scholarly journals Different selection dynamics of S and RdRp between SARS-CoV-2 genomes with and without the dominant mutations

2021 ◽  
Author(s):  
Necla Koçhan ◽  
Doğa Eskier ◽  
Aslı Suner ◽  
Gökhan Karakülah ◽  
Yavuz Oktay
Keyword(s):  
Viral Entry ◽  
Negative Selection ◽  
Pharmaceutical Research ◽  
Mutation Rates ◽  
Coding Region ◽  
S Gene ◽  
Selection Dynamics ◽  
Strong Negative Selection ◽  
Rdrp Region ◽  
Over Time

AbstractSARS-CoV-2 is a betacoronavirus responsible for the COVID-19 pandemic that has affected millions of people worldwide, with no dedicated treatment or vaccine currently available. As pharmaceutical research against and the most frequently used tests for SARS-CoV-2 infection both depend on the genomic and peptide sequences of the virus for their efficacy, understanding the mutation rates and content of the virus is critical. Two key proteins for SARS-CoV-2 infection and replication are the S protein, responsible for viral entry into the cells, and RdRp, the RNA polymerase responsible for replicating the viral genome. Due to their roles in the viral cycle, these proteins are crucial for the fitness and infectiousness of the virus. Our previous findings had shown that the two most frequently observed mutations in the SARS-CoV-2 genome, 14408C>T in the RdRp coding region, and 23403A>G in the S gene, are correlated with higher mutation density over time. In this study, we further detail the selection dynamics and the mutation rates of SARS-CoV-2 genes, comparing them between isolates carrying both mutations, and isolates carrying neither. We find that the S gene and the RdRp coding region show the highest variance between the genotypes, and their selection dynamics contrast each other over time. The S gene displays higher positive selection in mutant isolates early on, and undergoes increasing negative selection over time, whereas the RdRp region in the mutant isolates shows strong negative selection throughout the pandemic.

scholarly journals Sequence and phylogentic analysis of MERS-CoV in Saudi Arabia, 2012–2019

2021 ◽  
Vol 18 (1) ◽  
Author(s):  
Mohamed A. Farrag ◽  
Haitham M. Amer ◽  
Rauf Bhat ◽  
Fahad N. Almajhdi
Keyword(s):  
Middle East ◽  
Gene Sequence ◽  
Selective Pressure ◽  
Mutation Rates ◽  
Receptor Binding Domain ◽  
Sequence Comparisons ◽  
S Gene ◽  
Clade B ◽  
Human Coronaviruses ◽  
Early Phases

Abstract Background The Middle East Respiratory Syndrome-related Coronavirus (MERS-CoV) continues to exist in the Middle East sporadically. Thorough investigations of the evolution of human coronaviruses (HCoVs) are urgently required. In the current study, we studied amplified fragments of ORF1a/b, Spike (S) gene, ORF3/4a, and ORF4b of four human MERS-CoV strains for tracking the evolution of MERS-CoV over time. Methods RNA isolated from nasopharyngeal aspirate, sputum, and tracheal swabs/aspirates from hospitalized patients with suspected MERS-CoV infection were analyzed for amplification of nine variable genomic fragments. Sequence comparisons were done using different bioinformatics tools available. Results Several mutations were identified in ORF1a/b, ORF3/4a and ORF4b, with the highest mutation rates in the S gene. Five codons; 4 in ORF1a and 1 in the S gene, were found to be under selective pressure. Characteristic amino acid changes, potentially hosted and year specific were defined across the S protein and in the receptor-binding domain Phylogenetic analysis using S gene sequence revealed clustering of MERS-CoV strains into three main clades, A, B and C with subdivision of with clade B into B1 to B4. Conclusions In conclusion, MERS-CoV appears to continuously evolve. It is recommended that the molecular and pathobiological characteristics of future MERS-CoV strains should be analyzed on regular basis to prevent potential future outbreaks at early phases.

scholarly journals Seed Banks Alter the Rate and Direction of Molecular Evolution in Bacillus subtilis

