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10th Anniversary of Pathogens—Emerging and Re-emerging Viral Pathogens in a Pandemic World

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A special issue of Pathogens (ISSN 2076-0817). This special issue belongs to the section "Viral Pathogens".

Deadline for manuscript submissions: closed (31 December 2022) | Viewed by 17416

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Special Issue Editor

Dr. Anna Honko

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Guest Editor

Apriori Bio, Cambridge, MA, USA
Interests: filoviruses; emerging viruses; aerobiology; animal model development; medical countermeasures to hazard group 4 viruses; survival and inactivation of hazard group 4 viruses
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The year 2022 marks the 10th anniversary of the journal Pathogens. We are delighted and proud to celebrate with a series of Special Issues and events. We would like to express our sincerest thanks to our innumerable readers, authors, anonymous peer reviewers, editors, and all others who have worked in some way for the journal and made substantial contributions over the years. Reaching this landmark would not have been possible without your support.

To mark this important milestone, we have launched a dedicated Special Issue entitled “10th Anniversary of Pathogens—Emerging and Re-emerging Viral Pathogens in a Pandemic World”, which is now open for submissions.

We have been living in the new era of a pandemic world, and we would like to embrace and represent the research into many of these viral diseases that can lead to the occurrence of pandemics. Emerging viral diseases are those that have not been previously recognized within a particular geography or population, many of which are zoonoses and frequently involve arthropod vectors. In these cases, the emergence or re-emergence of these pathogens may be due to the increased expansion of humans into previously austere wilderness regions, or the changes in climate that have expanded the range of many pathogen vectors. In addition to the current coronavirus pandemic, other examples of emerging and re-emerging diseases include major outbreaks of Ebola virus, MERS virus, the original SARS virus as well as Zika virus, Hendra and Nipah viruses, hantaviruses, West Nile virus, and avian influenza viruses, among others. Many of these diseases are caused by viral pathogens that are studied under increased levels of containment. This Special Issue will consider any research article that has focused on emerging or re-emerging viral pathogens, from basic research on host-pathogen interactions and immune responses to viral pathogens to possible application, i.e., potential treatments or vaccines.

Dr. Anna Honko
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Pathogens is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

emerging diseases
viral pathogens
Ebola virus
Marburg virus
Sudan virus
Lassa virus
Zika virus
MERS
SARS
Hendra virus
Nipah virus
H5N1
H1N1
H7N9
avian influenza
West Nile virus
encephalitis virus
hemorrhagic fever virus

Published Papers (7 papers)

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Research

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11 pages, 772 KiB

Open AccessArticle

In Patients Hospitalized for Community-Acquired Pneumonia, SARS-CoV-2 Is Associated with Worse Clinical Outcomes When Compared to Influenza

by Jeffrey Spindel, Stephen Furmanek, Thomas Chandler, Julio A. Ramirez and Rodrigo Cavallazzi

Pathogens 2023, 12(4), 571; https://doi.org/10.3390/pathogens12040571 - 07 Apr 2023

Cited by 1 | Viewed by 1229

Abstract

SARS-CoV-2 and influenza are primary causes of viral community-acquired pneumonia (CAP). Both pathogens have exhibited high transmissibility and are recognized causes of pandemics. Controversy still exists regarding the clinical outcomes between patients hospitalized with CAP due to these viruses. This secondary analysis identified patients with either influenza or SARS-CoV-2 infections from three cohorts of patients hospitalized for CAP. Clinical outcomes between patients with CAP due to influenza or due to SARS-CoV-2 were evaluated. Primary outcomes included length of stay and in-hospital mortality. To account for population differences between cohorts, each case of influenza CAP was matched to two controls with SARS-CoV-2 CAP. Matching criteria included sex, age, and nursing home residency. Stratified cox-proportional hazards regression or conditional logistic regression were used where appropriate. A total of 259 patients with influenza CAP were matched to two controls with SARS-CoV-2 CAP, totaling to 518 controls. Patients with SARS-CoV-2 CAP were 2.23 times more likely to remain hospitalized at any point in time (95% confidence interval: 1.77–2.80), and had 3.84 times higher odds of dying in-hospital (95% confidence interval: 1.91–7.76) when compared to patients with influenza CAP. After matching and adjusting for confounding variables, patients admitted with SARS-CoV-2 CAP had consistently worse outcomes in comparison to their influenza CAP counterparts. This information can help clinicians decide on the level of care needed for patients with confirmed infections due to these pathogens. Additionally, estimates of disease burden can inform individuals at-risk for poor clinical outcomes, and further highlight the importance of effective preventative strategies. Full article

(This article belongs to the Special Issue 10th Anniversary of Pathogens—Emerging and Re-emerging Viral Pathogens in a Pandemic World)

