The Isolated in Utero Environment Is Conducive to the Emergence of RNA and DNA Virus Variants

The host’s immune status may affect virus evolution. Little is known about how developing fetal and placental immune milieus affect virus heterogeneity. This knowledge will help us better understand intra-host virus evolution and how new virus variants emerge. The goal of our study was to find out whether the isolated in utero environment—an environment with specialized placental immunity and developing fetal immunity—supports the emergence of RNA and DNA virus variants. We used well-established porcine models for isolated Zika virus (RNA virus) and porcine circovirus 2 (DNA virus) fetal infections. We found that the isolated in utero environment was conducive to the emergence of RNA and DNA virus variants. Next-generation sequencing of nearly whole virus genomes and validated bioinformatics pipelines identified both unique and convergent single nucleotide variations in virus genomes isolated from different fetuses. Zika virus and PCV2 in utero evolution also resulted in single nucleotide variations previously reported in the human and porcine field samples. These findings should encourage further studies on virus evolution in placenta and fetuses, to better understand how virus variants emerge and how in utero viral evolution affects congenital virus transmission and pathogenicity.

Download Full-text

COVID-19 CG enables SARS-CoV-2 mutation and lineage tracking by locations and dates of interest

eLife ◽

10.7554/elife.63409 ◽

2021 ◽

Vol 10 ◽

Author(s):

Albert Tian Chen ◽

Kevin Altschuler ◽

Shing Hei Zhan ◽

Yujia Alina Chan ◽

Benjamin E Deverman

Keyword(s):

Public Health ◽

Health Interventions ◽

Receptor Binding Domain ◽

Public Health Interventions ◽

Single Nucleotide ◽

Geographical Regions ◽

Single Nucleotide Variations ◽

Lineage Tracking ◽

Virus Genomes ◽

Design And Testing

COVID-19 CG (covidcg.org) is an open resource for tracking SARS-CoV-2 single-nucleotide variations (SNVs), lineages, and clades using the virus genomes on the GISAID database while filtering by location, date, gene, and mutation of interest. COVID-19 CG provides significant time, labor, and cost-saving utility to projects on SARS-CoV-2 transmission, evolution, diagnostics, therapeutics, vaccines, and intervention tracking. Here, we describe case studies in which users can interrogate (1) SNVs in the SARS-CoV-2 spike receptor binding domain (RBD) across different geographical regions to inform the design and testing of therapeutics, (2) SNVs that may impact the sensitivity of commonly used diagnostic primers, and (3) the emergence of a dominant lineage harboring an S477N RBD mutation in Australia in 2020. To accelerate COVID-19 efforts, COVID-19 CG will be upgraded with new features for users to rapidly pinpoint mutations as the virus evolves throughout the pandemic and in response to therapeutic and public health interventions.

Download Full-text

In Utero Environment Linked to Infant Hypertension

Pediatric News ◽

10.1016/s0031-398x(10)70078-3 ◽

2010 ◽

Vol 44 (2) ◽

pp. 42

Author(s):

PATRICE WENDLING

Keyword(s):

In Utero ◽

In Utero Environment

Download Full-text

Genomic Analyses of Globodera pallida, A Quarantine Agricultural Pathogen in Idaho

Pathogens ◽

10.3390/pathogens10030363 ◽

2021 ◽

Vol 10 (3) ◽

pp. 363

Author(s):

Sulochana K. Wasala ◽

Dana K. Howe ◽

Louise-Marie Dandurand ◽

Inga A. Zasada ◽

Dee R. Denver

Keyword(s):

Genetic Variation ◽

Potato Production ◽

Globodera Pallida ◽

Fixation Index ◽

Parasitic Nematodes ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Genome Wide ◽

