scholarly journals Intra-host evolution provides for continuous emergence of SARS-CoV-2 variants

2021 ◽  
Author(s):  
Justin Landis ◽  
Razia Moorad ◽  
Linda J. Pluta ◽  
Carolina Caro-Vegas ◽  
Ryan P. McNamara ◽  
...  
Keyword(s):  
Public Health ◽  
Sequence Evolution ◽  
Clinical Progression ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Viral Genomes ◽  
Synonymous Mutations ◽  
Health Measures ◽  
Broad Public Health ◽  
Host Evolution

Variants of concern (VOC) in SARS-CoV-2 refer to viral genomes that differ significantly from the ancestor virus and that show the potential for higher transmissibility and/or worse clinical progression. VOC have the potential to disrupt ongoing public health measures and vaccine efforts. Yet, little is known regarding how frequently different viral variants emerge and under what circumstances. We report a longitudinal study to determine the degree of SARS-CoV-2 sequence evolution in 94 COVID-19 cases and to estimate the frequency at which highly diverse variants emerge. 2 cases accumulated 9 single-nucleotide variants (SNVs) over a two-week period and 1 case accumulated 23 SNVs over a three-week period, including three non-synonymous mutations in the Spike protein (D138H, E554D, D614G). We estimate that in 2% of COVID cases, viral variants with multiple mutations, including in the Spike glycoprotein, can become the dominant strains in as little as one month of persistent in patient virus replication. This suggests the continued local emergence of VOC independent of travel patterns. Surveillance by sequencing for (i) viremic COVID-19 patients, (ii) patients suspected of re-infection, and (iii) patients with diminished immune function may offer broad public health benefits.

scholarly journals Variants in SARS-CoV-2 Associated with Mild or Severe Outcome

2020 ◽  
Author(s):  
Jameson D. Voss ◽  
Martin Skarzynski ◽  
Erin M. McAuley ◽  
Ezekiel J. Maier ◽  
Thomas Gibbons ◽  
...  
Keyword(s):  
Public Health ◽  
Regression Models ◽  
Molecular Characteristics ◽  
Median Frequency ◽  
Global Public Health ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Logistic Regression Models ◽  
Health Measures ◽  
And Gender

AbstractIntroductionThe coronavirus disease 2019 (COVID-19) pandemic is a global public health emergency causing a disparate burden of death and disability around the world. The molecular characteristics of the virus that predict better or worse outcome are largely still being discovered.MethodsWe downloaded 155,958 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes from GISAID and evaluated whether variants improved prediction of reported severity beyond age and region. We also evaluated specific variants to determine the magnitude of association with severity and the frequency of these variants among the genomes.ResultsLogistic regression models that included viral genomic variants outperformed other models (AUC=0.91 as compared with 0.68 for age and gender alone; p<0.001). Among individual variants, we found 17 single nucleotide variants in SARS-CoV-2 have more than two-fold greater odds of being associated with higher severity and 67 variants associated with ≤ 0.5 times the odds of severity. The median frequency of associated variants was 0.15% (interquartile range 0.09%-0.45%). Altogether 85% of genomes had at least one variant associated with patient outcome.ConclusionNumerous SARS-CoV-2 variants have two-fold or greater association with odds of mild or severe outcome and collectively, these variants are common. In addition to comprehensive mitigation efforts, public health measures should be prioritized to control the more severe manifestations of COVID-19 and the transmission chains linked to these severe cases.

scholarly journals Genomic Epidemiology of the Los Angeles COVID-19 Outbreak

2021 ◽  
Author(s):  
Longhua Guo​ ◽  
James Boocock​ ◽  
Evann E. Hilt​ ◽  
Sukantha Chandrasekaran​ ◽  
Yi Zhang​ ◽  
...  
Keyword(s):  
Public Health ◽  
Los Angeles ◽  
Severe Acute Respiratory Syndrome ◽  
Genome Sequencing ◽  
Transmission Rate ◽  
Washington State ◽  
Public Health Response ◽  
Viral Genomes ◽  
The Public ◽  
Health Measures

