Comment on "Genetic variants and source of introduction of SARS-CoV-2 in South America".
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ABSTRACT:
SUBMITTER: Romero PE
PROVIDER: S-EPMC7300916 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:After more than 4 months of the COVID-19 pandemics with genomic information of SARS-CoV-2 around the globe, there are more than 1000 complete genomes of this virus. We used 691 genomes from the GISAID database. Several studies have been reporting mutations and hotspots according to viral evolution. Our work intends to show and compare positions that have variants in 30 complete viral genomes from South American countries. We classified strains according to point alterations and portray the source where strains came into this region. Most viruses entered South America from Europe, followed by Oceania. Only Chilean isolates demonstrated a relationship with Asian isolates. Some changes in South American genomes are near to specific domains related to viral replication or the S protein. Our work contributes to the global understanding of which sort of strains are spreading throughout South America, and the differences among them according to the first isolates introduced to this region.
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Project description:In 2020, the emergence of SARS-CoV-2 caused a global public health crisis with significant mortality rates and a large socioeconomic burden. The rapid spread of this new virus has led to the appearance of new variants, making the characterization and monitoring of genetic diversity necessary to understand the population dynamics and evolution of the virus. Here, a population-genetics-based study was performed starting with South American genome sequences available in the GISAID database to investigate the genetic diversity of SARS-CoV-2 on this continent and the evolutionary mechanisms that modulate it.
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Project description:Since the zoonotic event from which SARS-CoV-2 started infecting humans late in 2019, the virus has caused more than 5 million deaths and has infected over 500 million people around the world. The pandemic has had a severe impact on social and economic activities, with greater repercussions in low-income countries. South America, with almost 5% of the world's population, has reckoned with almost a fifth of the total people infected and more than 26% (>1/4) of the deceased. Fortunately, the full genome structure and sequence of SARS-CoV-2 have been rapidly obtained and studied thanks to all the scientific efforts and data sharing around the world. Such molecular analysis of SARS-CoV-2 dynamics showed that rates of mutation, similar to other members of the Coronaviridae family, along with natural selection forces, could result in the emergence of new variants; few of them might be of high consequence. However, this is a serious threat to controlling the pandemic and, of course, enduring the process of returning to normalization with the implicit monetary cost of such a contingency. The lack of updated knowledge in South America justifies the need to develop a structured genomic surveillance program of current and emerging SARS-CoV-2 variants. The modeling of the molecular events and microevolution of the virus will contribute to making better decisions on public health management of the pandemic and developing accurate treatments and more efficient vaccines.
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Project description:SARS-CoV-2 is a new member of the genus Betacoronavirus, responsible for the COVID-19 pandemic. The virus crossed the species barrier and established in the human population taking advantage of the spike protein high affinity for the ACE receptor to infect the lower respiratory tract. The Nucleocapsid (N) and Spike (S) are highly immunogenic structural proteins and most commercial COVID-19 diagnostic assays target these proteins. In an unpredictable epidemic, it is essential to know about their genetic variability. The objective of this study was to describe the substitution frequency of the S and N proteins of SARS-CoV-2 in South America. A total of 504 amino acid and nucleotide sequences of the S and N proteins of SARS-CoV-2 from seven South American countries (Argentina, Brazil, Chile, Ecuador, Peru, Uruguay, and Colombia), reported as of June 3, and corresponding to samples collected between March and April 2020, were compared through substitution matrices using the Muscle algorithm. Forty-three sequences from 13 Colombian departments were obtained in this study using the Oxford Nanopore and Illumina MiSeq technologies, following the amplicon-based ARTIC network protocol. The substitutions D614G in S and R203K/G204R in N were the most frequent in South America, observed in 83% and 34% of the sequences respectively. Strikingly, genomes with the conserved position D614 were almost completely replaced by genomes with the G614 substitution between March to April 2020. A similar replacement pattern was observed with R203K/G204R although more marked in Chile, Argentina and Brazil, suggesting similar introduction history and/or control strategies of SARS-CoV-2 in these countries. It is necessary to continue with the genomic surveillance of S and N proteins during the SARS-CoV-2 pandemic as this information can be useful for developing vaccines, therapeutics and diagnostic tests.
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Project description:This study analyzes the evolution of the population structure and genetic diversity of Braford cattle in South America from 1949 to 2019 to suggest effective strategies for breeding in the future. The percentage of bulls historically increased. The average generational interval decreased to 11.78 years for the current population. Average inbreeding (F) and coancestry (C) are low and show a historically increasing trend (0.001% to 0.002%, respectively). The degree of nonrandom mating (α) increased from -0.0001 to 0.0001 denoting a change in the trend to mate similar individuals. The average relatedness coefficient (ΔR) increased in the current period from 0.002% to 0.004%. A single ancestor explained 4.55% to 7.22% of the population's gene pool. While the effective population size based on the individual inbreeding rate (NeFi) was 462.963, when based on the individual coancestry rate (NeCi), it was 420.168. Genetic diversity loss is small and mainly ascribed to bottlenecks (0.12%) and to unequal contributions of the founders (0.02%). Even if adequate levels of diversity can be found, practices that consider the overuse of individual bulls (conditioned by nature or not), could lead to a long-term reduction in diversity. The present results permit tailoring genetic management strategies that are perfectly adapted to the needs that the population demands internationally.
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Project description:Genetic mutation and recombination are driving the evolution of SARS-CoV-2, leaving many genetic imprints which could be utilized to track the evolutionary pathway of SARS-CoV-2 and explore the relationships among variants. Here, we constructed a complete genetic map, showing the explicit evolutionary relationship among all SARS-CoV-2 variants including 58 groups and 46 recombination types identified from 3,392,553 sequences, which enables us to keep well informed of the evolution of SARS-CoV-2 and quickly determine the parents of novel variants. We found that the 5' and 3' of the spike and nucleoprotein genes have high frequencies to form the recombination junctions and that the RBD region in S gene is always exchanged as a whole. Although these recombinants did not show advantages in community transmission, it is necessary to keep a wary eye on the novel genetic events, in particular, the mutants with mutations on spike and recombinants with exchanged moieties on spike gene.
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