Research exhibits the function of globalization and zoonosis within the improvement and unfold of SARS-CoV-2 variants
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), which is responsible for Coronavirus Disease 2019 (COVID-19), was originally detected in December 2019 in Wuhan, China. SARS-CoV-2 is a rapidly developing virus with a mutation rate of around 9.8 x 10-4 substitutions per site per year along with a high rate of line turnover.
To learn: The analysis of SARS-CoV-2 variants from 24,181 patients illustrates the role of globalization and zoonosis in pandemics. Image source: solarseven / Shutterstock.com
The different national curves of COVID-19 cases
Different epidemic patterns caused by SARS-CoV-2 have been observed in different countries around the world. A bell-shaped curve typical of seasonal respiratory viral infection has been observed in Asia. In comparison, the bell-shaped curve recorded in western countries experienced one or two peaks.
A bell-shaped curve was observed in Marseille, France during the first wave of COVID-19, which was followed by almost no incidence between May and June 2020.The curve of this city is different from the single bell-shaped curve typical of most respiratory viral infections . It was assumed that this increase in cases corresponds to the emergence of new genotypes of SARS-CoV-2.
Classification of SARS-CoV-2 variants
Next-generation sequencing studies revealed various SARS-CoV-2 lines that exhibited different genetic, clinical, and epidemiological characteristics. The classification and naming of these various lineages are required in order to communicate about them.
The naming of SARS-CoV-2 variants, however, turned out to be difficult for several reasons. First, the virus develops through continuous genetic variation, which leads to a high rate of mutation. Second, there is an association between SARS-CoV-2 and other animal reservoirs, particularly minks.
The SARS-CoV-2-specific naming systems include Nextstrain, GISAID, Pangolin and the World Health Organization. While these systems are useful, they are not helpful in providing information about local genetic trends and correlating the epidemiological and clinical features with their genotypic patterns.
A study recently published on the medRxiv * pre-print server aimed to use their own classification and naming of the various SARS-CoV-2 lines to monitor their genetic traits and geographic origins.
About the study
The current study collected daily COVID-19 death rates from John Hopkins University, which includes data collected from 221 countries and locations between April 22, 2020 through June 24, 2021. Data mining techniques were then used to determine the dynamics of COVID-19 at the country level.
The genotyping of SARS-CoV-2 from nasopharyngeal samples took place between February 2020 and August 2021. The samples that had a cycle threshold (Ct) less than 20 were sent for whole genome sequencing. Samples with a Ct value between 20 and 30 were used for comprehensive coverage of the study period, while samples with a Ct value greater than 30 were subjected to qualitative polymerase chain reaction (qPCR) assays.
In addition, a genome sequence analysis was performed to determine the number of nucleotide changes in the genome and the number of amino acid changes in the spike protein of SARS-CoV-2. Finally, a phylogenetic reconstruction was performed to determine all of the mutations in the newest strain that corresponded to each of the variants.
The results of the current study indicate that geographically or politically isolated countries faced only one epidemic episode and thus exhibited a single bell-shaped curve. While Europe and the United States have seen multiple epidemics in a row involving different variants of the virus.
The city of Marseille, which in the past was an important location for tracking down cholera and plague epidemics, also showed similar trends during the SARS-CoV-2 pandemic. The first SARS-CoV-2 infection has been observed to involve people living in northwest Italy and on the Franco-Italian border. The border was closed after the first phase of the epidemic, but opened in early summer 2020 and a brief epidemic quickly followed.
This epidemic indicated the emergence of a new variant called Marseille-1 that originated in sub-Saharan Africa. This epidemic ended within two months and the variant did not spread beyond Marseille.
This was followed by the introduction of a second variety called Marseille-2, which came from Spain in early summer 2020. In 2021, the alpha variant was introduced by French people returning from the UK. Two other variants, including the Beta and Marseille-501 strains, were introduced by people of Comorian origins.
The Delta variant was imported by an Indian sailor who traveled from India to Marseille in the spring of 2020. Two other variants were imported from Colombia and the Republic of Guinea in 2021. It was observed that travel played an important role in the introduction and distribution of new SARS-CoV-2 variants.
The results of the study also showed that the role of animal diseases in animal herds in the generation of new SARS-CoV-2 variants and their transmission to humans was not taken into account. Mink was found to play an important role in the spread of the pandemic.
In Denmark and the USA, mink was found to be a source of new SARS-CoV-2 variants. In fact, the Marseille 4 variant was also made from mink. A major epidemic across Europe was subsequently caused by the Marseille-4 variant.
The current study also showed that different variants of SARS-CoV-2 reported different clinical patterns of infection. For example, patients infected with Marseille-1 reported a lower incidence of rhinitis and dyspnea and were less likely to be hospitalized between February and May 2020 compared to Nextstrain Clade 20A in Marseille.
In addition, patients infected with Marseille-4 were hospitalized more often than those infected with Marseille-1. It was also observed that the patients infected with the alpha, beta and gamma variants were less likely to be hospitalized than those infected with the Marseille-1 variant.
Souvenirs for your studies
The authors came to the conclusion that the different waves of the epidemic are caused by different variants of SARS-CoV-2. The main sources of these variants are cross-border travel and animal reservoirs. Efficient border controls and regular monitoring of livestock farms can help reduce the occurrence of new SARS-CoV-2 variants and the occurrence of new epidemics.
medRxiv publishes preliminary scientific reports that are not peer-reviewed and therefore are not considered conclusive, guide clinical practice / health-related behavior, or should be treated as established information.