Variants in nucleocapsid protein and endoRNase are found to associate with severe COVID-19 in a case-control study in Washington State, USA

SARS-CoV-2 is spreading worldwide with continuously evolving variants, some of which occur in the Spike protein and appear to increase the viral transmissibility. However, variants that cause severe COVID-19 or lead to other breakthroughs have not been well characterized. To discover such viral variants, we assembled a cohort of 683 COVID-19 patients; 388 inpatients (“cases”) and 295 outpatients (“controls”) from April to August 2020 using electronically captured COVID test request forms and sequenced their viral genomes. To improve the analytic power, we accessed 7,137 viral sequences in Washington State to filter out viral single nucleotide variants (SNVs) that did not have significant expansions over the collection period. Applying this filter led to the identification of 53 SNVs that were statistically significant, of which 13 SNVs each had 3 or more variant copies in the discovery cohort. Correlating these selected SNVs with case/control status, eight SNVs were found to significantly associate with inpatient status (q-values<0.01). Using temporal synchrony, we identified a four SNV-haplotype (t19839-g28881-g28882-g28883) which was significantly associated with case/control status (Fisher’s exact p=2.84*10−11) that appeared in April 2020, peaked in June, and persisted into January 2021. This association was replicated (OR=5.46, p-value=4.71*10−12) in an independent cohort of 964 COVID-19 patients (June 1, 2020 to March 31, 2021). The haplotype included a synonymous change N73N in endoRNase, and three non-synonymous changes coding residues R203K, R203S and G204R in the nucleocapsid protein. This discovery points to the potential functional role of the nucleocapsid protein in triggering “cytokine storms” and severe COVID-19 that led to hospitalization. The study further emphasizes a need for tracking and analyzing viral sequences in correlations with clinical status.

Variants in nucleocapsid protein and endoRNase are found to associate with severe COVID-19 in a case-control study in Washington State, USA

SARS-CoV-2 is spreading worldwide with continuously evolving variants, some of which occur in the Spike protein and appear to increase the viral transmissibility. However, variants that cause severe COVID-19 or lead to other breakthroughs have not been well characterized. To discover such viral variants, we assembled a cohort of 683 COVID-19 patients; 388 inpatients (“cases”) and 295 outpatients (“controls”) from April to August 2020 using electronically captured COVID test request forms and sequenced their viral genomes. To improve the analytic power, we accessed 7,137 viral sequences in Washington State to filter out viral single nucleotide variants (SNVs) that did not have significant expansions over the collection period. Applying this filter led to the identification of 53 SNVs that were statistically significant, of which 13 SNVs each had 3 or more variant copies in the discovery cohort. Correlating these selected SNVs with case/control status, eight SNVs were found to significantly associate with inpatient status (q-values<0.01). Using temporal synchrony, we identified a four SNV-haplotype (t19839-g28881-g28882-g28883) which was significantly associated with case/control status (Fisher’s exact p=2.84*10-11) that appeared in April 2020, peaked in June, and persisted into January 2021. This association was replicated (OR=5.46, p-value=4.71*10-12) in an independent cohort of 964 COVID-19 patients (June 1, 2020 to March 31, 2021). The haplotype included a synonymous change N73N in endoRNase, and three non-synonymous changes coding residues R203K, R203S and G204R in the nucleocapsid protein. This discovery points to the potential functional role of the nucleocapsid protein in triggering “cytokine storms” and severe COVID-19 that led to hospitalization. The study further emphasizes a need for tracking and analyzing viral sequences in correlations with clinical status.

