Tag Archives: Coronavirus

Microbiology

Candida auris infection without epidemiologic links to a prior outbreak

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Dr. Priyom Bose, Ph.D.By Dr. Priyom Bose, Ph.D.Mar 23 2023Reviewed by Danielle Ellis, B.Sc.

The Centers for Disease Control and Prevention (CDC) has classified Candida auris (C. auris) as an urgent public threat due to its role in elevating mortality, its ability to persist in hospital environments, and the high possibility of developing pan-drug resistance.

Notably, a recent study published in the journal Open Forum Infectious Diseases has pointed out that surfaces near patients with C. auris quickly become re-contaminated after cleaning.

Existing research has not adequately elucidated the environmental reservoirs of C. auris. Further, few studies have reported epidemiologic links associated with C. auris infection. 

Study: The Emergence and Persistence of Candida auris in Western New York with no Epidemiologic Links: A Failure of Stewardship?. Image Credit: Kateryna Kon / ShutterstockStudy: The Emergence and Persistence of Candida auris in Western New York with no Epidemiologic Links: A Failure of Stewardship? Image Credit: Kateryna Kon / Shutterstock

Background

C. auris is a species of fungus that grows as yeast. It is one of the few species of the genus Candida which cause candidiasis in humans. In the past, C. auris infection was primarily found in cancer patients or those subjected to feeding tubes.

In the United States (US), the emergence of C. auris was traced to New York, and surveillance for this fungal infection was focused mainly on New York City to detect outbreaks. Recently, scientists investigated the association between genomic epidemiology and C. auris infection in Western New York.

A Case Study

The study describes the emergence of C. auris in a patient hospitalized at a small community hospital in Genesee County, New York (NY). In January 2022, C. auris was isolated from the urine culture of a 68-year-old male on the 51st day of hospitalization.

This patient had no known epidemiological connections outside his immediate community. Before his hospitalization, he was not exposed to other patients or family members associated with C. auris infection.

This patient had no history of organ transplantation, decubitus ulcers, hemodialysis, feeding tubes, or nursing home stays. He had an active lifestyle with a history of mild vascular dementia. He was hospitalized due to pneumonia and was prescribed azithromycin treatment.

Post hospitalization, he tested positive for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and was treated with dexamethasone (6 mg) daily for 10 days and remdesivir (200 mg) once, followed by 100 mg daily for five days.

Since the patient’s chest radiograph showed left lobar consolidation, he was further treated with empiric ceftriaxone and azithromycin. As the respiratory symptoms deteriorated, he received non-invasive positive pressure ventilation, with subsequent endotracheal intubation for eight days. He was successfully extubated. He developed a fever and received antimicrobial therapy for 73 days. The patient had a urinary catheter and a peripherally inserted central line in his arm for 35 days. 

Microbiology culture test and serum procalcitonin levels remained negative and within normal levels. On the 22nd day of hospitalization, Candida albicans were isolated from respiratory samples. On the 51st day, the urine culture revealed the presence of azole-resistant C. auris.

The isolated C. auris (MRSN101498) was forwarded to the Multidrug-resistant organism Repository and Surveillance Network (MRSN), where genomic sequencing was performed. After the patient was discharged, the hospital room was cleaned using hydrogen peroxide and peracetic acid, followed by ultraviolet-C light. Other patients who shared rooms with the patient with C. auris were tested for infection.

Study Outcomes

C. auris was not detected in the Western NY community hospital in the past year. Physicians stated that the patient received excessive antibiotic treatment for a prolonged period. Genomic studies revealed that the MRSN101498 genome sequence was closely related to the 2013 Indian strain with minor genomic differences. Interestingly, the K143R mutation in ERG11 was found in MRSN101498, which is associated with triazole resistance in Candida albicans.

Whole genome single nucleotide polymorphism (SNP) analysis also highlighted that MRSN101498 was strongly genetically related to four other isolates, with marginal differences.

These isolates were linked to an outbreak in March 2017 in a hospital 47 miles northeast of Rochester, NY. Based on the current findings, it is highly likely that isolates from Western NY share a recent common ancestor.

Study Importance

This case study is important for several reasons, including the absence of epidemiologic links to C.auris infection. Since reports from rural sectors are rare, this study addresses a vital surveillance ‘blind spot.’ 

However, the current study failed to identify the potential reservoirs of MRSN101498 in Western NY. Sporicidal disinfectants were inefficient for both Clostridioides difficile and C. auris. However, terminal cleaning protocols that included UV irradiation and sporicidal cleaning agents were able to eradicate C. auris effectively.

The current study highlights the role of excessive antibiotic exposure in the emergence of C. auris. It also indicates the challenges in eliminating fungi from hospital settings. The authors recommend proper antibiotic treatment and cleaning procedures for drug-resistant pathogens.

Journal reference:
Microbiology

New SARS-CoV-2 Omicron XBB.1.5 variant has high transmissibility and infectivity, study finds

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Mar 20 2023Reviewed by Danielle Ellis, B.Sc.

COVID-19 has caused significant global panic after its rapid emergence more than 3 years ago. Although we now have highly effective vaccines against the SARS-CoV-2 virus, which causes COVID-19, scientists continue to study emerging SARS-CoV-2 variants in order to safeguard public health and devise global preventive strategies against emerging variants. A team led by Japanese researchers has recently discovered that the SARS-CoV-2 Omicron XBB.1.5 variant, prevalent in the Western hemisphere, has high transmissibility and infectivity.