Abstract Background The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global disruption to human health and activity. Being able to trace the early outbreak of SARS-CoV-2 within a locality will inform public health measures and provide insights to contain or prevent the viral transmission to save lives. Investigation of the transmission history requires efficient sequencing methods and analytic strategy, which can be generally useful in the study of viral outbreaks. Methods Los Angeles (LA) County has sustained a large outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To learn about the transmission history, we carried out surveillance viral genome sequencing to determine 142 viral genomes from unique patients seeking care at UCLA Health System. 86 of these genomes are from samples collected before April 19, 2020. Results We found that the early outbreak in LA, as in other international air travel hubs, was seeded by multiple introductions of strains from Asia and Europe. We identified a US-specific strain, B.1.43, which has been found predominantly in California and Washington State. While samples from LA County carry the ancestral B.1.43 genome, viral genomes from neighboring counties in California and from counties in Washington State carry additional mutations, suggesting a potential origin of B.1.43 in Southern California. We quantified the transmission rate of SARS-CoV-2 over time, and found evidence that the public health measures put in place in LA County to control the virus were effective at preventing transmission, but may have been undermined by the many introductions of SARS-CoV-2 into the region. Conclusion Our work demonstrates that genome sequencing can be a powerful tool for investigating outbreaks and informing the public health response. Our results reinforce the critical need for the U.S. to have coordinated inter-state responses to the pandemic.

scholarly journals A short plus long-amplicon based sequencing approach improves genomic coverage and variant detection in the SARS-CoV-2 genome

PLoS ONE ◽  
2022 ◽  
Vol 17 (1) ◽  
pp. e0261014
Author(s):  
Carlos Arana ◽  
Chaoying Liang ◽  
Matthew Brock ◽  
Bo Zhang ◽  
Jinchun Zhou ◽  
...  
Keyword(s):  
Virus Genome ◽  
Positive Control ◽  
Nasopharyngeal Swab ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Spike Gene ◽  
Synonymous Mutations ◽  
Variant Detection ◽  
Variant Analysis ◽  
New Mutations

High viral transmission in the COVID-19 pandemic has enabled SARS‐CoV‐2 to acquire new mutations that may impact genome sequencing methods. The ARTIC.v3 primer pool that amplifies short amplicons in a multiplex-PCR reaction is one of the most widely used methods for sequencing the SARS-CoV-2 genome. We observed that some genomic intervals are poorly captured with ARTIC primers. To improve the genomic coverage and variant detection across these intervals, we designed long amplicon primers and evaluated the performance of a short (ARTIC) plus long amplicon (MRL) sequencing approach. Sequencing assays were optimized on VR-1986D-ATCC RNA followed by sequencing of nasopharyngeal swab specimens from fifteen COVID-19 positive patients. ARTIC data covered 94.47% of the virus genome fraction in the positive control and patient samples. Variant analysis in the ARTIC data detected 217 mutations, including 209 single nucleotide variants (SNVs) and eight insertions & deletions. On the other hand, long-amplicon data detected 156 mutations, of which 80% were concordant with ARTIC data. Combined analysis of ARTIC + MRL data improved the genomic coverage to 97.03% and identified 214 high confidence mutations. The combined final set of 214 mutations included 203 SNVs, 8 deletions and 3 insertions. Analysis showed 26 SARS-CoV-2 lineage defining mutations including 4 known variants of concern K417N, E484K, N501Y, P618H in spike gene. Hybrid analysis identified 7 nonsynonymous and 5 synonymous mutations across the genome that were either ambiguous or not called in ARTIC data. For example, G172V mutation in the ORF3a protein and A2A mutation in Membrane protein were missed by the ARTIC assay. Thus, we show that while the short amplicon (ARTIC) assay provides good genomic coverage with high throughput, complementation of poorly captured intervals with long amplicon data can significantly improve SARS-CoV-2 genomic coverage and variant detection.

