Tag: Remdesivir

Analysis finds significant variations in national COVID-19 treatment recommendations

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National clinical guidelines for the treatment of COVID-19 vary significantly around the world, with under-resourced countries the most likely to diverge from gold standard (World Health Organization; WHO) treatment recommendations, finds a comparative analysis published in the open access journal BMJ Global Health.

And nearly every national guideline recommends at least one treatment proven not to work, the analysis shows.

Significant variations in national COVID-19 treatment recommendations have been suspected since the advent of the pandemic, but these haven’t been formally quantified or studied in depth, note the researchers.

And despite the fact that COVID-19 is no longer taking the toll on lives and health that it once did, the virus is still evolving and active around the globe, they emphasize. The WHO only rescinded COVID-19’s status as a public health emergency in April 2023.

To assess how well national clinical practice followed the recommendations of the WHO (11th version; July 2022)—regarded as the gold standard—-for the treatment of COVID-19, the researchers analysed the content of all 194 WHO member states’ most recent national guidelines at the end of 2022.

Each set of guidelines was scored according to how closely they aligned with the WHO recommendations. Extra points were awarded for those that had been updated within the preceding 6 months; those that made recommendations in line with the strength of evidence; and those that included assessments of the effectiveness of treatments and their side effects.

The wealth and resources of each country were then compared using per capita World Bank gross domestic product (GDP) in US dollars for 2021, the Human Development Index 2021, and the Global Health Security Index 2021.

Of the 194 countries contacted, 72 didn’t respond. Of the remaining 122, 9 had no formal guidelines or couldn’t be accessed (1) and a further 4 didn’t recommend any treatments, so these were excluded, leaving a total of 109.

The countries for which guidelines weren’t obtained had, on average, smaller populations, lower GDP per head, and a lower Global Health Security Index, indicative of greater economic challenges and less ability to respond to health emergencies.

The 11th iteration of the WHO guidelines categorises disease severity, but most of the reviewed guidelines (84%; 92) didn’t define COVID-19 severity in the same way, and some didn’t define severity at all (6.5%; 7). Only 10 guidelines (9%) used disease severity definitions that were comparable with those of the WHO.

Most (77%; 84) guidelines didn’t include an assessment of the strength or certainty of the therapeutic recommendation. And the range of recommended drugs, irrespective of severity, varied from 1 to 22. The WHO guidelines recommend a total of 10.

In all, 105 guidelines included at least one treatment recommended by the WHO, but 4 didn’t recommend any. Countries in the African region had a significantly lower proportion of therapies recommended by the WHO, compared with countries in Europe and SouthEast Asia.

The most commonly recommended drugs were corticosteroids (92%;100), with 80% (88) of guidelines recommending them for the same disease severity as the WHO. But corticosteroids weren’t recommended in severe disease in nearly 1 in 10 guidelines despite overwhelming evidence of their benefit.

Remdesivir was recommended for severe or critical disease in half the guidelines (51%;72). But the WHO guidelines only indicate remdesivir conditionally for mild disease in patients at highest risk of hospital admission.

In late 2022, many guidelines continued to recommend treatments that the WHO had advised against, including chloroquine, lopinavir-ritonavir, azithromycin; vitamins and/or zinc.

One in three guidelines (36; 33%) recommended at least one neutralising monoclonal antibody directed against SARS-CoV-2, the virus responsible for COVID-19.These guidelines were issued by wealthier countries.

But 2 of these monoclonal antibodies—bamlanivimab plus or minus etesivamab and regdanivimab—appeared consistently in clinical guidelines, despite not being recommended by the WHO.

Doses of the most commonly recommended drugs also varied. And many guidelines hadn’t been updated for more than 6 months.

Guidelines from under-resourced countries diverged the most from the WHO recommendations, when stratified by annual GDP, the Human Development Index, and the Global Health Security Index.

The researchers acknowledge several limitations to their findings, including the scoring used to assess the guidelines, which hasn’t been validated by other studies, and the inability to assess all national guidelines.

But they nevertheless ask: “Why do [national guidelines] differ so much in their treatment guidance for such a widespread and potentially serious infection when all have access to the same information?

“Apart from the prohibitive cost of some medications for low-resource settings we do not have a satisfactory explanation.”

They offer some possible explanations, including variations in how the severity of, and therefore the most appropriate treatment for, COVID-19 is defined; the evolution of the evidence; and the research chaos and confusion of the early stages of the pandemic, leading to claims and counterclaims, compounded by intense political and media interest.