New SARS-CoV-2 Omicron XBB.1.5 variant has high transmissibility and infectivity, study finds
New SARS-CoV-2 variant may jeopardize public health across the globe. The SARS-CoV-2 Omicron XBB.1.5 variant spreads rapidly and is more infectious than its historic precursor. Image Credit: The University of Tokyo

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been responsible for millions of deaths worldwide. Although scientists have designed novel vaccines to counter COVID-19, they are constantly on the lookout for emerging variants that can bypass vaccine resistance and potentially jeopardize global public health. A team led by Japanese researchers has recently been successful in characterizing the new SARS-CoV-2 Omicron XBB.1.5 variant, which was first detected in October 2022. Their findings were published on January 31, 2023 in volume 23 of The Lancet Infectious Diseases.​​​

Says senior author Prof. Kei Sato from the Division of Systems Virology, The Institute of Medical Science, The University of Tokyo, Japan, “Because the Omicron XBB.1.5 variant can spread more rapidly than previous variants and has a potential to cause the next epidemic surge, we should carefully monitor it to safeguard public health.”

While studying emerging variants of the SARs-CoV-2 Omicron lineage, the research team made a startling discovery: the SARS-CoV-2 Omicron XBB.1.5 variant has a novel mutation in the spike (S) protein—the protein that anchors the virus firmly to the human angiotensin converting enzyme-2 (ACE2) receptor, thus facilitating the invasion of human cells. The serine-to-proline amino acid mutation noted at residue no. 486 in the S protein is virologically concerning because of a variety of reasons.

Sharing his concerns, first author Keiya Uriu from the Division of Systems Virology, Department of Microbiology and Immunology, The University of Tokyo, Japan, says, “In late 2022, the SARS-CoV-2 Omicron BQ.1 and XBB lineages, characterized by amino acid substitutions in the S protein and increased viral fitness, had become predominant in the Western and Eastern Hemisphere, respectively. In 2022, we elucidated the characteristics of a variety of newly emerging SARS-CoV-2 Omicron subvariants. At the end of 2022, the XBB.1.5 variant, a descendant of XBB.1 that acquired the S:S486P substitution, emerged and was rapidly spreading in the USA.”

To gain mechanistic insights into the infectivity, transmissibility, and immune response associated with XBB.1.5, the team conducted a series of experiments. For instance, upon conducting epidemic dynamics analysis—statistical modeling that facilitates the analysis of the general characteristics of any epidemic—the team realized that the relative effective reproduction number (Re) of XBB.1.5 was 1.2-fold greater than that of the parental XBB.1. This indicated that an individual with the XBB.1.5 variant could infect 1.2 times more people in the population than someone with the parental XBB.1 variant. Moreover, the team also realized that, as of December 2022, XBB.1.5 was rapidly outcompeting BQ.1.1, the predominant lineage in the United States.

Co-first-author Jumpei Ito from the Division of Systems Virology, remarks, “Our data suggest that XBB.1.5 will rapidly spread worldwide in the near future.”

The team also studied the virological features of XBB.1.5 to determine how tightly the S protein of the new variant interacts with the human ACE2 receptor. To this end, the researchers conducted a yeast surface display assay. The results showed that the dissociation constant (KD) corresponding to the physical interaction between the XBB.1.5 S receptor-binding domain (RBD) and the human ACE2 receptor is significantly (4.3-fold) lower than that for XBB.1 S RBD. “In other words, the XBB.1.5 variant binds to human ACE2 receptor with very high affinity,” explains Shigeru Fujita from the Division of Systems Virology.

Further experiments using lentivirus-based pseudoviruses also showed that XBB.1.5 had approximately 3-fold higher infectivity than XBB.1. These results suggest that XBB.1.5 exhibits a remarkably strong affinity to the human ACE2 receptor, which can be attributed to the S486P substitution.

The study by Prof. Sato and his team led to another important discovery from an immunization perspective. The XBB.1.5 S protein was found to be highly resistant to neutralization antibodies elicited by breakthrough infection with the BA.2/BA.5 subvariants. In other words, patients with prior infection from the BA.2/BA.5 subvariants may not show robust immunity against XBB.1.5, increasing their chances of infection and disease.

The results of our virological experiments explain why the Omicron XBB.1.5 variant has a higher transmissibility than past variants: This variant acquired strong binding ability to human ACE2 while maintaining a higher ability to escape from neutralizing antibodies.”

​​​​​​​Yusuke Kosugi, Division of Systems Virology, Department of Microbiology and Immunology, The University of Tokyo, Japan

Contributing members of The Genotype to Phenotype Japan (G2P-Japan) Consortium conclude, “The SARS-CoV-2 Omicron XBB.1.5 variant does show enhanced transmissibility. Although few cases have been detected in the Eastern hemisphere, it could become a looming threat. Imminent prevention measures are needed.”

​​​​​​​Thanks to the research team for the early warning! Meanwhile, we must continue adopting safe practices to defend ourselves from XBB.1.5. 