scholarly journals Updated SARS-CoV-2 Single Nucleotide Variants and Mortality Association

2021 ◽  
Author(s):  
Shuyi Fang ◽  
Sheng Liu ◽  
Jikui Shen ◽  
Alex Z Lu ◽  
Yucheng Zhang ◽  
...  
Keyword(s):  
Protein Structure ◽  
Critical Role ◽  
Single Nucleotide Variants ◽  
Protein Structure Analysis ◽  
Single Nucleotide ◽  
Synonymous Mutations ◽  
Conformation Changes ◽  
The Difference ◽  
Distinct Distribution

AbstractSince its outbreak in December 2019, COVID-19 has caused 100,5844,555 cases and 2,167,313 deaths as of Jan 27, 2021. Comparing our previous study of SARS-CoV-2 single nucleotide variants (SNVs) before June 2020, we found out that the SNV clustering had changed considerably since June 2020. Apart from that the group SNVs represented by two non-synonymous mutations A23403G (S: D614G) and C14408T (ORF1ab: P4715L) became dominant and carried by over 95% genomes, a few emerging groups of SNVs were recognized with sharply increased monthly occurrence ratios up to 70% in November 2020. Further investigation revealed that several SNVs were strongly associated with the mortality, but they presented distinct distribution in specific countries, e.g., Brazil, USA, Saudi Arabia, India, and Italy. SNVs including G25088T, T25A, G29861T and G29864A were adopted in a regularized logistic regression model to predict the mortality status in Brazil with the AUC of 0.84. Protein structure analysis showed that the emerging subgroups of non-synonymous SNVs and those mortality-related ones in Brazil were located on protein surface area. The clashes in protein structure introduced by these mutations might in turn affect virus pathogenesis through conformation changes, leading to the difference in transmission and virulence. Particularly, we found that SNVs tended to occur in intrinsic disordered regions (IDRs) of Spike (S) and ORF1ab, suggesting a critical role of SNVs in protein IDRs to determine protein folding and immune evasion.

scholarly journals Genomic characterization of a novel SARS-CoV-2 lineage from Rio de Janeiro, Brazil

2020 ◽  
Author(s):  
Carolina M Voloch ◽  
Ronaldo da Silva F ◽  
Luiz G P de Almeida ◽  
Cynthia C Cardoso ◽  
Otavio J. Brustolini ◽  
...  
Keyword(s):  
Rio De Janeiro ◽  
Neutralizing Antibodies ◽  
Health Management ◽  
The State ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Viral Genomes ◽  
Genomic Characterization ◽  
Second Wave

AbstractIn this study, we report the sequencing of 180 new viral genomes obtained from different municipalities of the state of Rio de Janeiro from April to December 2020. We identified a novel lineage of SARS-CoV-2, originated from B.1.1.28, distinguished by five single-nucleotide variants (SNVs): C100U, C28253U, G28628U, G28975U, and C29754U. The SNV G23012A (E484K), in the receptor-binding domain of Spike protein, was widely spread across the samples. This mutation was previously associated with escape from neutralizing antibodies against SARS-CoV-2. This novel lineage emerged in late July being first detected by us in late October and still mainly restricted to the capital of the state. However, as observed for other strains it can be rapidly spread in the state. The significant increase in the frequency of this lineage raises concerns about public health management and continuous need for genomic surveillance during the second wave of infections.Article Summary LineWe identified a novel circulating lineage of SARS-CoV-2 in the state of Rio de Janeiro Brazil originated from B.1.1.28 lineage.

scholarly journals RNA viromics of Southern California wastewater and detection of SARS-CoV-2 single nucleotide variants.

