Chinese Scientists Identify New SARS-CoV-2 Gamma Variants In Shandong


Researchers, from the Shandong Provincial Center For Disease Control And Prevention has released information to the media (CCTV-Chinese Language News) that a new SARS-CoV-2 Gamma variant has been identified among infected individuals in the county of Roncheng.

The new variants were discovered among 4 asymptomatic individuals whose viral samples were sent for genomic sequencing at the Weihai City Centre For Disease Control and Prevention labs.
According to the Chinese scientists, when compared with the Wuhan reference strain (NC-D45512), the genome sequences of the 4 cases of local infection of the new coronavirus variant are highly homologous and there were 36 nucleotide mutation sites that correspond to those found on the VOC/Gamma Variant strain (P.1.15 evolutionary branch).
The three defining and concerning mutations of the Gamma variant ie N501Y, E484K and K417T were found on the genomic sequences of the new variant as well.
These genomic sequences when compared on the GISAID global databases were found to be highly homologous to previous sequences uploaded from Chile.
The four individuals had no previous travel history and were also not known to be in proximity to any foreigners.
Chinese authorities are conduction more tracking studies and also conducting more vigorous testing and genomic sequencing if individuals in Roncheng county.

Currently, SARS-CoV-2 variants that present a threat to global health are classified as Variants of Interest (VOIs) and Variants of Concern (VOCs)3. To date, all VOCs are descendants of the SARS-CoV-2 strain containing a Spike (S) D614G mutation, which is associated with increased viral fitness by enhancing viral load in the upper respiratory tract favoring viral spread and transmission 4,5.

As of December 2021, five reported lineages had been defined as VOCs, four of them first detected in late 2020: B.1.1.7 (Alpha), first detected in the United Kingdom (UK), has been associated with enhanced transmissibility, higher severity of disease6,7, and lower neutralization potential by vaccine and convalescent sera8; B.1.351 (Beta), a variant first detected in South Africa, has been associated with an increased risk of transmission and reduced neutralization by monoclonal antibody therapy, convalescent sera, and post-vaccination sera9,10,11,12; Gamma (P.1), a Brazilian variant derived from the B.1.1.28 lineage, shares some critical mutations in the Spike protein with B.1.35113; and B.1.617.2 (Delta), detected in India, has spread and replaced other variants circulating and currently is the dominant lineage globally, and showed significantly reduced neutralizing antibody activity compared with the wild-type strain and other VOCs14. The B.1.1.5 29 variant, first reported to WHO from South Africa on 24 November 2021, was recently advertised as a VOC and named Omicron15. It is unclear whether Omicron is more transmissible or causes more severe disease than infections with other variants15. However, this decision was based on Omicron’s large number of mutations, especially in the Spike gene (more than 30 mutations)16.

The Brazilian VOC, Gamma lineage, was first detected in early December in Manaus, the capital of Amazonas state17, and rapidly spread throughout Brazil and to more than 60 countries2. Gamma lineage emerged after a period of rapid genetic diversification17 and accumulated 17 non-synonymous defining mutations, ten of which are located in the S gene 13,17, of which K417T:E484K:N501Y were demonstrated to be involved in immune escape 18,19.

Recent studies have reported that Gamma lineage presents an increase in ACE2 receptor affinity due to the presence of the N501Y mutation18,20, which considerable impacts its transmissibility rate, shown to be 1.4–2.2-fold higher than the wild type strain13. Moreover, Gamma also exhibited a reduction of anti-RBD antibody neutralization21, and it has been implicated in breakthrough infections of vaccinated individuals and reinfections 22,23,24.

Although several studies documented, Gamma’s increased transmissibility 17,25 and immune evasion 22,24,26,27,28, little is known about its association with the severity of COVID-19 disease and mortality risk, which is crucial to better understand and mitigate the severe impact of the ongoing pandemic.

In addition to Gamma lineages emergence and dissemination, Brazil has faced a slow vaccination roll-out, which contributed to prolonging the pandemic and the emergence of additional SARS-CoV-2 variants. The immunization campaign started in February 2021, in descending age order. As of July 26, 2021, 131,946,091 doses of COVID-19 vaccine have been administered, with 44.11% and 17.3% of the population receiving the first and second doses, respectively 29.

Brazil has approved the use of four COVID-19 vaccines: ChAdOx1 nCoV-19 (AZD1222; Oxford-AstraZeneca), CoronaVac (Butantan Institute, São Paulo, Brazil, and Sinovac Life Sciences, Beijing, China), BNT162b2 mRNA (Pfizer/BioNTech), and Ad26.COV2.S (Janssen/Johnson & Johnson), corresponding to 46.4%, 40.8%, 9.9%, and 2.9% of the administered doses29, respectively. While most vaccines show high efficacy in preventing severe COVID-19 disease and death 30,31,32,33,34,35, the impact of slow vaccination rates on the circulation and spread of VOCs on the epidemiological profiles at the national and local level is still unclear.

Here, we report the rapid spread of the Gamma variant following its introduction and dissemination in São José do Rio Preto (SJdRP), Brazil, the municipality with the third-highest number of confirmed COVID-19 cases in São Paulo and where based Hospital de Base (HB), the main responsible for SARS-CoV-2 diagnosis and one of the leading in COVID-19 care and treatment in the state. Moreover, the new lineage introduction drove a clade replacement event, associated with a change in the epidemiological profile, with increased severe COVID-19 cases and deaths, especially in the unvaccinated population.

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