“In this ‘fog of war’ countries clearly felt the need to say something and do something, even if it was based on very little evidence,” explain the researchers. “But why many of these unproven remedies continued to be recommended as evidence of their ineffectiveness accrued is much less clear,” they add.

“There is clearly more variation in national guidelines for COVID-19 therapeutics than there should be to ensure optimum treatment,” which aren’t justified by significant differences between populations or geographic variation in SARS-CoV-2 antiviral susceptibility, they write.

Global health inequalities clearly have a part to play, leading to the recommendation of ineffective, unaffordable and unavailable therapies, they suggest.

“The formalisation of processes in the development of [national guidelines] for COVID-19 and other infectious diseases is essential for ensuring that these guidelines are grounded in the best available evidence,” they conclude.

“A systematic and structured approach would not only enhance the credibility of the guidelines but could also contribute to their effectiveness in guiding public health interventions, especially in a pandemic setting.”

Source:

Journal reference:

Cokljat, M., et al. (2024) Comparison of WHO versus national COVID-19 therapeutic guidelines across the world: not exactly a perfect match. BMJ Global Health. doi.org/10.1136/bmjgh-2023-014188.

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April 23, 2024
Study reveals how SARS-CoV-2 hijacks lung cells to drive COVID-19 severity

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In a recent study published in the Journal of Experimental Medicine, researchers identified the cellular tropism and transcriptome consequences of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by infecting human lung tissue and using single-cell ribonucleic acid sequencing (scRNA-seq) to rebuild the transcriptional program in “infection pseudotime” for distinct lung cell types.

Lower respiratory infections, such as coronavirus disease 2019 (COVID-19), are a leading cause of death worldwide, producing pneumonia and acute respiratory distress syndrome. Understanding their early phases is difficult. Researchers used classical histopathological approaches and single-cell multi-omic profiling to infer early phases in human pathogenesis from lung lavage, biopsy, or autopsy materials. These approaches reveal a thorough picture of COVID-19 pneumonia at unparalleled cellular and molecular resolution, implying infection models including alveolar epithelium, capillaries, macrophages, and myeloid cells.

Study: Interstitial macrophages are a focus of viral takeover and inflammation in COVID-19 initiation in human lung. Image Credit: Dotted Yeti / Shutterstock

About the study

In the present study, researchers developed an experimental COVID-19 model to investigate early molecular processes and pathogenic mechanisms of SARS-CoV-2 infection at the cellular level in native tissues of the human lung.

The researchers established SARS-CoV-2’s cellular tropism and its unique and dynamic impacts on host cellular gene expression in specific types of lung cells. Prominent targets were lung-resident macrophages, of which one SARS-CoV-2 takes over transcriptomes, inducing a targeted host interferon (IFN) antiviral program, and several chemokines and pro-fibrotic and pro-inflammatory and cytokines signaling to various structural and immunological cells of the lung.

To determine the early stages of COVID-19 in human lungs, the researchers sliced lung tissue obtained from surgical specimens or organ donor individuals into thick sections and used them for tissue culture analysis. Subsequently, they exposed the tissues to the SARS-CoV-2 USA-WA1 2020 strain at 1.0 multiplicity of infection (MOI) for two hours before allowing the SARS-CoV-2 infection to continue for two to three days. They performed a plaque test on culture supernatants.

The researchers separated the slices and examined them by scRNA-seq to evaluate host and viral genetic expression during the SARS-CoV-2 infection. They also examined the viral RNA molecules’ junctional structure and processing by analyzing the scRNA-seq dataset with the SICILIAN framework. They used molecular atlas markers to distinguish lung cell types in healthy lung slices and measure viral RNA levels in infected cells.

The team performed multiplexed single-molecule fluorescence in situ hybridization (smFISH) to confirm lung cell tropism findings and show infected cells. They used single-cell gene expression patterns to identify cellular targets for inflammatory and pro-fibrotic signals elicited by the SARS-CoV-2 infection of a-IMs. They devised a technique for purifying macrophage populations from human lungs with a SARS-CoV-2 spike (S) protein-pseudotyped lentivirus (lenti-S-NLuc-tdT) to investigate lung macrophage entrance routes.

The researchers productively infected human lung slices cultivated ex vivo with SARS-CoV-2, with production rising between 24 and 72 hours of culture. They heat-inactivated, ultraviolet (UV)-treated, or administered 10.0 µM remdesivir, an RNA-dependent RNA polymerase inhibitor used as a COVID-19 therapeutic, to prevent viral stock infection.

