Co-infection with other respiratory pathogens in COVID-19 patients

Calcagno, Andrea; Ghisetti, Valeria; Burdino, Elisa; Trunfio, Mattia; Allice, Tiziano; Boglione, Lucio; Bonora, Stefano; Perri, Giovanni Di

doi:10.1016/j.cmi.2020.08.012

Cited by 52 publications

(64 citation statements)

References 6 publications

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“…Influenza A, metapneumovirus, parainfluenza virus) on their early hospitalization, to verify whether and how the present observations apply only to SARS-CoV-2 and not to other viruses. The exclusion of concurrent viral pneumonia circulation during the SARS-CoV-2 epidemic prevented from parallel evaluation in this regard [28]. Although to our knowledge this is the first time that these alterations in NK cell subsets and function are reported during primary viral pneumonia, future work will need to verify uniqueness of this phenomenon.…”

Section: Discussionmentioning

confidence: 98%

“…Disease severity was defined based on the need for oxygen support during the whole hospital stay until discharge. According to a modified WHO clinical progression scale [28], patients were grouped according to their need for inspiratory oxygen fraction support, as judged by the PLOS PATHOGENS clinical team physicians, into the following categories: Grade 1, from 24% to �60% (WHO 4-5); Grade 2, 60% to non-invasive ventilation (WHO 6); Grade 3, mechanical ventilation requirements (WHO 7-9).…”

Section: Patientsmentioning

confidence: 99%

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Extensive activation, tissue trafficking, turnover and functional impairment of NK cells in COVID-19 patients at disease onset associates with subsequent disease severity

et al. 2021

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The SARS-CoV-2 infection causes severe respiratory involvement (COVID-19) in 5–20% of patients through initial immune derangement, followed by intense cytokine production and vascular leakage. Evidence of immune involvement point to the participation of T, B, and NK cells in the lack of control of virus replication leading to COVID-19. NK cells contribute to early phases of virus control and to the regulation of adaptive responses. The precise mechanism of NK cell dysregulation is poorly understood, with little information on tissue margination or turnover. We investigated these aspects by multiparameter flow cytometry in a cohort of 28 patients hospitalized with early COVID-19. Relevant decreases in CD56brightCD16+/- NK subsets were detected, with a shift of circulating NK cells toward more mature CD56dimCD16+KIR+NKG2A+ and “memory” KIR+CD57+CD85j+ cells with increased inhibitory NKG2A and KIR molecules. Impaired cytotoxicity and IFN-γ production were associated with conserved expression of natural cytotoxicity receptors and perforin. Moreover, intense NK cell activation with increased HLA-DR and CD69 expression was associated with the circulation of CD69+CD103+ CXCR6+ tissue-resident NK cells and of CD34+DNAM-1brightCXCR4+ inflammatory precursors to mature functional NK cells. Severe disease trajectories were directly associated with the proportion of CD34+DNAM-1brightCXCR4+ precursors and inversely associated with the proportion of NKG2D+ and of CD103+ NK cells. Intense NK cell activation and trafficking to and from tissues occurs early in COVID-19, and is associated with subsequent disease progression, providing an insight into the mechanism of clinical deterioration. Strategies to positively manipulate tissue-resident NK cell responses may provide advantages to future therapeutic and vaccine approaches.

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Section: Discussionmentioning

confidence: 98%

Section: Patientsmentioning

confidence: 99%

Extensive activation, tissue trafficking, turnover and functional impairment of NK cells in COVID-19 patients at disease onset associates with subsequent disease severity

et al. 2021

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“…As many microorganisms in the agricultural setting also have clinical significance, we can begin to reconcile agricultural findings with clinical research. This is especially important now as we begin to explore novel SARS-CoV2 and its interaction with polymicrobial communities in the lung that are made up of bacterial and fungal organisms [ 97 ].…”

Section: Discussionmentioning

confidence: 99%

Let’s Get Physical: Bacterial-Fungal Interactions and Their Consequences in Agriculture and Health