Field Samples ◽

Multiple Introduction

Globodera pallida is among the most significant plant-parasitic nematodes worldwide, causing major damage to potato production. Since it was discovered in Idaho in 2006, eradication efforts have aimed to contain and eradicate G. pallida through phytosanitary action and soil fumigation. In this study, we investigated genome-wide patterns of G. pallida genetic variation across Idaho fields to evaluate whether the infestation resulted from a single or multiple introduction(s) and to investigate potential evolutionary responses since the time of infestation. A total of 53 G. pallida samples (~1,042,000 individuals) were collected and analyzed, representing five different fields in Idaho, a greenhouse population, and a field in Scotland that was used for external comparison. According to genome-wide allele frequency and fixation index (Fst) analyses, most of the genetic variation was shared among the G. pallida populations in Idaho fields pre-fumigation, indicating that the infestation likely resulted from a single introduction. Temporal patterns of genome-wide polymorphisms involving (1) pre-fumigation field samples collected in 2007 and 2014 and (2) pre- and post-fumigation samples revealed nucleotide variants (SNPs, single-nucleotide polymorphisms) with significantly differentiated allele frequencies indicating genetic differentiation. This study provides insights into the genetic origins and adaptive potential of G. pallida invading new environments.

Download Full-text

Association between Genetic Variants in NOS2 and TNF Genes with Congenital Zika Syndrome and Severe Microcephaly

Viruses ◽

10.3390/v13020325 ◽

2021 ◽

Vol 13 (2) ◽

pp. 325

Author(s):

Julia A. Gomes ◽

Eduarda Sgarioni ◽

Juliano A. Boquett ◽

Ana Cláudia P. Terças-Trettel ◽

Juliana H. da Silva ◽

...

Keyword(s):

Risk Factors ◽

Zika Virus ◽

Genetic Variants ◽

Educational Level ◽

Congenital Anomalies ◽

Family Income ◽

First Trimester ◽

In Utero ◽

Zikv Infection ◽

Congenital Zika Syndrome

Zika virus (ZIKV) causes Congenital Zika Syndrome (CZS) in individuals exposed prenatally. Here, we investigated polymorphisms in VEGFA, PTGS2, NOS3, TNF, and NOS2 genes as risk factors to CZS. Forty children with CZS and forty-eight children who were in utero exposed to ZIKV infection, but born without congenital anomalies, were evaluated. Children with CZS were predominantly infected by ZIKV in the first trimester (p < 0.001) and had mothers with lower educational level (p < 0.001) and family income (p < 0.001). We found higher risk of CZS due the allele rs2297518[A] of NOS2 (OR = 2.28, CI 95% 1.17–4.50, p = 0.015). T allele and TT/CT genotypes of the TNF rs1799724 and haplotypes associated with higher expression of TNF were more prevalent in children with CZS and severe microcephaly (p = 0.029, p = 0.041 and p = 0.030, respectively). Our findings showed higher risk of CZS due ZIKV infection in the first trimester and suggested that polymorphisms in NOS2 and TNF genes affect the risk of CZS and severe microcephaly.

Download Full-text

Myocarditis and heart function impairment occur in neonatal mice following in utero exposure to the Zika virus

Journal of Cellular and Molecular Medicine ◽

10.1111/jcmm.16064 ◽

2021 ◽

Vol 25 (5) ◽

pp. 2730-2733

Author(s):

Chongzhi Bai ◽

Jianqing Hao ◽

Shihua Li ◽

George Fu Gao ◽

Yu Nie ◽

...

Keyword(s):

Zika Virus ◽

Heart Function ◽

In Utero ◽

In Utero Exposure ◽

Neonatal Mice ◽

Function Impairment

Download Full-text

Cytosine and adenine deaminase base-editors induce broad and nonspecific changes in gene expression and splicing

Communications Biology ◽

10.1038/s42003-021-02406-5 ◽

2021 ◽

Vol 4 (1) ◽

Author(s):

Jiao Fan ◽

Yige Ding ◽

Chao Ren ◽

Ziguo Song ◽

Jie Yuan ◽

...

Keyword(s):

Gene Expression ◽

Double Strand Breaks ◽

Great Promise ◽

Single Nucleotide ◽

Strand Breaks ◽

Dna Base ◽

Target Dna ◽

Single Nucleotide Variations ◽

Adenine Deaminase ◽

Target Rna

AbstractCytosine or adenine base editors (CBEs or ABEs) hold great promise in therapeutic applications because they enable the precise conversion of targeted base changes without generating of double-strand breaks. However, both CBEs and ABEs induce substantial off-target DNA editing, and extensive off-target RNA single nucleotide variations in transfected cells. Therefore, the potential effects of deaminases induced by DNA base editors are of great importance for their clinical applicability. Here, the transcriptome-wide deaminase effects on gene expression and splicing is examined. Differentially expressed genes (DEGs) and differential alternative splicing (DAS) events, induced by base editors, are identified. Both CBEs and ABEs generated thousands of DEGs and hundreds of DAS events. For engineered CBEs or ABEs, base editor-induced variants had little effect on the elimination of DEGs and DAS events. Interestingly, more DEGs and DAS events are observed as a result of over expressions of cytosine and adenine deaminases. This study reveals a previously overlooked aspect of deaminase effects in transcriptome-wide gene expression and splicing, and underscores the need to fully characterize such effects of deaminase enzymes in base editor platforms.