Source:

The University of Tokyo

Journal reference:

Uriu, K., et al. (2023) Enhanced transmissibility, infectivity, and immune resistance of the SARS-CoV-2 omicron XBB.1.5 variant. The Lancet Infectious Diseases. doi.org/10.1016/S1473-3099(23)00051-8.

Microbiology

Real-world data on the effectiveness of Sotrovimab as a prophylactic against COVID-19

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Bhavana KunkalikarBy Bhavana KunkalikarMar 16 2023Reviewed by Danielle Ellis, B.Sc.

*Important notice: medRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.

In a recent study posted in the medRxiv* preprint server, scientists assessed the efficacy of sotrovimab for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) treatment.

Emerging SARS-CoV-2 variants have lowered the fold change in half maximal effective concentration (EC50) for the SARS-CoV-2 Omicron BA.2 sublineage and subsequent sublineages. Yet, the association between this decrease and clinical efficacy outcomes is unknown. With a lack of clinical trials evaluating the efficacy of sotrovimab against novel variants, real-world evidence becomes an essential data source.

Study: Real-world effectiveness of sotrovimab for the treatment of SARS-CoV-2 infection during Omicron BA.2 subvariant predominance: a systematic literature review. Image Credit: Cryptographer / ShutterstockStudy: Real-world effectiveness of sotrovimab for the treatment of SARS-CoV-2 infection during Omicron BA.2 subvariant predominance: a systematic literature review. Image Credit: Cryptographer / Shutterstock

About the study

In the present study, researchers assessed the efficacy of sotrovimab on severe coronavirus disease 2019 (COVID-19) outcomes throughout the period of the prevalence of the SARS-CoV-2 Omicron BA.2 subvariant.

This systematic literature review (SLR) comprised observational papers assessing clinical outcomes as well as the viral load in sotrovimab-treated patients, which were published between 1 January 2022 and 3 November 2022 in preprint articles, peer-reviewed journal publications, and conference abstracts. To identify data related to Omicron BA.2 and the following subvariants, the team chose a suitable publication period for the systematic review.

The following electronic databases were searched on 3 November 2022: MEDLINE, LitCovid, Embase, EcoLit, and Cochrane COVID-19 Study Registry. Further searches were undertaken in medRvix, bioRvix, arRvix, xhemRvix, Preprints.org, SSRN, and ResearchSquare for relevant preprints. In addition, relevant abstracts from the following conferences were indexed beginning in January 2022: Infectious Diseases Week, International Conference on Emerging Infectious Diseases, European Respiratory Society, and European Congress of Clinical Microbiology and Infectious Diseases.

Data extraction from the listed studies was conducted by a single extractor using a Microsoft Excel-designed data extraction file. Information extracted included the study’s title and citation, data source, study design and details, country, number of patients, study population, data collection period and circulating SARS-CoV-2 variants, duration of follow-up, key baseline features, and clinical outcomes. The clinical outcomes taken into account for the study included hospital admission, intensive care admission, respiratory support, emergency department visits, mortality, COVID-19 progression, the relative and absolute change in viral load observed during the acute phase after sotrovimab therapy, and the number of patients having undetectable viral load after sotrovimab treatment.

Results

Initial searches of electronic databases generated 257 studies. Another 263 studies were found by searching preprints, conference abstracts, and citation chasing from appropriate SLRs. After removing duplicates, 343 unique abstracts and titles were evaluated, of which 89 were deemed eligible for full-text review. Five observational trials reporting viral load or clinical outcome data associated with sotrovimab during the era of BA.2 predominance were deemed appropriate for inclusion in the present SLR.

Point estimates for hospitalization or mortality (as a composite endpoint) or clinical progression for sotrovimab-treated patients. a95 CIs calculated via Clopper-Pearson methods using reported data. bDefined as March through April 2022 in source and assumes homogeneity in the distribution of SARS-CoV-2 variants across all US states. cOnly COVID-19-specific outcome shown; all-cause outcome also reported in source. dHospitalizations were COVID-19-specific; deaths could be due to any cause. CI confidence interval

Point estimates for hospitalization or mortality (as a composite endpoint) or clinical progression for sotrovimab-treated patients. a95 CIs calculated via Clopper-Pearson methods using reported data. bDefined as March through April 2022 in source and assumes homogeneity in the distribution of SARS-CoV-2 variants across all US states. cOnly COVID-19-specific outcome shown; all-cause outcome also reported in source. dHospitalizations were COVID-19-specific; deaths could be due to any cause. CI confidence interval

The number of patients reporting hospitalization or fatality due to COVID-19 was consistently low for all investigations and periods of the prevalence of Omicron BA.1 and BA.2 variants. COVID-19-related hospital admission or mortality rates were between 1.0% and 3.1% for sotrovimab-treated patients during Omicron BA.1 prevalence and from 1.0% and 3.6% when BA.2 was predominant. The number of patients who reported hospitalization and mortality due to all causes ranged from 2.1% to 2.7% for the BA.1 predominance era, and from 1.7% to 2.0% for the BA.2 era. During Omicron BA.1 predominance, COVID-19-related mortality was projected to be 0.21% for the sotrovimab group versus 0.67% for the molnupiravir group, and 0.15% versus 0.96% for the BA.2 era, respectively.