2021 ◽  
Author(s):  
William R. Shoemaker ◽  
Evgeniya Polezhaeva ◽  
Kenzie B. Givens ◽  
Jay T. Lennon
Keyword(s):  
Bacillus Subtilis ◽  
Molecular Evolution ◽  
Seed Bank ◽  
Negative Selection ◽  
Evolutionary Dynamics ◽  
Genetic Manipulation ◽  
Seed Banks ◽  
Rate Of Molecular Evolution ◽  
Over Time ◽  
Growth And Reproduction

Fluctuations in the availability of resources constrains the growth and reproduction of individuals, which in turn effects the evolution of their respective populations. Many organisms are able to respond to fluctuations by entering a reversible state of reduced metabolic activity, a phenomenon known as dormancy. This pool of dormant individuals (i.e., a seed bank) does not reproduce and is expected to act as an evolutionary buffer, though it is difficult to observe this effect directly over an extended evolutionary timescale. Through genetic manipulation, we analyze the molecular evolutionary dynamics of Bacillus subtilis populations in the presence and absence of a seed bank over 700 days. We find that the ability to enter a dormant state increases the accumulation of genetic diversity over time and alters the trajectory of mutations, findings that are recapitulated using simulations based on a simple mathematical model. While the ability to form a seed bank does not alter the degree of negative selection, we find that it consistently alters the direction of molecular evolution across genes. Together, these results show that the ability to form a seed bank affects the direction and rate of molecular evolution over an extended evolutionary timescale.

Sequence Length of HIV-1 Subtype B Increases Over Time: Analyzing a Cohort of Patients with Hemophilia Over 30 Years

2021 ◽  
Author(s):  
Young-Keol Cho ◽  
Jung-eun Kim ◽  
Brian Foley
Keyword(s):  
Direct Sequencing ◽  
National Laboratory ◽  
Sequence Length ◽  
Coding Region ◽  
Los Alamos National Laboratory ◽  
Subtype B ◽  
Combined Antiretroviral Therapy ◽  
Signature Pattern ◽  
Hiv 1 ◽  
Over Time

The objective of this study is to investigate whether the sequence length of HIV-1 increases over time. A longitudinal analysis of full-length coding region sequences (FLs) in an outbreak of HIV-1 infection among patients with hemophilia and local controls identified as infected with the Korean subclade B of HIV-1 (KSB). Genes amplified by overlapping RT-PCR or nested PCR were subjected to direct sequencing. In total, 141 FLs were sequentially determined over 30 years in 62 KSB-infected patients. Non-KSB sequences were retrieved from the Los Alamos National Laboratory HIV Database. Phylogenetic analysis indicated that within KSB, 2 FLs from plasma donors O and P comprised two clusters together with 8 and 12 patients with hemophilia, respectively. Signature pattern analysis for the KSB of HIV-1 revealed signature nucleotide residues at 1.05%, compared with local controls. Additionally, in-depth FLs sequence analysis over 30 years in KSB indicates that the KSB FL significantly increases over time before combined antiretroviral therapy (cART) and decreases on cART. Furthermore, the increase in FLs over time significantly occurred in the subtypes B, C and G, but, there was no increase in the subtypes D, A, and F1. Consequently, subtypes F1 and D had the shortest sequence length. Our analysis was extended to compare HIV-1 with HIV-2 and SIVs. Essentially, the longer the sequence length (SIVsm > HIV-2 > SIVcpz > HIV-1), the longer the survival period. The increase in the length of the HIV-1 sequence over time suggests that it might be an evolutionary direction toward attenuated pathogenicity.

The possible role of S gene mutations of hepatitis B virus in intrauterine transmission

2020 ◽  
Author(s):  
Jiaxin Wu ◽  
Yongliang Feng ◽  
Zhiqing Yang ◽  
Ruijun Zhang ◽  
Dandan Wang ◽  
...  
Keyword(s):  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Hepatitis B Surface Antigen ◽  
Gene Mutations ◽  
Hbv Dna ◽  
Mutation Rates ◽  
Control Group ◽  
Intrauterine Transmission ◽  
S Gene ◽  
B Virus

