automatically rejected from repositories, suggesting that the frequency of this new lineage is underestimated using public data.
Recent dynamics based on 339 samples obtained in Santa Cruz County, CA, USA suggest that B.1.x may be increasing in frequency at a rate similar to that of B.1.1.7 in Southern California. At present the functional differences between this variant B.1.x and other circulating SARS-CoV-2 variants are unknown, and further studies on secondary attack rates, viral loads, immune evasion and/or disease severity are needed to determine if it poses a public health concern.
BiorXiv preprint: A new SARS-CoV-2 lineage that shares mutations with known Variants of Concern is rejected by automated sequence repository quality control
Scientists have examined the Nextstrain and GISAID databases and found that the L452R mutation is present in more than 400 SARS-CoV-2 genomes isolated from over 20 countries. This indicates a strong positive selection for L452R mutation.
The scientists identified L452R amino acid substitution in the spike region as the dominant mutation in specimens collected since November 2020. Specifically, they observed that two independent SARS-CoV-2 variants (CAL.20C and CAL.20A) containing spike L452R mutation emerged recently in the state of California. Of these variants, CAL.20C (clade 20C; lineage B.1.429) is considered to be the predominant variant in California since November 2020. However, the CAL.20A variant (clade 20A; lineage B.1.232) identified in this study has emerged much more recently than CAL.20C and is primarily circulating in California. Based on the phylogenetic analysis, the scientists indicated that L452R mutation is the primary driving force behind the emergence of both variants. Such an increase in L452R mutation frequency in recent SARS-CoV-2 variants directly indicates its crucial involvement in viral adaptive evolution due to positive selection.
Interestingly, they found CAL.20A variant from a gorilla at the San Diego Zoo, which contains two additional mutations in the non-structural protein 2 (NSP2).
In contrast to CAL.20C, no massive clonal expansion was observed for CAL.20A. According to the study findings, CAL.20C contains two additional spike mutations along with L452R, which are missing in CAL.20A. The scientists believe that these additional mutations may be responsible for increasing the adaptive benefits of L452R, and because of this reason, CAL.20A could not achieve the same expansion rate as CAL.20C.
The CAL.20C variant accounts for nearly half of COVID-19 cases in Southern California and about a third of cases in the state based on an analysis of viral genomes posted to a global database called GISAID.
What’s more, the researchers found that by the end of January, the variant had spread to 19 other states, up from five states in November 2020. It has also spread beyond the U.S. to six other countries — Australia, Denmark, Israel, New Zealand, Singapore and the United Kingdom.
“We detected a novel strain descended from cluster 20C and defined by five mutations (ORF1a: I4205V, ORF1b:D1183Y, S: S13I;W152C;L452R)(Figure 1). This strain, CAL.20C, was first observed in July 2020 in 1/1230 samples from LA county and not detected in Southern California again until October. Since then, this strain’s prevalence has increased absolutely and relatively in Southern California, where by December it accounted for 24% of all samples (Figure 2A) and 36.4% (66/181) of our local Los Angeles cohort.”
A troop of gorillas at the San Diego Zoo’s Safari Park is recovering from an outbreak of COVID-19 that sickened several of the group’s eight members, the zoo said in a news release on Monday.
The gorillas began to fall ill on Jan. 6, when two of them started coughing, the statement by San Diego Zoo Global said.
The strain that infected them was “a new, highly contagious strain of the coronavirus, recently identified in California,” the zoo said.
Thousands of new coronavirus cases continue to emerge on college campuses. A New York Times survey of more than 1,700 American colleges and universities — including every four-year public institution and every private college that competes in N.C.A.A. sports — has revealed more than 252,000 cases and at least 80 deaths since the pandemic began.
Most of the cases have been announced since students returned to campus for the fall term. Most of the deaths were reported in the spring and involved college employees, not students.
But at least three students — Jamain Stephens, a football player at California University of Pennsylvania; Chad Dorrill, a sophomore at Appalachian State; and Bethany Nesbitt, a student at Grace College — have died in recent weeks after contracting the virus.
Three inmates in California prisons died of COVID-19 in the past week, state prison officials reported, as coronavirus outbreaks continued to devastate the state’s prison population.
The latest death was that of an inmate at Avenal State Prison. He was the 79th incarcerated person in California to die from complications of the illness