During the BA.1 and BA.2 subvariant surges, sotrovimab was associated with a significantly decreased incidence of 28-day SARS-CoV-2-related hospital admission or fatality compared to molnupiravir. After statistical adjustment for demographics, vaccination status, high-risk cohort categories, body mass index, calendar time, and other comorbidities, the findings indicated that sotrovimab was associated with a significantly lower risk of COVID-19-related hospital admission or mortality compared to molnupiravir during the BA.1 and BA.2 periods.

During the BA.2 subvariant surge, sotrovimab was linked with a decreased risk of 30-day hospitalization or mortality from all causes compared to no mAb treatment. In March 2022, sotrovimab was considerably more successful than non-mAb-treated patients, with an adjusted reduction of 59% in relative risk and a propensity score-matched relative risk reduction of 64% with respect to 30-day all-cause hospital admission or mortality. Similar risks of hospitalization were associated with BA.1 and BA.2 patients treated with sotrovimab.

Conclusion

The study findings showed that sotrovimab continued to be clinically effective in mitigating severe clinical outcomes associated with SARS-CoV-2 infections during the period of SARS-CoV-2 Omicron BA.2 predominance compared to the control/comparator and relative to Omicron BA.1 predominance. During Omicron BA.1 and BA.2 subvariant predominance, the studies consistently reported low rates of poor clinical outcomes in individuals treated with sotrovimab.

*Important notice: medRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.

Journal reference:
Microbiology

Study finds community-onset bacterial coinfection in children with critical COVID-19 is infrequent but empiric antibiotics are commonly prescribed

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Pooja Toshniwal PahariaBy Pooja Toshniwal PahariaMar 8 2023Reviewed by Danielle Ellis, B.Sc.

In a recent study published in Open Forum Infectious Diseases, researchers evaluated the use of empiric antibiotics to determine the prevalence rates of community-acquired bacterial coinfections among hospitalized pediatric critical coronavirus disease 2019 (COVID-19) patients and to identify opportunities for de-escalating antibiotic usage in case of no bacteria-caused sepsis among high-risk individuals, and those presenting with shock.

Study: Community-onset bacterial coinfection in children critically ill with SARS-CoV-2 infection. Image Credit: nokwalai/Shutterstock
Study: Community-onset bacterial coinfection in children critically ill with SARS-CoV-2 infection. Image Credit: nokwalai/Shutterstock

Background

Community-acquired bacterial coinfections among hospitalized adult coronavirus disease 2019 (COVID-19) patients are uncommon; however, empiric antibiotic usage is reportedly high. Data on empiric antibiotic usage and bacterial coinfections among pediatric individuals with critical severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections are limited.

The clinical manifestations of severe SARS-CoV-2 infections often include pulmonary distress and fever, findings that could be difficult to discriminate from serious bacterial infections, which might prompt the use of empiric antibiotics in the initial days of hospitalization, particularly among high-risk individuals.

About the study

In the present study, researchers investigated whether any radiographic, laboratory, or clinical features ascertainable during hospitalization were related to empiric antibiotic usage or were estimative of bacterial coinfections acquired in community settings.

The team evaluated individuals below 19.0 years and admitted to pediatric high-acuity units (HAU) or intensive care units (ICU) due to SARS-CoV-2 infections from March 2020 to December 2020. On the basis of microbiology reports from the initial 72 hours of hospitalization, the team adjudicated if patients had community-acquired bacterial coinfections.

Clinical and demographic variables of individuals with and without antibiotic prescriptions and bacterial coinfections in the initial days of hospitalization were compared. Poisson regression modeling was performed to assess factors related to the outcome, and the adjusted relative risk (aRR) values were calculated.

Data were obtained from patient electronic medical records and data from the nationwide overcoming COVID-19 population health active surveillance registry of patients hospitalized due to COVID-19-associated complications between 15 March 2020 and 31 December 2020 across >70.0 pediatric hospitals in 25 states.

COVID-19 diagnosis was confirmed using polymerase chain reaction (PCR). The team excluded multisystem inflammatory syndrome among children (MIS-C) patients diagnosed using the Centers for Disease Control and Prevention (CDC) criteria. Data were obtained on demographic parameters, clinical symptoms and signs, comorbidities, radiographical and laboratory investigations, and data on antibiotics prescribed at admission and the course of critical COVID-19, including clinical outcomes and hemodynamic and respiratory support needed.

The primary study outcome assessed was the prescriptions of empirical antimicrobials, for which enteral or intravenous antimicrobials administered in the initial two days of hospital admission were assessed. The second outcome evaluated community-acquired bacterial infection presence, for which relevant case report form (CRF) information from individuals with SARS-CoV-2-positive microbiological cultures, and PCR, were analyzed in the initial 72 hours of hospital admission.

Results

Out of 532 individuals, 63.0% were administered empiric antibiotics; however, only seven percent developed bacterial coinfections, of which only three percent were respiratory-type. Empirical antibiotics had a greater likelihood of being prescribed to immunosuppressed individuals (aRR of 1.3), requiring non-mechanical ventilator-type respiratory aid (aRR of 1.4), or requiring invasive-type mechanical ventilators (aRR of 1.8), than no respiratory aid.

