Coronastream May 2022: SARS-CoV-2’s party-going friends

Posted on May 31, 2022   by Dr Tim Inglis

In this special blog series, medical microbiologists led by Dr Tim Inglis summarise some of the research that will be essential to inform COVID-19 countermeasures. Find out more about the project in Dr Inglis' Editorial 'Logic in the time of coronavirus', published in theJournal of Medical Microbiology


It seems many places have rushed headlong into abandoning COVID restrictions as public health authorities bow to public pressure over individual freedom. Even in this risk-averse corner of the COVID world, mask mandates have been axed, large gatherings have resumed, and long-distance travel has re-commenced. An anticipated rise in confirmed case numbers followed these administrative changes, the figures surpassing previous daily case-load records. Locally, peak cases occur early to mid-week and fall as the weekend approaches. The more cynical among us suggest this reflects a preoccupation with risk: the risk of losing a weekend to COVID.

This blog has mentioned previously the decoupling of case numbers, hospital admissions, intensive care bed demand and deaths. Though this phenomenon is now widely observed where Omicron and its progeny predominate, there is growing concern about influenza co-infection. The theme of dual infections may prove to be a sting in the tail of this pandemic, considering some of the other co-infections that have appeared de novo or resurfaced recently; friends of SARS-CoV-2 that have joined the party.

CONGRUENCE: Clinical microbiology of SARS-CoV-2 co-infection

Opportunistic Infections in COVID-19: A Systematic Review and Meta-Analysis

A good place to start on COVID-19 co-infections is a recent systematic review, such as this one from a group that scoured the medical literature to understand the infections that occur as a result of an initial SARS-CoV-2 infection. The commonest were other viruses, followed by bacteria and then fungi. While there was considerable heterogeneity in the studies reviewed, the authors conclude that critically ill COVID-19 patients were at greater risk of opportunist infections, notably including Epstein-Barr virus, Pseudomonas aeruginosa, Escherichia coli, Acinetobacter baumannii, Hemophilus influenzae, and Aspergillus species. 

SARS-CoV-2 co-infection with influenza viruses, respiratory syncytial virus, or adenoviruses

In this correspondence, a multicentre group report on clinical outcomes of influenza virus, respiratory syncytial virus and adenovirus infection in 212,466 adults with SARS-CoV-2 infection admitted to UK hospitals between February 2020 and December 2021. The odds in favour of mechanical ventilation increased with influenza co-infection and for death in hospital increased for influenza and adenovirus co-infection. The authors highlight the importance of laboratory tests for respiratory viruses other than SARS-CoV-2 and recognise a need to promote influenza vaccination because relaxed public health restrictions allow greater circulation of other viral respiratory pathogens.

CONSISTENCY: India-wide epidemiology of SARS-CoV-2 and influenza co-infection

SARS-CoV-2 and Influenza Virus Co-Infection Cases Identified through ILI/SARI Sentinel Surveillance: A Pan-India Report

This report describes findings from an India-wide sentinel surveillance programme that examined community data on co-infection in addition to hospital reporting. Only five of 13,467 samples collected between July 2021 and January 2022 indicated SARS-CoV-2 and influenza co-infection, and no deaths were attributed. These cases are described in detail, hence the format of a case report. Figure 1 shows the different timing of peak SARS-CoV-2 and influenza virus infection, which may explain the small number of co-infections. The authors recognise that the COVID peak triggered an increase in public health restrictions, which may have reduced circulation of influenza virus in the community.

CUMULATIVE DISSONANCE: Mouse model of co-infection; fungal microbiome disruption

Coinfection with SARS-CoV-2 and Influenza A Virus Increases Disease Severity and Impairs Neutralizing Antibody and CD4+ T Cell Responses

As public health restrictions against COVID-19 ease, community circulation of other respiratory viruses increases, raising concern that dual infections may have worse outcomes than COVID-19 alone, as noted above. In Kim and colleagues' study of SARS-CoV-2 and influenza, co-infection in a mouse model showed an increased mortality and prolonged influenza virus shedding. Their study documented a prolonged primary viral infection period, increased cellular infiltration and raised cytokine levels in bronchoalveolar fluid, with consequent lung damage. Their conclusion was that viral co-infection aggravated the pathology through an impaired neutralising antibody response.

The Fungal Gut Microbiome Exhibits Reduced Diversity and Increased Relative Abundance of Ascomycota in Severe COVID-19 Illness and Distinct Interconnected Communities in SARS-CoV-2 Positive Patients

During COVID-19, the gut microbiome is disrupted, resulting in a loss of bacterial diversity, increased Enterobacteriaceae and a loss of immunomodulating bacteria.  This study applies those insights to the fungal microbiome of patients with SARS-CoV-2 infection. They found similar disruption of fungal diversity and richness, plus depletion of fungal taxa in severe disease. There was also an increase in the Ascomycetes in non-severe disease. There was considerable between-patient variation in the dominant fungal species. The cross-sectional study design leaves important questions about the significance of fungal microbiome changes to the course of COVID-19 and their effect on disease severity.

CURTAILMENT: Antiviral properties of metallic film surfaces

Nanoscale copper and silver thin film systems display differences in antiviral and antibacterial properties. Scientific Reports

Previously, this blog referenced work on the effect of different inanimate surfaces on SARS-CoV-2 persistence. At that time, there was concern that these surfaces were an important vehicle for viral transmission. Since then, the emphasis has shifted to airborne transmission in droplets and bioaerosols. However, the issue of surface contamination has not completely disappeared, so that enhanced cleaning procedures are still practiced in high-risk locations. This study considers the antiviral properties of two candidate metals; copper and silver. Its interesting conclusion is that surfaces coated by magnetron sputtering as thin copper films or as composite copper and silver ultrathin nanopatches had an antiviral effect, but silver alone did not. This observation differs from the antibacterial effect of silver coatings and has obvious implications for the development of anti-SARS-CoV-2 surface coatings for high transmission risk areas.


SARS-CoV-2 phylogeny summarised. Omicron's new identities. Nature.