2021 ◽  
Author(s):  
Jason A Rothman ◽  
Theresa B Loveless ◽  
Joseph Kapcia ◽  
Eric D Adams ◽  
Joshua A Steele ◽  
...  
Keyword(s):  
Public Health ◽  
Los Angeles ◽  
Southern California ◽  
Municipal Wastewater ◽  
Rna Viruses ◽  
Disease Outbreaks ◽  
Clinical Samples ◽  
Human Populations ◽  
Single Nucleotide Variants ◽  
Single Nucleotide

Abstract: Municipal wastewater provides an integrated sample of a diversity of human-associated microbes across a sewershed, including viruses. Wastewater-based epidemiology (WBE) is a promising strategy to detect pathogens and may serve as an early-warning system for disease outbreaks. Notably, WBE has garnered substantial interest during the COVID-19 pandemic to track disease burden through analyses of SARS-CoV-2 RNA. Throughout the COVID-19 outbreak, tracking SARS-CoV-2 in wastewater has been an important tool for understanding the spread of the virus. Unlike traditional sequencing of SARS-CoV-2 isolated from clinical samples, which adds testing burden to the healthcare system, in this study, metatranscriptomics was used to sequence virus directly from wastewater. Here, we present a study in which we explored RNA viral diversity through sequencing 94 wastewater influent samples across seven treatment plants (WTPs), collected August 2020 - January 2021, representing approximately 16 million people in Southern California. Enriched viral libraries identified a wide diversity of RNA viruses that differed between WTPs and over time, with detected viruses including coronaviruses, influenza A, and noroviruses. Furthermore, single nucleotide variants (SNVs) of SARS-CoV-2 were identified in wastewater and we measured proportions of overall virus and SNVs across several months. We detected several SNVs that are markers for clinically-important SARS-CoV-2 variants, along with SNVs of unknown function, prevalence, or epidemiological consequence. Our study shows the potential of WBE to detect viruses in wastewater and to track the diversity and spread of viral variants in urban and suburban locations, which may aid public health efforts to monitor disease outbreaks. Importance: Wastewater based epidemiology (WBE) can detect pathogens across sewersheds, which represents the collective waste of human populations. As there is a wide diversity of RNA viruses in wastewater, monitoring the presence of these viruses is useful for public health, industry, and ecological studies. Specific to public health, WBE has proven valuable during the COVID-19 pandemic to track the spread of SARS-CoV-2 without adding burden to healthcare systems. In this study, we used metatranscriptomics and RT-ddPCR to assay RNA viruses across Southern California wastewater from August 2020 - January 2021, representing approximately 16 million people from Los Angeles, Orange, and San Diego counties. We found that SARS-CoV-2 quantification in wastewater correlates well with county-wide COVID-19 case data, and that we can detect SARS-CoV-2 single nucleotide variants through sequencing. Likewise, WTPs harbored different viromes, and we detected other human pathogens such as noroviruses and adenoviruses, furthering our understanding of wastewater viral ecology.

scholarly journals RNA viromics of Southern California wastewater and detection of SARS-CoV-2 single nucleotide variants.

2021 ◽  
Author(s):  
Jason A. Rothman ◽  
Theresa B. Loveless ◽  
Joseph Kapcia ◽  
Eric D. Adams ◽  
Joshua A. Steele ◽  
...  
Keyword(s):  
Public Health ◽  
Los Angeles ◽  
Southern California ◽  
Municipal Wastewater ◽  
Rna Viruses ◽  
Disease Outbreaks ◽  
Clinical Samples ◽  
Human Populations ◽  
Single Nucleotide Variants ◽  
Single Nucleotide

