“We also observed that the spike protein of the Lambda variant presented increased infectivity when compared with the spike protein of the Alpha and Gamma variants, both of them with reported increased infectivity and transmissibility. Together, our data show for the first time that mutations present in the spike protein of the Lambda variant confer escape to neutralizing antibodies and increased infectivity.”
“The evidence presented here reinforces the idea that massive vaccination campaigns in countries with high SARS-CoV-2 circulation rates must be accompanied by strict genomic surveillance aimed to rapidly identify new viral isolates carrying spike mutations as well as studies aimed to analyze the impact of these mutations in immune escape and vaccines breakthrough.”
We report the emergence of a novel lineage of SARS-CoV-2 in South America, termed C.37. It presents seven nonsynonymous mutations in the Spike gene (Δ247-253, G75V, T76I, L452Q, F490S, T859N) and a deletion in the ORF1a gene (Δ3675-3677) also found in variants of concern (VOCs) Alpha, Beta, and Gamma. Initially reported in Lima, Peru, in late December 2020, it now accounts for 97% of Peruvian public genomes in April 2021. It is expanding in Chile and Argentina, and there is evidence of onward transmission in Colombia, Ecuador, Mexico, the USA, Germany, and Israel. On June 15, 2021, the World Health Organization designated C.37 as Variant of Interest (VOI) Lambda.
According to Dr. Roberto Ovilla Martínez, head of hematology and bone marrow transplants at Hospital Ángeles Lomas, the patient Francisco Aguirre, an engineer by profession, is receiving treatment based on intravenous immunoglobulin that has helped to improve the condition. This would be the first case of a thrombosis caused by the AstraZeneca vaccine registered in Mexico and in the entire American continent.
Dr. Ovilla Martínez said that on April 2, together with his colleague, Víctor Manuel Vidal, a member of the Naucalpan Satellite Hospital, they diagnosed the patient who is currently hospitalized.
According to the doctor, a graduate from the Autonomous University of Chiapas (UNACH), the 94-year-old patient was inoculated last Wednesday, March 31, with the first dose of the drug developed by the University of Oxford and the AstraZeneca laboratory.
After 42 hours, the patient began to have symptoms such as extreme fatigue and lack of appetite, so his family transferred him to the Corporate Hospital Satélite.
We report the distribution of the Spike mutation S:T478K and its recent growth in prevalence in the SARS-CoV-2 population. While there is currently no report of association of this variant with clinical features, S:T478K’s rapid growth may indicate an increased adaption of SARS-CoV-2 variants carrying it, particularly lineage B.1.1.222.
The distribution of this mutation is higher in North America, but we could detect it also in several European countries. The location of S:T478K in the interaction complex with human ACE2 may affect the affinity with human cells and therefore influence viral infectivity.
We detected this growth starting at the beginning of 2021, and S:T478K is, at the time of writing (March 26, 2021) characterizing almost 2.0% of all sequenced SARS-CoV-2
An in silico molecular dynamics study on the protein structure of Spike has predicted that the T478K mutation, substituting a non-charged amino acid (Threonine) with a positive one (Lysine) may significantly alter the electrostatic surface of the protein, and therefore the interaction with ACE2, drugs or antibodies, and that the effect can be increased if combined by other co-occurring Spike mutations.
Another experiment showed that T478K and T478R mutants were enriched when SARS-CoV-2 viral cultures were tested against weak neutralizing antibodies, highlighting, at least in vitro, a possible genetic route the virus can follow to escape immune recognition. Everything considered, we believe that the continued genetical and clinical monitoring of S:T478K and other Spike mutations is of paramount importance to better understand COVID-19 and be able to better counteract its future developments.
This is the first study focused on the presence of SARS-CoV-2 in different freshwater environments of an urban setting. Groundwater and surface water reservoirs for drinking water as well as water from receiving rivers of Monterrey Metropolitan Area were sampled repeatedly during a peak phase between October 2020 and January 2021, and the virus RNA was measured by quantitative reverse transcription polymerase chain reaction.
Forty-four percent of groundwater samples demonstrated detectable virus loads between 2.9 and 5.6 copies/ml. A significant correlation with sucralose concentration in groundwater reaffirmed the hypothesis of leaching and infiltration of effluents from surface and/or failing sewage pipes, and emphases the importance of water disinfection. Thirteen percent of surface water dam samples tested positive, with values varying between 3.3 and 3.8 copies/ml. Finally, 21% of river samples marked positive for viral RNA, with concentrations ranging from 0.3 to 7.0 copies/ml. Raw wastewater samples taken in the same period show viral loads of up to 3535 copies/ml
This what we know about the strain found in San Luis Potosí, Mexico: The mutation is known as E-484k and it was also identified in people from Jalisco and Tamaulipas. However, unlike the PFS patient, the other residents did have contact with foreigners.
According to specialists, the E484K mutation recognizes the virus less, which can reduce neutralization by antibodies, it can also evade immune protection due to vaccination.
The health authorities highlighted that the patient showed a favorable evolution without the need for hospitalization.
The Brazilian variant called P.1, which is related to the San Luis Potosí strain, has already appeared in several Latin American countries such as Mexico, the World Health Organization ( WHO ) reported.
If it is not associated with the Brazilian strain of Covid-19, it would be a new strain of the virus, said Andreu Comas García, a doctor at the UASLP.
Sofía Bernal, one of the doctors who coordinates the University Laboratory, assured that more variants of COVID-19 that circulate in the world will reach Mexico, for which she called for reinforcing prevention measures at all times.
The new SARS-CoV-2 mutation, E484K, detected in four patients from Jalisco, has some characteristics of its own and differences with the strain identified in Brazil and South Africa, according to the University of Guadalajara.
“What we can confirm is that we did detect the E484K mutation and this is an important finding, since it had not been reported in Mexico,” said the head of the Laboratory for Diagnosis in Emerging and Reemerging Diseases (LaDEER), Nataly Vega Magaña, at the University Center for Health Sciences (CUCS) of the University of Guadalajara.