Results

The analysis showed that SARS-CoV-2 preferentially infects active interstitial macrophages (IMs), which can amass hundreds of SARS-CoV-2 RNA molecules, comprising >60% of the cell transcriptome and producing dense viral RNA bodies. Infected alveolar macrophages (AMs) exhibit no severe reactions, with spike (S) protein-dependent viral entrance into AMs utilizing angiotensin-converting enzyme 2 (ACE2) and the cluster of differentiation 169 (CD169) and IM entry via CD209.

They found canonical sub-genomic junctions between the unusual sequence reads beyond their 39 terminal regions, indicating canonical-type SARS-CoV-2 messenger RNA (mRNA) production in the pulmonary cultures. They also found hundreds of new subgenomic junctions, showing a wide range of non-canonical and canonical sub-genomic SARS-CoV-2 RNAs produced during pulmonary infection.

Model of initiation, transition, and pathogenesis of COVID-19 and the viral lifecycle in AMs and IMs. (a–d) Model of COVID-19 initiation in the human lung and transition from viral pneumonia to lethal COVID-19 ARDS. (a) SARS-CoV-2 virion dissemination and arrival in the alveoli. Luminal AM encounter virions shed from the upper respiratory tract that enter the lung. AMs can express low to moderate numbers of viral RNA molecules and can propagate the infection but “contain” the viral RNA from taking over the total transcriptome and show only a very limited host cell inflammatory response to viral infection. (b) Replication and epithelial injury. SARS-CoV-2 virions enter AT2 cells through ACE2, its canonical receptor, and “replicate” to high viral RNA levels, producing infectious virions and initiating viral pneumonia. (c) a-IM takeover and inflammation signaling. SARS-CoV-2 virions spread to the interstitial space through either transepithelial release of virions by AT2 cells or injury of the epithelial barrier, and enter a-IMs. Infected a-IMs can express very high levels of viral RNA that dominate (“take over”) the host transcriptome and can propagate the infection. Viral takeover triggers induction of the chemokines and cytokines shown, forming a focus of inflammatory and fibrotic signaling. (d) Endothelial breach and immune infiltration. The a-IM inflammatory cytokine IL6 targets structural cells of the alveolus causing epithelial and endothelial breakdown, and the inflammatory cytokines recruit the indicated immune cells from the interstitium or bloodstream, which flood and infiltrate the alveolus causing COVID-19 ARDS. Local inflammatory molecules are amplified by circulating immune cells, and reciprocally can spread through the bloodstream to cause systemic symptoms of cytokine storm. (e) Comparison of the SARS-CoV-2 viral lifecycle in AMs and IMs. Although both can produce infectious virions, note differences in viral entry receptors (AMs can use ACE2 and CD169/SIGLEC1, whereas IMs use CD209); viral RNA transcription of dsRNA intermediates (greater in AMs); replication of full-length genomic RNA (greater in IMs); viral takeover, formation of RNA bodies, and induction of a robust host cell inflammatory response (only in IMs), and cell destruction/death (only in IMs).

Heat, UV-C inactivation, or remdesivir therapy prevented the development of canonical and non-canonical connections. The team observed SARS-CoV-2 takeover of an activated IM subtype in 176,382 cells with high-quality transcriptomes obtained from infected lung slices of four donor lungs and in 112,359 cells from mock-infected slices (cultured without viral addition) and 95,389 uncultured control cells (directly from freshly cut lung slices). A differential gene expression study of a-IMs over infection pseudotime revealed host gene expression alterations corresponding to SARS-CoV-2 RNA levels.

The study found that COVID-19 pneumonia infection and takeover cause an early antiviral cell response specific to activated interstitial macrophages, resulting in a powerful immunological and fibrotic signaling center. Inflammasome activation is uncommon and only detectable late in a-IM infection. Blocking antibodies against CD169 and CD209 prevented entrance into IMs and AMs. The study also highlighted IMs as the most vulnerable lung target, with initial emphasis on inflammation and fibrosis. Two unique molecular lineages of macrophage targets react differently to SARS-CoV-2, influencing etiology and treatments.

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April 15, 2024
Molnupiravir influences SARS-CoV-2 evolution in immunocompromised patients

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In a recent study published in The Lancet Microbe, researchers investigated the effects of molnupiravir on the evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in immunocompromised patients.