A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation

SummaryWhile SARS-CoV-2 likely has animal origins1, the viral genetic changes necessary to adapt this animal-derived ancestral virus to humans are largely unknown, mostly due to low levels of sequence polymorphism and the notorious difficulties in experimental manipulations of coronavirus genomes. We scanned more than 182,000 SARS-CoV-2 genomes for selective sweep signatures and found that a distinct footprint of positive selection is located around a non-synonymous change (A1114G; T372A) within the Receptor-Binding Domain of the Spike protein, which likely played a critical role in overcoming species barriers and accomplishing interspecies transmission from animals to humans. Structural analysis indicated that the substitution of threonine with an alanine in SARS-CoV-2 concomitantly removes a predicted glycosylation site at N370, resulting in more favorable binding predictions to human ACE2, the cellular receptor. Using a novel bacteria-free cloning system for manipulating RNA virus genomes, we experimentally validated that this SARS-CoV-2-unique substitution significantly increases replication in human cells relative to its putative ancestral variant. Notably, this mutation’s impact on virus replication in human cells was much greater than that of the Spike D614G mutant, which has been widely reported to have been selected for during human-to-human transmission2,3.

Genomic epidemiology and evolutionary dynamics of respiratory syncytial virus group B in Kilifi, Kenya, 2015-17

Respiratory syncytial virus (RSV) circulates worldwide and is a leading cause of acute respiratory illness in young children. There is paucity of genomic data from purposively sampled populations by which to investigate evolutionary dynamics and transmission patterns of RSV. Here we present an analysis of 295 RSV group B genomes from Kilifi, coastal Kenya, sampled from individuals seeking outpatient care in 9 health facilities across a defined geographical area (890 km2), over 2 RSV epidemics between 2015 and 2017. RSVB diversity was characterized by multiple viral introductions into the area and co-circulation of distinct genetic groups or clusters, which transmitted and diversified locally but with varying frequency. Bayesian analyses indicated a strong spatially and temporally structured viral population suggesting extensive within-epidemic virus transmission. Phylogeographic analysis provided a strong support for epidemiological linkage from one central health facility to other facilities. Increase in relative diversity paralleled increase in seasonal viral incidence. Importantly, we identified a cluster of viruses (n=91) that emerged in the 2016/17 epidemic, carrying distinct amino-acid signatures including a novel non-synonymous change (K68Q) in antigenic site Ø in the Fusion gene. A different non-synonymous change K68N was recently associated with escape from a potent neutralizing monoclonal antibody (MEDI8897). RSVB diversity was additionally marked by signature non-synonymous substitutions that were unique to particular genomic clusters, some of which were under diversifying selection. Our findings provide insights into recent evolutionary and epidemiologic behaviors of RSV group B, and highlight possible emergence of a novel antigenic variant, which has implications on current prophylactic development strategies.

Absence of pathogenic mutations in CD59 in chronic inflammatory demyelinating polyradiculoneuropathy

ABSTRACTObjectiveMutations in CD59 cause CIDP-like polyneuropathy in children with inherited chronic hemolysis. We hypothesized that mutations in CD59 might be found in a subset of sporadic CIDP patients.Methods5 patients from two centers, fulfilling the EFNS/PNS diagnostic criteria for CIDP were included. CD59 coding region was amplified by PCR and Sanger sequenced.ResultsOne rare variant was detected in a patient which resulted in a synonymous change and predicted to be neutral. Pathogenic variants were absent in our cohort.InterpretationOur pilot study suggests that mutations in CD59 are absent in adult-onset sporadic CIDP.

Language and cognitive impairment associated to a novel p.Cys63Arg change in the MED13L gene

ABSTRACTMutations of the MED13L gene, which encodes a subunit of a transcriptional regulatory complex, result in a complex phenotype entailing physical and cognitive anomalies. Deep language impairment has been reported, mostly in patients with CNV. Case presentation. We report on a child who presents with a non-synonymous change p.Cys63Arg in MED13L (Chr12:116675396A>G, GRCh37) and who exhibits profound language impairment in the expressive domain, cognitive delay, behavioral disturbances, and some autistic features. Conclusions. Because of the brain areas in which MED13L is expressed and because of the functional links between MED13L and the products of some candidate genes for language disorders, the proband’s linguistic phenotype may result from changes in a functional network important for language development.