Download Full-text

In utero Zika virus exposure and schizophrenia

The World Journal of Biological Psychiatry ◽

10.1080/15622975.2018.1533995 ◽

2019 ◽

Vol 21 (1) ◽

pp. 12-12 ◽

Cited By ~ 1

Author(s):

Beuy Joob ◽

Viroj Wiwanitkit

Keyword(s):

Zika Virus ◽

In Utero ◽

Virus Exposure

Download Full-text

Proteome-Wide Analysis of Single-Nucleotide Variations in the N-Glycosylation Sequon of Human Genes

PLoS ONE ◽

10.1371/journal.pone.0036212 ◽

2012 ◽

Vol 7 (5) ◽

pp. e36212 ◽

Cited By ~ 26

Author(s):

Raja Mazumder ◽

Krishna Sudeep Morampudi ◽

Mona Motwani ◽

Sona Vasudevan ◽

Radoslav Goldman

Keyword(s):

Single Nucleotide ◽

Human Genes ◽

Single Nucleotide Variations

Download Full-text

Sequential Neuroimaging of the Fetus and Newborn With In Utero Zika Virus Exposure

JAMA Pediatrics ◽

10.1001/jamapediatrics.2018.4138 ◽

2019 ◽

Vol 173 (1) ◽

pp. 52 ◽

Cited By ~ 11

Author(s):

Sarah B. Mulkey ◽

Dorothy I. Bulas ◽

Gilbert Vezina ◽

Yamil Fourzali ◽

Armando Morales ◽

...

Keyword(s):

Zika Virus ◽

In Utero ◽

Virus Exposure

Download Full-text

Sequence variability ofChrysanthemum stunt viroidin different chrysanthemum cultivars

PeerJ ◽

10.7717/peerj.2933 ◽

2017 ◽

Vol 5 ◽

pp. e2933 ◽

Cited By ~ 4

Author(s):

Hoseong Choi ◽

Yeonhwa Jo ◽

Ju-Yeon Yoon ◽

Seung-Kook Choi ◽

Won Kyong Cho

Keyword(s):

Infectious Agents ◽

Sequence Variability ◽

Rt Pcr ◽

Genome Sequences ◽

Single Nucleotide ◽

Genomic Variations ◽

The Family ◽

Chrysanthemum Plant ◽

Single Nucleotide Variations ◽

Polymerase Chain

Viroids are the smallest infectious agents, and their genomes consist of a short single strand of RNA that does not encode any protein.Chrysanthemum stunt viroid(CSVd), a member of the familyPospiviroidae, causes chrysanthemum stunt disease. Here, we report the genomic variations of CSVd to understand the sequence variability of CSVd in different chrysanthemum cultivars. We randomly sampled 36 different chrysanthemum cultivars and examined the infection of CSVd in each cultivar by reverse transcription polymerase chain reaction (RT-PCR). Eleven cultivars were infected by CSVd. Cloning followed by Sanger sequencing successfully identified a total of 271 CSVd genomes derived from 12 plants from 11 cultivars. They were further classified into 105 CSVd variants. Each single chrysanthemum plant had a different set of CSVd variants. Moreover, different single plants from the same cultivar had different sets of CSVd variants but identical consensus genome sequences. A phylogenetic tree using 12 consensus genome sequences revealed three groups of CSVd genomes, while six different groups were defined by the phylogenetic analysis using 105 variants. Based on the consensus CSVd genome, by combining all variant sequences, we identified 99 single-nucleotide variations (SNVs) as well as three nucleotide positions showing high mutation rates. Although 99 SNVs were identified, most CSVd genomes in this study were derived from variant 1, which is identical to known CSVd SK1 showing pathogenicity.

Download Full-text