Municipal wastewater provides an integrated sample of a diversity of human-associated microbes across a sewershed, including viruses. Wastewater-based epidemiology (WBE) is a promising strategy to detect pathogens and may serve as an early-warning system for disease outbreaks. Notably, WBE has garnered substantial interest during the COVID-19 pandemic to track disease burden through analyses of SARS-CoV-2 RNA. Throughout the COVID-19 outbreak, tracking SARS-CoV-2 in wastewater has been an important tool for understanding the spread of the virus. Unlike traditional sequencing of SARS-CoV-2 isolated from clinical samples, which adds testing burden to the healthcare system, in this study, metatranscriptomics was used to sequence virus directly from wastewater. Here, we present a study in which we explored RNA viral diversity through sequencing 94 wastewater influent samples across seven treatment plants (WTPs), collected August 2020 – January 2021, representing approximately 16 million people in Southern California. Enriched viral libraries identified a wide diversity of RNA viruses that differed between WTPs and over time, with detected viruses including coronaviruses, influenza A, and noroviruses. Furthermore, single nucleotide variants (SNVs) of SARS-CoV-2 were identified in wastewater and we measured proportions of overall virus and SNVs across several months. We detected several SNVs that are markers for clinically-important SARS-CoV-2 variants, along with SNVs of unknown function, prevalence, or epidemiological consequence. Our study shows the potential of WBE to detect viruses in wastewater and to track the diversity and spread of viral variants in urban and suburban locations, which may aid public health efforts to monitor disease outbreaks. Importance: Wastewater based epidemiology (WBE) can detect pathogens across sewersheds, which represents the collective waste of human populations. As there is a wide diversity of RNA viruses in wastewater, monitoring the presence of these viruses is useful for public health, industry, and ecological studies. Specific to public health, WBE has proven valuable during the COVID-19 pandemic to track the spread of SARS-CoV-2 without adding burden to healthcare systems. In this study, we used metatranscriptomics and RT-ddPCR to assay RNA viruses across Southern California wastewater from August 2020 – January 2021, representing approximately 16 million people from Los Angeles, Orange, and San Diego counties. We found that SARS-CoV-2 quantification in wastewater correlates well with county-wide COVID-19 case data, and that we can detect SARS-CoV-2 single nucleotide variants through sequencing. Likewise, WTPs harbored different viromes, and we detected other human pathogens such as noroviruses and adenoviruses, furthering our understanding of wastewater viral ecology.

scholarly journals Vibrio choleraegenomic diversity within and between patients

2017 ◽  
Author(s):  
Inès Levade ◽  
Yves Terrat ◽  
Jean-Baptiste Leducq ◽  
Ana A. Weil ◽  
Leslie M. Mayo-Smith ◽  
...  
Keyword(s):  
Biofilm Formation ◽  
Diarrheal Disease ◽  
Point Mutations ◽  
Gene Gain ◽  
Chronic Infections ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Content Variation ◽  
Gain Loss ◽  
Host Evolution

AbstractCholera is a severe, waterborne diarrheal disease caused by toxin-producing strains of the bacteriumVibrio cholerae. Comparative genomics has revealed “waves” of cholera transmission and evolution, in which clones are successively replaced over decades and centuries. However, the extent ofV. choleraegenetic diversity within an epidemic or even within an individual patient is poorly understood. Here, we characterizedV. choleraegenomic diversity at a micro-epidemiological level within and between individual patients from Bangladesh and Haiti. To capture within-patient diversity, we isolated multiple (8 to 20)V. choleraecolonies from each of eight patients, sequenced their genomes and identified point mutations and gene gain/loss events. We found limited but detectable diversity at the level of point mutations within hosts (zero to three single nucleotide variants within each patient), and comparatively higher gene content variation within hosts (at least one gain/loss event per patient, and up to 103 events in one patient). Much of the gene content variation appeared to be due to gain and loss of phage and plasmids within theV. choleraepopulation, with occasional exchanges betweenV. choleraeand other members of the gut microbiota. We also show that certain intra-host variants have phenotypic consequences. For example, the acquisition of aBacteroidesplasmid and nonsynonymous mutations in a sensor histidine kinase gene both reduced biofilm formation, an important trait for environmental survival. Together, our results show thatV. choleraeis measurably evolving within patients, with possible implications for disease outcomes and transmission dynamics.Author SummaryVibrio choleraeis the etiological agent of cholera, a severe diarrheal disease endemic to Bangladesh and responsible for global outbreaks, including one ongoing in Haiti. Certain bacterial pathogens can evolve and diversify within the human host, often altering virulence and antibiotic resistance. However, most examples of within-host evolution have come from chronic infections, in which the pathogen has sufficient time to mutate and diversify, and little attention has been paid to more acute infections such as the one caused byV. cholerae. The goal of this study was to measure the extent of within-host evolution ofV. choleraewithin individual infected patients. By sequencing multiple bacterial isolates_from each of eight patients from Bangladesh and Haiti, we found that cholera patients can harbor a diverse population ofV. cholerae. As expected for an acute infection, this diversity is limited, ranging from zero to three point mutations (single nucleotide variants) per patient. However, gene gain/loss events are more prevalent than point mutations, occurring in every single patient, and sometimes involving the transfer of dozens of genes on plasmids. Even if rare, point mutations and gene gain/loss events may be maintained by natural selection, and can alter clinically-and environmentally-relevant phenotypes such as biofilm formation. Therefore, within-patient evolution has the potential to impact clinical and epidemiological outcomes. Together, our results demonstrate that within-patient evolution may be a general feature of both acute and chronic infections, and that gene gain/loss may be an important but under-appreciated feature of within-host evolution.