The most frequently prescribed antimicrobials were ceftriaxone (41%) and vancomycin (28%), followed by cefepime (20%). Most individuals were prescribed multiple antimicrobials, with 21%, 10%, and 18% receiving 2.0, 3.0, and ≥4.0 antibiotics in the initial two days of hospital admission. More than 33% of individuals received antibiotics for ≥5.0 days, despite no evidence of bacterial coinfections. The median social vulnerability index (SVI) values were significantly greater among those who received antibiotics than those who did not.

The median C-reactive protein (CRP) levels were greater among those who received antibiotics versus those who did not (4.6 mg per dL vs. 2.2 mg per dL), as were the median procalcitonin levels (0.4 ng per mL vs. 0.1 ng per mL). The median leukocyte counts showed no significant differences between the two groups. Antibiotic usage was related to COVID-19 severity, indicated by greater median values for PEdiatric Logistic Organ Dysfunction-2 (PELOD-2) scores at hospitalization among individuals who received antibiotics than those who did not.

Seven percent (n=38) of individuals had true community-onset bacterial coinfections, of which 13, 16, 8.0, and 4.0 were bloodstream infections, respiratory infections, urinary tract infections, and bacterial infections at other sites (peritonitis, colitis, meningitis, and pharyngitis), respectively.

No particular pathogenic organism predominantly caused bacterial coinfections, although most pulmonary coinfections were caused by Staphylococcus aureus and/or Pseudomonas aeruginosa. Greater PELOD-2 scores at admission were associated with bacterial coinfections (aRR of 1.2), in addition to age, sex, and pulmonary conditions other than asthma (aRR 2.3).

Conclusion

Overall, the study findings showed that community-onset bacterial coinfections among children with critical COVID-19 are not frequent; however, empiric antibiotics are usually prescribed. The study findings inform antibiotic use and underpin swift de-escalation in case assessments indicating that coinfections are not likely.

Journal reference:
Microbiology

The SARS-CoV-2 virus and the illness it causes, COVID-19, have made an indelible mark on our lives. It …

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The SARS-CoV-2 virus and the illness it causes, COVID-19, have made an indelible mark on our lives. It seems that is also true in more ways than one; new research has shown that when the virus infects cells, portions of the viral genome integrate into the genome of host cells in a phenomenon known as reverse transcription. While this is a relatively rare even for SARS-CoV-2, so many people have been infected with the virus that integration has probably happened many times. Scientists have now used several techniques to show that SARS-CoV-2 can integrate into a host cell genome, and the findings have been reported in the journal Viruses. This study is confirmation of previous work reported in the Proceedings of the National Academy of Sciences in 2021.

Colorized scanning electron micrograph of a cell (red) infected with the Omicron strain of SARS-CoV-2 virus particles (blue), isolated from a patient sample. Image captured at the NIAID Integrated Research Facility (IRF) in Fort Detrick, Maryland. Credit: NIAID

This research may help explain why some people continue to test positive for the virus long after their infection has subsided and they have recovered. In reverse transcription, RNA molecules, in this case from SARS-CoV-2, are transcribed into cDNA, a flip of the typical process in which active genes are transcribed into RNA molecules. Those reverse-transcribed cDNA molecules are then stitched into the host cell genome. If some of those cells are captured during a COVID-19 test, PCR would recognize and amplify the viral DNA in the host cell, causing a positive test result.

This study has also shown that simply inserting viral RNA into cells is not enough to cause genomic integration, so it seems unlikely based on the evidence we have now that mRNA from the COVID-19 vaccines would cause integration into cells’ DNA.

“This paper puts our data on a very firm footing. Hopefully, it will clarify some of the issues raised in the discussion that followed the first paper, and provide some reassurance to people who were worried about the implications for the vaccine,” said corresponding study author Rudolf Jaenisch, a founding member of the Whitehead Institute.

Since the integration of the SARS-CoV-2 genome into cells’ DNA is unusual, the researchers had to use a very sensitive method called digital PCR, which detects very specific genetic sequences, to identify instances in which viral RNA had been integrated into the genome of a cell.

The digital PCR results found viral RNA that had been reverse-transcribed to cDNA in about 4 to 20 of every 1,000 cells, but this includes all molecules of the sort, whether they ended up being integrated into a genome or not. Thus, the researchers suggested that viral integration is even more rare than that.

Whole genome sequencing can be used to show when that integration also occurred, because those events are typically accompanied by a reverse transcription complex called LINE1. The LINE1 sequences act as an indicator of integration. However, WGS is usually only used on a handful of cells, so when other investigators looked for those sequences, they could not usually be found.

“Because the human cell genome coverage by whole genome sequencing is very limited, you would need to run the sequencing experiment many times in order to have a good chance of detecting one viral genome copy,” explained postdoctoral researcher and first study author Liguo Zhang.

In this study, the researchers created cells that would overexpress LINE1, and make viral integration more common artificially. This time, the digital PCR showed that viral cDNA appeared in fourteen to twenty of every 1,000 cells, and WGS identified instances of integration along with LINE1. Further work with a tool called TagMap confirmed viral integration without overexpressing LINE1.

“This is unambiguous proof of viral genomic integration,” Zhang said. When this approach was repeated with cells that were treated with SARS-CoV-2 vaccine, there was no evidence of integration.