Abstract Background: Many hepatitis B virus (HBV) substances could inevitably enter fetuses and occurred neonatal intrauterine transmission. HBV often occurs mutation, especially S gene, and may lead to different outcomes on intrauterine transmission. We explored the associations between HBV S gene mutations of hepatitis B surface antigen positive (HBsAg-positive) mothers and intrauterine transmission. Methods: A total of 399 HBsAg-positive mothers and neonates were recruited and their general demographic information was collected between June 2011 and July 2013. The mothers with HBV DNA levels ≥ 106 IU/ml were selected, 22 mothers whose neonates occurred HBV intrauterine transmission were in the HBV intrauterine transmission group (GT) and 22 mothers were randomly selected from the remaining controls were in the control group (GC). Maternal whole-genome HBV DNA was extracted, amplified, cloned, and sequenced. Obtained sequences were adjusted, genotyped, and analyzed for mutation rates. A case-control study was designed to analyze the relationship between mutations in the S gene of HBV and intrauterine transmission. Results: Fifty-five neonates were found to have experienced intrauterine transmission (13.78%). Genotype B (4.55%), genotype C (88.64%) and inter-genotype B/C (6.81%) were found in the 44 HBsAg-positive mothers. The mutation rates of the S gene, in both genotypes B (0.58% vs 1.41%, P = 0.040) and C (7.56% vs 14.71%, P＜0.001), were lower in group T than in group C. Missense substitutions such as L84I, P47S, K10Q, A41P, M133L, A60V, and I42T only existed in group C. The mutation rates of G73S, I126T, and I126S in group C were higher (P < 0.001, P < 0.001, P = 0.010). Deletions occurred in the S gene. The occurrence of intrauterine transmission with maternal mutation A90V was higher (P < 0.001). This may have increased the risk of neonatal HBsAg expression (P = 0.022). Conclusions: The HBV S gene mutations of HBsAg-positive mothers may reduce the occurrence of HBV intrauterine transmission. It is possible for HBsAg-positive mothers infected with A90V to develop HBV chronic infection and transmit it to the fetus during pregnancy, resulting in neonatal HBV infection.

Genomic Variations in ORF3a and ORF1ab Genes of SARS-nCoV2 Strain from Southern Pakistan

2020 ◽  
Author(s):  
Rashid Saif ◽  
Aniqa Ejaz ◽  
Tania Mahmood ◽  
Saeeda Zia ◽  
Abdul Rasheed Qureshi
Keyword(s):  
Host Cell ◽  
Viral Entry ◽  
Binding Capacity ◽  
Its Sequence ◽  
Genomic Variations ◽  
S Gene ◽  
Variation Rate ◽  
Codon Change ◽  
Different Strains

Emergence of COVID-19 pandemic has resulted in 8,578,283 total cases and 456,286 deaths worldwide as of June 19, 2020. We previously analysed genomic variants in two Northern Pakistani SARS-nCoV2 strains against USA and Chinese strains as reference, and hypothesized the putative role of observed variants in low severity of COVID-19 in Pakistan. Due to high variation rate in this virus, we further analysed the whole genome of Southern Pakistani SARS-nCoV2 MT500122 strain (Karachi-Pak) vs NC_045512 (Wuhan1-China) and observed 4 variants (3=SNPs,1=del). Three of variants at g.1604 (del ND447N), SNPs at g.1912 (p.=), g.10582 (p.=) and g.26022 (p.=) in ORF1ab and ORF3a genes respectively. ORF1ab encodes 16 non-structural polyproteins (nsps1-16) and plays role in viral replication. The codon change deletion in its sequence (as observed in MT500122) might have caused conformational alterations particularly in nsp2&amp;5 structures which may obstruct its effectiveness. ORF3a is unique to SARS-nCoV2 and located in-between envelope and spike genes, which assist viral entry into the host cell by interacting with S gene. Alteration in its sequence might have hampered the activation of S gene and affect its binding capacity to host cell ACE2 and NRP1 receptors, which may greatly weaken its pathogenicity in its different strains and hence may vary severity of COVID-19. Nevertheless, intensive data and conclusive wet lab experiments are needed for validating this postulated hypothesis. Moreover, these variants have modifier to silent impact on further 9 genes e.g. M, N, S, E, ORFs 6, 7a, 7b, 8 and 10 as well. Advancements in understanding the role of these Pakistani SARS-nCoV2 genomic variations will be helpful in developing indigenous vaccines, diagnostic kits and drug development.

scholarly journals Nucleotide sequence analyses of the MRP 1 gene in four populations suggest negative selection on its coding region