scholarly journals Impact of Pregnancy on Intra-Host Genetic Diversity of Influenza A Viruses in Hospitalised Women: A Retrospective Cohort Study

2019 ◽  
Vol 8 (11) ◽  
pp. 1974 ◽  
Author(s):  
Gregory Destras ◽  
Maxime Pichon ◽  
Bruno Simon ◽  
Martine Valette ◽  
Vanessa Escuret ◽  
...  
Keyword(s):  
Influenza A ◽  
Immune Modulation ◽  
Pregnant Mouse ◽  
Influenza A Viruses ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Host Diversity ◽  
Significant Difference ◽  
Host Genetic ◽  
Host Evolution

Characterising dynamics of Influenza A Viruses (IAV) within-host evolution is an active field of research which may lead to a better understanding of viral pathogenesis. Using a pregnant mouse model, a study has recently suggested that immune modulation during pregnancy could promote the emergence of IAV quasispecies with increased virulence. Herein, we assess the clinical relevance of these findings in humans. We studied IAV intra-host diversity (ihD) in pregnant (n = 36) and non-pregnant (n = 23) women hospitalized in Lyon for IAV infection (01/2015–05/2018). Whole IAV genomes present in nasopharyngeal samples were sequenced in duplicate to analyze reproducible intra-host single nucleotide variants (ihSNV). Counts, relative frequencies and locations of ihSNV were used as indicators of ihD. The median ihSNV/kb counts per segment were between 0 and 1.3. There was >81% ihSNV at relative frequencies between 1–5% for H1N1 and >51% for H3N2 IAV. No significant difference was noted between pregnant and non-pregnant women when considering all or only non-synonymous ihSNV. Seven convergent non-synonymous ihSNV were found; none were significantly associated with pregnancy. These results suggest that modulation of the immune system during pregnancy in humans does not impact IAV ihD, in contrast to mice.

scholarly journals Rapid and ongoing evolution of repetitive sequence structures in human centromeres

2020 ◽  
Vol 6 (50) ◽  
pp. eabd9230
Author(s):  
Yuta Suzuki ◽  
Eugene W. Myers ◽  
Shinichi Morishita
Keyword(s):  
Sequence Variation ◽  
Structural Diversity ◽  
Higher Order ◽  
Human Populations ◽  
Sequence Evolution ◽  
Diverse Populations ◽  
Sequencing Data ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Long Read

Our understanding of centromere sequence variation across human populations is limited by its extremely long nested repeat structures called higher-order repeats that are challenging to sequence. Here, we analyzed chromosomes 11, 17, and X using long-read sequencing data for 36 individuals from diverse populations including a Han Chinese trio and 21 Japanese. We revealed substantial structural diversity with many previously unidentified variant higher-order repeats specific to individuals characterizing rapid, haplotype-specific evolution of human centromeric arrays, while frequent single-nucleotide variants are largely conserved. We found a characteristic pattern shared among prevalent variants in human and chimpanzee. Our findings pave the way for studying sequence evolution in human and primate centromeres.

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