“We need to do further testing, but our results are consistent with vaccine RNA not integrating,” Jaenisch said.

Sources: Whitehead Institute for Biomedical Research, Viruses


Carmen Leitch

Microbiology

Study finds unique epigenetic biosignature in individuals with post-COVID syndrome

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Reviewed by Emily Henderson, B.Sc.Feb 28 2023

A reprogramming of which genes are active, and which are not, is visible in post-COVID sufferers. This is shown in a study from Linköping University, Sweden, on a small group of individuals. The researchers can see that genes associated with taste and smell, as well as cell metabolism, are affected in individuals with post-COVID syndrome. These findings may ultimately contribute to the development of new diagnostic tools for this and similar diseases.

There are many external factors that can affect which of all the genes in a cell are used at a certain point in time. The body’s ability to switch genes on and off contributes to our ability to adapt to various conditions. This gene use regulation is called epigenetics.

One of the regulation mechanisms entails that a small chemical group, a methyl group, is switched on and removed from the DNA strand. Reduced methylation of a gene may be a sign of it becoming easier for the cell to read and use, whereas high methylation most often means that the gene is not used. The researchers in Maria Lerm’s research group at Linköping University have previously found that exposure to the tuberculosis bacteria is visible in individuals’ DNA by looking at certain epigenetic changes.

In their new study, published in Clinical Epigenetics, the researchers studied blood samples from ten individuals having had persistent post-COVID symptoms for more than 12 weeks. The most common symptoms were a feeling of not being able to draw in enough air, palpitations, muscle weakness and loss of smell and taste.

These individuals were compared with two other groups: healthy COVID-19 convalescents, and individuals who had not had COVID-19 when the samples were taken. The researchers measured the methylation pattern on 850,000 sites of the DNA and then used an algorithm that can find data similarities and differences. It turned out that the three groups differed from each other and had distinct methylation profiles. The researchers then identified the genes that differ in methylation patterns between the groups.

“We have found that, for example, signaling pathways that control taste and smell have been affected. This confirms that the epigenetic differences may in fact be associated with the set of symptoms and be physiologically relevant,” says Maria Lerm, Professor of Medical Microbiology at the Department of Biomedical and Clinical Sciences, BKV, at Linköping University.

A previous study conducted by the research group concerned individuals who had recently recovered from COVID-19 and who showed a similar epigenetic reprogramming of signaling pathways associated with taste and smell.

In their new study, the researchers also found epigenetic changes in what is known as the angiotensin-2 system in post-COVID sufferers. This could be biologically relevant as the coronavirus which causes COVID-19, i.e., the SARS-CoV-2 virus, uses the angiotensin-2 system to enter and infect cells.

One of several conditions similar to post-covid is chronic fatigue syndrome, CFS, which is also known as myalgic encephalomyelitis, ME.

“One important finding is that we can see that the cells’ energy factories, the mitochondria, are affected in the post-COVID group. Other studies have shown that the cells’ energy factories have also been affected in cases of chronic fatigue,” says Maria Lerm.

There is currently no test that doctors can use to decide whether a person has post-COVID syndrome. The researchers are hoping that their recent findings can contribute to the development of diagnostic tools for health care providers, tools that might perhaps even make it possible to distinguish post-COVID from similar conditions.

The study was financed with support from the Swedish Heart Lung Foundation and the Swedish Research Council. The methylation pattern of study participants’ DNA was analyzed at Clinical Genomics, a SciLifeLab platform at Linköping University and Region östergötland.

Source:

Linköping University

Journal reference:

Defining post-acute COVID-19 syndrome (PACS) by an epigenetic biosignature in peripheral blood mononuclear cells, Frida Nikesjö, Shumaila Sayyab, Lovisa Karlsson, Eirini Apostolou, Anders Rosén, Kristofer Hedman and Maria Lerm, (2022), Clinical Epigenetics 14:172, published online on 14 December 2022 https://doi.org/10.1186/s13148-022-01398-1

Microbiology

Though the COVID-19 pandemic has waned, SARS-CoV-2 is still with us, and we still need diagnostic tests. Scientists …

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Though the COVID-19 pandemic has waned, SARS-CoV-2 is still with us, and we still need diagnostic tests. Scientists have been improving those tests in several ways. Researchers are developing a test that can rapidly diagnose new COVID-19 infections within hours of exposure. A combination flu and COVID-19 test has recently been approved by the US Food and Drug Administration (FDA) and is now available to consumers for use at home. A COVID-19 home test with greater sensitivity has also been created and will hopefully reach the market soon.

Image credit: Pixabay

Typical COVID-19 tests identify viral particles in swabs of the nostrils, throat, and/or cheeks. But those tests are best used during certain windows, and they can miss active infections when there isn’t much viral material available because a person is asymptomatic, or the infection has not yet set in and begun to replicate robustly. A totally new type of test uses a different approach, and aims to detect the immune response to the virus. The work has been published in Cell Reports Methods.

A viral infection activates the expression of a variety of immune genes, which are transcribed into mRNA molecules. The test detects certain levels of those mRNA molecules. The researchers used blood samples collected during the COVID-19 pandemic to validate their results; the test detected COVID-19 infections, even in asymptomatic people, with 98.4 percent accuracy.