Comprehensive family-based SNV association analysis shows new alleles associated to mealy traits in Prunus persica

Identification of DNA markers associated with mealiness trait is an important tool to agricultural industry. Many peach breeding initiatives have as aim to improve early selection of varieties with better postharvest performance. We present a family-based approach to identify and develop an association panel to evaluate potential varieties susceptible to mealiness induced by chilling. We used whole-genome sequencing and SNV genotyping of parents and ten contrasting siblings (Juicy and mealy) obtained from segregating population of self-cross ‘Venus’. Results show that there are differences regarding SNVs and structural variants (SVs) that could be associated with mealy to be contrasted with individuals without such damage phenotype. Preliminary results showed a total of 30.564 SNVs and 2.297 SVs having a non-synonymous change in genes. Comparison of SNVs between segregants and parental revealed 1.963 SNVs associated genes presents in juicy segregants and 6.162 SNVs associated genes in segregants mealiness. We found 230 and 244 SVs with functional impact in genomes mealy and juicy. As proof of concept, all SNVs obtained were correlated with the information published in peach related to chilling injury (QTL genomic region, dbSNP, SDR chillpeach, upeach and RNA-seq available). Guided by preliminary analysis, we selected pools of alleles that display a frequency difference between mealy and juicy fruit and a selective sweep is observed around those alleles. Some of the SNVs have been previously correlated with chilling injury through transcriptome analysis. Additionally, we identify new genome regions associated with mealy susceptibility. Most of these genes were related to negative regulation of programmed cell death, cell surface receptors signaling pathways and cell wall remodeling. On the other hand, the genes affected by SV in the juicy segregating are classified according to the biological process in metabolism of sugars and fatty acid biosynthetic process. These results provide insights into genetics determinants related with susceptibility to mealiness. Analysis of the sequences revealed the existence of a high polymorphism rate in nectarines, and statistical analysis showed that the segments could be used as genetic barcodes that should be informative enough to allow reliable identification of cultivars. This study proposes a predictive panel of biomarkers to identify varieties at susceptible for mealiness and identifies new candidates genes linked to mealiness in peach.

Comprehensive family-based SNV association analysis shows new alleles associated to mealy traits in Prunus persica

Identification of DNA markers associated with mealiness trait is an important tool to agricultural industry. Many peach breeding initiatives have as aim to improve early selection of varieties with better postharvest performance. We present a family-based approach to identify and develop an association panel to evaluate potential varieties susceptible to mealiness induced by chilling. We used whole-genome sequencing and SNV genotyping of parents and ten contrasting siblings (Juicy and mealy) obtained from segregating population of self-cross ‘Venus’. Results show that there are differences regarding SNVs and structural variants (SVs) that could be associated with mealy to be contrasted with individuals without such damage phenotype. Preliminary results showed a total of 30.564 SNVs and 2.297 SVs having a non-synonymous change in genes. Comparison of SNVs between segregants and parental revealed 1.963 SNVs associated genes presents in juicy segregants and 6.162 SNVs associated genes in segregants mealiness. We found 230 and 244 SVs with functional impact in genomes mealy and juicy. As proof of concept, all SNVs obtained were correlated with the information published in peach related to chilling injury (QTL genomic region, dbSNP, SDR chillpeach, upeach and RNA-seq available). Guided by preliminary analysis, we selected pools of alleles that display a frequency difference between mealy and juicy fruit and a selective sweep is observed around those alleles. Some of the SNVs have been previously correlated with chilling injury through transcriptome analysis. Additionally, we identify new genome regions associated with mealy susceptibility. Most of these genes were related to negative regulation of programmed cell death, cell surface receptors signaling pathways and cell wall remodeling. On the other hand, the genes affected by SV in the juicy segregating are classified according to the biological process in metabolism of sugars and fatty acid biosynthetic process. These results provide insights into genetics determinants related with susceptibility to mealiness. Analysis of the sequences revealed the existence of a high polymorphism rate in nectarines, and statistical analysis showed that the segments could be used as genetic barcodes that should be informative enough to allow reliable identification of cultivars. This study proposes a predictive panel of biomarkers to identify varieties at susceptible for mealiness and identifies new candidates genes linked to mealiness in peach.