Steffan

Venkatesh

Keller

2020

JoF

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Fungi serve as a biological scaffold for bacterial attachment. In some specialized interactions, the bacteria will invade the fungal host, which in turn provides protection and nutrients for the bacteria. Mechanisms of the physical interactions between fungi and bacteria have been studied in both clinical and agricultural settings, as discussed in this review. Fungi and bacteria that are a part of these dynamic interactions can have altered growth and development as well as changes in microbial fitness as it pertains to antibiotic resistance, nutrient acquisition, and microbial dispersal. Consequences of these interactions are not just limited to the respective microorganisms, but also have major impacts in the health of humans and plants alike. Examining the mechanisms behind the physical interactions of fungi and bacteria will provide us with an understanding of multi-kingdom community processes and allow for the development of therapeutic approaches for disease in both ecological settings.

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“…The genetic diversity of SARS-CoV-2 has been extensively studied, evidencing the presence of recurrent mutations across the world (Takahiko Koyama et al; Laamarti et al 2020; van Dorp et al 2020), their impact on pathogenicity and transmissibility of the virus (Korber et al 2020; Li et al 2020; Toyoshima et al 2020; Volz et al 2020), and on the role of mutations in the development of new vaccines (Dearlove et al 2020). In addition to SARS-CoV-2 mutations, co-infection with other pathogens may be associated with poor clinical outcomes, although these rates appear to be limited (Calcagno et al 2020; Kim et al 2020; Nowak et al 2020; Peddu et al 2020).…”

Section: Introductionmentioning

confidence: 99%

Genomic Epidemiology of SARS-CoV-2 in Esteio, Rio Grande do Sul, Brazil

Franceschi

Caldana

Mayer

et al. 2021

Preprint

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Brazil is the third country most affected by Covid-19 pandemic. In spite of this, viral evolution in municipality resolution is poorly understood in Brazil and it is crucial to understand the epidemiology of viral spread. We identified four main circulating lineages in Esteio (Southern Brazil) and their relationship with global, national and regional lineages using phylogenetics and phylodynamics inferences from 21 SARS-CoV-2 genome sequences. We provided a comprehensive view of viral mutations from a time- and age-representative sampling from May to October 2020, in Esteio (RS, Brazil), highlighting two frequent mutations in Spike glycoprotein (D614G and V1176F), an emergent mutation (E484K) in Spike Receptor Binding Domain (RBD) characteristic of the South African lineage B.1.351, and the adjacent replacement of 2 amino acids in Nucleocapsid phosphoprotein (R203K and G204R). A significant viral diversity was evidenced with the identification of 80 different SNPs. The E484K replacement was found in two genomes (9.5%) from samples obtained in mid-October, which is to our best knowledge the earliest description of E484K harboring SARS-CoV-2 in South Brazil. This mutation identified in a small municipality from the RS state demonstrates that it was probably widely distributed in the Brazilian territory, but went unnoticed so far by the lack of genomic surveillance in Brazil. The introduction of E484K mutants shows temporal correlation with later increases in new cases in our state. Importantly, since it has been associated with immune evasion and enhanced interaction with hACE-2, lineages containing this substitution must be the subject of intense surveillance. Our date demonstrates multiple introductions of the most prevalent lineages (B.1.1.33 and B.1.1.248) and the major role of community transmission in viral spreading and the establishment of Brazilian lineages. This represents an important contribution to the epidemiology of SARS-CoV-2.

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Co-infection with other respiratory pathogens in COVID-19 patients

Cited by 52 publications

References 6 publications

Extensive activation, tissue trafficking, turnover and functional impairment of NK cells in COVID-19 patients at disease onset associates with subsequent disease severity

Extensive activation, tissue trafficking, turnover and functional impairment of NK cells in COVID-19 patients at disease onset associates with subsequent disease severity

Let’s Get Physical: Bacterial-Fungal Interactions and Their Consequences in Agriculture and Health

Genomic Epidemiology of SARS-CoV-2 in Esteio, Rio Grande do Sul, Brazil

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