More work is still needed to improve the test. For example, it uses blood samples and not nasal swabs. The scientists also need to verify that it can distinguish between different types of viral infections, like COVID-19 and the flu. But the researchers are hopeful that the diagnostic test will be available in the near future.

A combination flu and COVID-19 test is already on the market. The FDA recommends the test for anyone with symptoms of a respiratory tract infection symptoms. It’s called the Lucira COVID-19 & Flu Home test. It does not require a prescription, requires nasal swabs that can be collected by the user at home, and results are available in about 30 minutes.

While samples have to be collected by an adult, the test can be used on anyone older than 2. There is a small risk of false negatives, noted the FDA, so if respiratory infection symptoms exist and the test is negative, people may still want to follow up with their healthcare provider.

Scientists have also developed a much more sensitive test for COVID-19 that can be used at home. The work was reported in ACS Infectious Diseases.

At-home tests change color when an antibody-linked reporter molecule latches onto viral particles in a sample. But that color change is very faint when few viral particles are present. PCR-based tests are good for disease detection because only very small amounts of viral material have to be present; they are then amplified by PCR. But special equipment is needed for PCR.

This new, sensitive test has added an amplification step to a test that can be used at home. A hybridization chain reaction (HCR) boosts the signal of reporter molecules instead. The viral protein gets tagged with a DNA molecule, which can act as a scaffold that more reporter molecules can bind to. Thus, every viral particle triggers the emission of a much stronger signal.

When the sensitive test was compared to tests that are on the market, it was 2.5 times more sensitive than the best, and 100 times more sensitive than the worst. The researchers are now working to get the new test to the market.

Sources: California Institute of Technology, ACS Infectious Diseases, The Associated Press, Simons Foundation, Cell Reports Methods


Carmen Leitch

Microbiology

A variety of studies have shown that when the air is drier, viral particles can linger there longer. …

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A variety of studies have shown that when the air is drier, viral particles can linger there longer. These findings have now been confirmed in an analysis of particles of a virus that is very similar to the one that causes COVID-19, SARS-CoV-2. Although previous work has shown that relative humidity levels affect the length of time of a virus stays infectious in the air, this is the first to factor in the effect of saliva, which helps shield viral particles. The data can help explain why people tend to get more sick during winter, when humidity levels drop significantly indoors. It also stresses the importance of good ventilation systems and other mitigation efforts for preventing the spread of illness. The work has been reported in PNAS Nexus.

Dr. Mark Hernandez, S. J. Archuleta Professor of Civil and Environmental Engineering, and CU PhD graduate Marina Nieto-Caballero, now a postdoctoral researcher at Colorado State University, standing inside a bioaerosol chamber in the Environmental Engineering disinfection laboratory at the Sustainability, Energy and Environment Complex (SEEC). Credit Patrick Campbell/University of Colorado

This study used a mammalian coronavirus that is very similar to SARS-CoV-2. Particles containing this virus remained infectious for twice as long when air was drier. These particles are normally expelled with saliva, which acts like a protective shield, particularly when humidity is low.

Although civil engineers typically design and maintain buildings so their indoor relative humidity will stay between 40 and 60 percent, the reality is a bit different, and varies widely depending on the climate of the region. The researchers suspected that these humidity levels were influencing the spread of SARS-CoV-2.

To test that theory, the investigators engineered airborne particles containing virus, with and without saliva. These were then released into large, sealed chambers with relative humidity levels of 25, 40, and 60 percent.

The saliva protected the virus at every humidity level, and at 40 and 60 percent relative humidity, half of the airborne viral particles were still infectious one hour after release. Half of the airborne particles were still infectious two hours after release at 25 percent humidity; as the relative humidity dropped, the virus was still pathogenic for much longer.

“It shows this virus can hang around for quite a while, hours even. It’s longer than a class, longer than the time you’re in a restaurant, longer than the time you take to hang out in the cafe. An occupant may come in, spread coronavirus in the air, and leave. Depending on architectural factors, then someone else could walk into that space with potent doses still hanging around,” said senior study author Mark Hernandez, a Professor of Civil and Environmental Engineering at the University of Colorado at Boulder.

The virus is probably also contaminating air for longer than it takes typical ventilation systems to eliminate it. Thus, additional mitigation strategies like filtration could reduce transmission, suggested the study authors.

“I hope this paper has an engineering impact in our buildings, for example, in schools and hospitals, so that we can minimize the infectivity of these viruses in the air,” said lead study author Marina Nieto-Caballero, PhD.

Increasing indoor humidity levels could help reduce risk for people who live in naturally arid environments, but that can be inefficient and expensive, said Hernandez. We can use strategies that we already know about instead, like opening windows, using inexpensive air filters, and increasing ventilation rates to introduce more fresh air, Hernandez added.

Sources: University of Colorado at Boulder, PNAS Nexus


Carmen Leitch

Microbiology

Long COVID still affects many people who had a case of COVID-19; even people who had mild cases …

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Long COVID still affects many people who had a case of COVID-19; even people who had mild cases and were not hospitalized are at risk for the chronic disorder. Scientists and clinicians are still learning about the illness, which causes a wide range of symptoms and happens for unknown reasons. There are several hypotheses, however, and the disorder may also arise in different people for different reasons. New research has suggested that long COVID happens because particles of SARS-CoV-2, the virus that causes COVID-19, hide away in parts of the body, and the immune system becomes overactivated trying to eliminate them. The study has been reported in PLOS Pathogens.