Persistent SARS-CoV-2 infection in individuals who are immunocompromised offers genomic variation and has been linked to viral evolution. Antiviral therapy is recommended in immunocompromised patients with acute infection to prevent severe disease. Molnupiravir is the only alternative when first-line therapies (remdesivir and ritonavir-boosted nirmatrelvir) are not feasible, available, or appropriate.

Study: Effect of molnupiravir on SARS-CoV-2 evolution in immunocompromised patients: a retrospective observational study. Image Credit: creativeneko / Shutterstock

Molnupiravir has been used worldwide in hospital and community settings as well as for immunocompromised patients. Nevertheless, it has been ineffective at reducing coronavirus disease 2019 (COVID-19) hospitalization and mortality rates in high-risk groups, and consequently, it has been designated a third-line therapeutic option. The drug triggers mutagenesis by introducing β-D-N4-hydroxycytidine, the prodrug, into the viral ribonucleic acid (RNA).

The viral RNA polymerase uses this modified RNA as the template, and an error catastrophe occurs, inhibiting the viral replication. During RNA synthesis, molnupiravir behaves like a cytosine (C) and pairs with guanine (G); however, once incorporated, it transforms into a tautomer analogous to uracil (U), leading to G-to-A mutations in the subsequent round of replication. Likewise, it can induce C-to-U (or -thymine [T]) mutations during the synthesis of the positive-sense genome.

Reverse T-to-C and A-to-G mutations are also possible but are less frequent. G-to-A mutations indicate molnupiravir treatment; distinctive mutational profiles with extensive G-to-A mutations have been found in global sequences and phylogenetic trees. This is linked to the use of molnupiravir as countries showing long G-to-A branches had increased use of the drug. Contrastingly, countries with infrequent G-to-A branches have not authorized molnupiravir.

About the study

In the present study, researchers analyzed the sequencing data from immunocompromised patients with SARS-CoV-2 infection to assess the effects of molnupiravir on viral evolution. The team sequenced around 100 genomes weekly from December 2021 to September 2022, specifically focusing on samples from reinfections, hospitalized patients, overseas travelers, and suspected residential care- and healthcare-related infections.

Immunocompromised patients with protracted infection were also covered. The team selected nine patients with the same variant with multiple samples (from distinct time points). Four patients (controls) were tested before molnupiravir was available, and five were sampled pre- and post-molnupiravir treatment. All molnupiravir recipients and two controls were immunocompromised. Seven patients received ≥ two vaccine doses, and two were non-vaccinated.

Patients’ prior infection status was unknown. Patients infected with similar variants and high-quality genomes were selected for group comparisons across time points. Accumulated mutations were compared between groups. The ultrafast sample placement on existing trees (UShER) pipeline and the University of California Santa Cruz genome viewer were leveraged to compare variants from patients with global reference sequences and visualize the locations of mutations.

Findings

The team noted that SARS-CoV-2 genomes acquired an average of 30 new low/mid frequency variants by 10 days post-molnupiravir treatment. These changes in viral diversity were not observed in patients who did not receive molnupiravir. On average, 3.3 mutations were acquired per day in the molnupiravir group.

The probability of observing no mutations among controls during the study period was extremely low. Non-synonymous mutations were common in the spike protein, and subsequent samples indicated that some mutations were fixed. In one patient, 10 non-synonymous mutations were fixed by 35 days post-treatment.

Accrued mutations were scattered throughout the genome, including those not detected in global Omicron genomes. Mutations acquired in the spike protein clustered at two locations, and their functional relevance was unclear. No known drug-resistance mutations were observed; however, non-synonymous mutations in the open reading frame 1b (ORF1b) were noted.

The UShER analysis revealed potentially rare/novel mutations in the sequences following treatment. Some samples could not be placed on the global SARS-CoV-2 phylogeny as many mutations were phylogenetically distinct. Mutational profiles post-treatment revealed dominant G-to-A and C-to-T mutations, representing 70% of mutations, which persisted up to 44 days post-treatment.

Conclusions

In sum, the findings showed that molnupiravir use in immunocompromised patients modified the patterns of viral evolution, with effects lasting beyond the five-day treatment period. This highlights the risks of treating this subgroup of patients with an error-generating antiviral. The evolution rate in molnupiravir recipients exceeded that observed in non-recipients in this study and globally. Overall, the researchers provided more evidence of the causal link between molnupiravir and the altered mutational landscape of SARS-CoV-2.

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March 26, 2024