A team of researchers from various institutions in the USA used RNA-sequencing data and other methods to profile unique genes and other characteristics associated with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in New York City (NYC).
Their findings could help with keeping a record of genomic data that could aid in the management of future pandemics. The researchers also find a benefit of using ACE inhibitors or angiotensin receptor blockers to prevent severe infection.
The study was recently published in the journal Nature Communications.
Methods
The team designed a 30-minute colorimetric assay to evaluate the viral load of nasal swabs. They validated the assay using two synthetic RNAs with matched sequences to ones found from COVID-19 patients in Wuhan, China, and Melbourne, Australia.
The assay was used on 201 samples from NYC patients suspected of COVID-19 infection in early March. There was a total of 69 positive nasopharyngeal swab samples and 132 samples that tested negative. Results showed an increased overall sensitivity of 95.6% and specificity of 99.2%. There was also higher LAMP sensitivity at higher viral loads.
The researchers also developed a large-scale shotgun metatranscriptomics platform using total RNA sequencing to evaluate the various RNA profiles associated with COVID-19 samples. They sequenced 857 RNA-sequencing libraries from 723 nasal swab samples from 669 patients who presented to the hospital with flu-like symptoms.
Nasal samples positive for SARS-CoV-2 showed massive amounts of bacterial and SARS-CoV-2 RNA but minor quantities of fungi, archaea, or other viral RNAs. Positive samples had an abundance of SARS-CoV-2 genome alignments compared to samples that tested negative.
The system also had a low rate of false negatives, with only 7 or 1.3% of negative samples having 0.01% of reads corresponding to SARS-CoV-2 RNA.
Findings showed sample differences for non-SARS-CoV-2 viruses and bacteria
The researchers found more non-SARS-CoV-2 respiratory viruses in the negative samples versus the positive samples. Patients with SARS-CoV-2 showed lower amounts of bacterial species, including A. xylosoxidans, E. faecalis, and L. bacterium.
Approximately 23% of viral cases in both positive and negative samples were from Influenza A. Others included the rhinovirus A at 16% and the human metapneumovirus at 12%.
The researchers were also able to analyze the rate of co-infection among patients with COVID-19. They found that about 3.2% of patients had sequences that belonged to other respiratory viruses such as human coronaviruses 229E, NL63 and HKU1, influenza A, and human mastadenovirus metapneumovirus — suggesting a low incidence of coinfection.
Further testing found the NYC samples were enriched with a clade 20C clade. “Investigating the geographical and temporal distribution of non-NYC samples in 20C, we found a global distribution with a likely origin in Western Europe,” wrote the researchers.
They note the first few COVID-19 cases with clade 20c were found in France, but over 70% of current clade20 SARS-CoV-2 cases from March to May 2020 were in NYC.
Changes in gene expression caused by SARS-CoV-2
Shotgun metatranscriptomics also helped uncover a small selection of genomic information that supports the creation of heterogenous variants.
Genomic information from the host transcriptome showed that SARS-CoV-2 had about 757 significant differentially expressed genes related to infection. Of these, 350 genes were upregulated, and 407 genes were downregulated. A total of 8,851 genes were considered unique. The greatest amounts of differentially expressed genes in the SARS-CoV-2 host transcriptome were associated with having a higher viral titer.
Among the genes were some that promoted antiviral activity and increases in ACE2 expression. Decreases in gene expression were observed for the TMPRSS-11B that modulates lung cell growth and olfactory receptor pathway genes, potentially explaining the loss of smell associated with COVID-19 infection.
Medication use in response to increased ACE2 expression
The researchers evaluated 50,821 medical records of patients suspected of COVID-19 and their outcomes after being given an ACE inhibitor or angiotensin receptor blocker. The team proposes these types of medications could help with the increased ACE2 gene expression caused by the virus. They found patients given either inhibitor decreased the risk of intubation and death.
Spatial transcriptomic data from four autopsies of people who died from COVID-19 showed the distribution of genes across tissues. They found unique ACE2 expression loci, the presence of SARS-CoV-2, and high macrophage and neutrophil levels in the lungs.
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