BMC Genomics ◽  
2006 ◽  
Vol 7 (1) ◽  
Author(s):  
Zihua Wang ◽  
Pui-Hoon Sew ◽  
Helen Ambrose ◽  
Stephen Ryan ◽  
Samuel S Chong ◽  
...  
Keyword(s):  
Nucleotide Sequence ◽  
Negative Selection ◽  
Coding Region ◽  
Sequence Analyses

scholarly journals Use of signals of positive and negative selection to distinguish cancer genes and passenger genes

2020 ◽  
Author(s):  
László Bányai ◽  
Mária Trexler ◽  
Krisztina Kerekes ◽  
Orsolya Csuka ◽  
László Patthy
Keyword(s):  
Negative Selection ◽  
Cancer Genomics ◽  
Tumor Evolution ◽  
Cancer Genes ◽  
Cancer Evolution ◽  
Human Genes ◽  
Strong Negative Selection ◽  
Selection For ◽  
Inactivating Mutations

AbstractA major goal of cancer genomics is to identify all genes that play critical roles in carcinogenesis. Most approaches focused on genes that are positively selected for mutations that drive carcinogenesis and neglected the role of negative selection. Some studies have actually concluded that negative selection has no role in cancer evolution. In the present work we have re-examined the role of negative selection in tumor evolution through the analysis of the patterns of somatic mutations affecting the coding sequences of human genes. Our analyses have confirmed that tumor suppressor genes are positively selected for inactivating mutations. Oncogenes, however, were found to display signals of both negative selection for inactivating mutations and positive selection for activating mutations. Significantly, we have identified numerous human genes that show signs of strong negative selection during tumor evolution, suggesting that their functional integrity is essential for the growth and survival of tumor cells.

scholarly journals Adaptive Approaches Towards Better GA Performance in Dynamic Fitness Landscapes

1994 ◽  
Vol 23 (487) ◽  
Author(s):  
Henrik Hautop Lund
Keyword(s):  
Fitness Landscape ◽  
Dynamic Environments ◽  
Mutation Rates ◽  
Landscape Changes ◽  
Correlation Measure ◽  
The Right ◽  
Changes Over Time ◽  
Adaptive Approaches ◽  
Over Time ◽  
Selection Of

We review different techniques for improving GA performance. By analysing the fitness landscape, a correlation measure between parents and offspring can be provided, and we can estimate effectively which genetic operator to use in the GA for a given fitness landscape. The response to selection equation further tells us how well the GA will do, and combining the two approaches gives us a powerful tool to automatically ensure the selection of the right parameter settings for a given problem. In dynamic environments the fitness landscape changes over time, and the evolved systems should be able to adapt to such changes. By introducing evolvable mutation rates and evolvable fitness formulae, we obtain such systems. The systems are shown to be able to adapt to both internal and external constraints and changes.

scholarly journals Identification of Genes under Purifying Selection in Human Cancers

2017 ◽  
Author(s):  
Robert A. Mathis ◽  
Ethan S. Sokol ◽  
Piyush B. Gupta
Keyword(s):  
Negative Selection ◽  
Somatic Mutations ◽  
Purifying Selection ◽  
Sequencing Data ◽  
Systematic Assessment ◽  
Coding Regions ◽  
Strong Negative Selection ◽  
Cancer Genomes ◽  
Lung Adenocarcinomas ◽  
Widespread Interest

AbstractThere is widespread interest in finding therapeutic vulnerabilities by analyzing the somatic mutations in cancers. Most analyses have focused on identifying driver oncogenes mutated in patient tumors, but this approach is incapable of discovering genes essential for tumor growth yet not activated through mutation. We show that such genes can be systematically discovered by mining cancer sequencing data for evidence of purifying selection. We show that purifying selection reduces substitution rates in coding regions of cancer genomes, depleting up to 90% of mutations for some genes. Moreover, mutations resulting in non-conservative amino acid substitutions are under strong negative selection in tumors, whereas conservative substitutions are more tolerated. Genes under purifying selection include members of the EGFR and FGFR pathways in lung adenocarcinomas, and DNA repair pathways in melanomas. A systematic assessment of purifying selection in tumors would identify hundreds of tumor-specific enablers and thus novel targets for therapy.

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