Colorized scanning electron micrograph of a cell (brown) infected with the Omicron strain of SARS-CoV-2 virus particles (purple), isolated from a patient sample. Image captured at the NIAID Integrated Research Facility (IRF) in Fort Detrick, Maryland. Credit: NIAID

Symptoms of long COVID can include fatigue, brain fog, cough, shortness of breath, and chest pain, and these symptoms last more than four weeks after the acute phase of COVID-19. The illness is thought to impact about 20 percent of people who get COVID, noted Brent Palmer, Ph.D., an associate professor at the University of Colorado School of Medicine.

In this study, the researchers followed forty COVID-19 patients; twenty of them totally eliminated the infection and twenty developed long COVID, also known as  post-acute sequelae of COVID (PASC). The investigators used blood and stool samples from the study volunteers to identify T cells that were specific to COVID-19 and remained active after the initial infection was over.

These cells were then incubated with bits of the virus, and the scientists were able to see how frequently CD4 and CD8 T cells were reacting by generating cytokines. They found that long COVID patients carried levels of cytotoxic CD8 T cells that were as much as 100 times higher compared to people who cleared the infection.

Palmer also studies HIV infection, and he was astonished to find that about 50 percent of T cells were still directed against COVID-19 six months after their initial infection. “That’s an amazingly high frequency, much higher than we typically see in HIV, where you have ongoing viral replication all the time,” he added. “These responses were in most cases higher than what we see in HIV.”

CU pulmonologist Sarah Jolley, MD was a study co-author who obtained pulmonary data for the study volunteers. The researchers found that pulmonary function decreased as the level of COVID-19-specific T cells increased.

“That showed a really strong connection between these T cells that were potentially driving disease and an actual readout of disease, which was reduced pulmonary function. That was a critical discovery.”

The researchers have suggested that long COVID is drive by the immune system, which is increasing inflammation as it attempts to remove residual SARS-CoV-2 particles that cannot be detected with a nasal swab, but nonetheless remain. Palmer noted that some autopsies of COVID-19 patients have revealed the virus in many organs including the lungs, gut and kidney.

 

Additional work by Palmer and colleagues was reported in the journal Gut; this study indicated that the composition of the gut microbiomes of long COVID patients reflects an elevation of inflammatory markers. There may also be a link between the gut microbiome and the inflammation that is observed in long COVID, noted the researchers.

Palmer added that some studies have shown that antiviral medications like Paxlovid, or doses of vaccine may help relieve the symptoms of long COVID patients. This may happen because their immune systems are being given enough of a stimulatory bump to finally remove the infection, and it would show that a hidden reservoir of virus likely exists in these patients.

Sources: CU Anschutz Medical Campus, PLOS Pathogens, Gut


Carmen Leitch

Microbiology

Hundreds of research studies have now investigated long COVID, in which symptoms of COVID-19 and other health issues …

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Hundreds of research studies have now investigated long COVID, in which symptoms of COVID-19 and other health issues linger for months after the acute phase of infection has passed. Long COVID can occur in people who have had any type of case of COVID-19, from the mild to the severe. Researchers have been categorizing various symptoms of long COVID, and have proposed that there are subtypes of the disease. Scientists have also been following long COVID cases to determine how long symptoms might last.

Colorized scanning electron micrograph of a cell (green) infected with the Omicron strain of SARS-CoV-2 virus particles (pink), isolated from a patient sample. Image captured at the NIAID Integrated Research Facility (IRF) in Fort Detrick, Maryland. Credit: NIAID

In a new report published in the Journal of the Royal Society of Medicine, scientists have shown that organ damage continued to occur in 59 percent of long COVID patients twelve months after their symptoms started. This was true even for some people who had not experienced severe COVID-19.

This research included 536 long COVID patients, 13 percent of whom had been hospitalized when they were diagnosed with COVID-19. Patients who had reported poor quality of life, extreme breathlessness, and cognitive dysfunction were a focus of this study.

Out of 536 study participants, 331 (62 percent) had persistent organ dysfunction six months after they’d been initially diagnosed. There was a followup with the study volunteers six months later, in which they received an organ MRI scan. This revealed that 29 percent of long COVID patients were having trouble with multiple organs, such as reduced function and other symptoms specific to the organ. At the one-year followup, there was impairment in a single organ in 59 percent of the study participants.

Symptoms of breathlessness began to go away between six and twelve months, but only for some patients; the individuals reporting breathlessness at six months was 38 percent, and it dropped to 30 percent at one year; cognitive dysfunction decreased from affecting 48 to 38 percent of particpants; quality of life disruptions were experienced by 57 percent, then 45 percent of patients.

“Several studies confirm persistence of symptoms in individuals with long COVID up to one year. We now add that three in five people with long COVID have impairment in at least one organ, and one in four have impairment in two or more organs, in some cases without symptoms,” said study co-author Professor Amitava Banerjee of the UCL Institute of Health.

More research will still be needed to understand the mechanisms underlying the development of long COVID.

Sources: Eurekalert! via SAGE Publications, Journal of the Royal Society of Medicine


Carmen Leitch