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17 pages, 2387 KiB

Open AccessArticle

Integration of Epidemiological and Genomic Data to Investigate H5N1 HPAI Outbreaks in Northern Italy in 2021–2022

by Diletta Fornasiero, Alice Fusaro, Bianca Zecchin, Matteo Mazzucato, Francesca Scolamacchia, Grazia Manca, Calogero Terregino, Tiziano Dorotea and Paolo Mulatti

Pathogens 2023, 12(1), 100; https://doi.org/10.3390/pathogens12010100 - 06 Jan 2023

Cited by 2 | Viewed by 2246

Abstract

Between October 2021 and April 2022, 317 outbreaks caused by highly pathogenic avian influenza (HPAI) H5N1 viruses were notified in poultry farms in the northeastern Italian regions. The complete genomes of 214 strains were used to estimate the genetic network based on the similarity of the viruses. An exponential random graph model (ERGM) was used to assess the effect of ‘at-risk contacts’, ‘same owners’, ‘in-bound/out-bound risk windows overlap’, ‘genetic differences’, ‘geographic distances’, ‘same species’, and ‘poultry company’ on the probability of observing a link within the genetic network, which can be interpreted as the potential propagation of the epidemic via lateral spread or a common source of infection. The variables ‘same poultry company’ (Est. = 0.548, C.I. = [0.179; 0.918]) and ‘risk windows overlap’ (Est. = 0.339, C.I. = [0.309; 0.368]) were associated with a higher probability of link formation, while the ‘genetic differences’ (Est. = −0.563, C.I. = [−0.640; −0.486]) and ‘geographic distances’ (Est. = −0.058, C.I. = [−0.078; −0.038]) indicated a reduced probability. The integration of epidemiological data with genomic analyses allows us to monitor the epidemic evolution and helps to explain the dynamics of lateral spreads casting light on the potential diffusion routes. The 2021–2022 epidemic stresses the need to further strengthen the biosecurity measures, and to encourage the reorganization of the poultry production sector to minimize the impact of future epidemics. Full article

(This article belongs to the Special Issue 10th Anniversary of Pathogens—Emerging and Re-emerging Viral Pathogens in a Pandemic World)

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17 pages, 2641 KiB

Open AccessArticle

Phylogenetic Inference of the 2022 Highly Pathogenic H7N3 Avian Influenza Outbreak in Northern Mexico

by Roberto Navarro-Lopez, Wanhong Xu, Ninnet Gomez-Romero, Lauro Velazquez-Salinas and Yohannes Berhane

Pathogens 2022, 11(11), 1284; https://doi.org/10.3390/pathogens11111284 - 01 Nov 2022

Cited by 4 | Viewed by 1941

Abstract

The Mexican lineage H7N3 highly pathogenic avian influenza virus (HPAIV) has persisted in Mexican poultry since its first isolation in 2012. To date, the detection of this virus has gradually expanded from the initial one state to 18 states in Mexico. Despite the HPAIV H7N3 outbreak occurring yearly, the transmission pathways have never been studied, disallowing the establishment of effective control measures. We used a phylogenetic approach to unravel the transmission pathways of 2022 H7N3 HPAIVs in the new outbreak areas in Northern Mexico. We present genetic data of H7N3 viruses produced from 18 poultry farms infected in the spring of 2022. Our results indicate that the virus responsible for the current outbreak in Northern Mexico evolved from the Mexican lineage H7N3 HPAIV discovered in 2012. In the current outbreak, we identified five clusters of infection with four noticeably different genetic backgrounds. It is a cluster IV-like virus that was transmitted into one northern state causing an outbreak, then spreading to another neighboring northern state, possibly via a human-mediated mechanical transmission mechanism. The long-distance transmission event highlights the necessity for the more rigorous enforcement of biosafety measures in outbreaks. Additionally, we examined the evolutionary processes shaping the viral genetic and antigenic diversities. It is imperative to enhance active surveillance to include birds, the environment, and humans to detect HPAI in domestic poultry at an earlier point and eliminate it. Full article

(This article belongs to the Special Issue 10th Anniversary of Pathogens—Emerging and Re-emerging Viral Pathogens in a Pandemic World)

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17 pages, 1603 KiB

Open AccessArticle

Ultraviolet-C Irradiation, Heat, and Storage as Potential Methods of Inactivating SARS-CoV-2 and Bacterial Pathogens on Filtering Facepiece Respirators

by Rhodri Harfoot, Deborah B. Y. Yung, William A. Anderson, Cervantée E. K. Wild, Nicolene Coetzee, Leonor C. Hernández, Blair Lawley, Daniel Pletzer, José G. B. Derraik, Yvonne C. Anderson and Miguel E. Quiñones-Mateu

Pathogens 2022, 11(1), 83; https://doi.org/10.3390/pathogens11010083 - 10 Jan 2022

Cited by 5 | Viewed by 4189

Abstract

The arrival of SARS-CoV-2 to Aotearoa/New Zealand in February 2020 triggered a massive response at multiple levels. Procurement and sustainability of medical supplies to hospitals and clinics during the then upcoming COVID-19 pandemic was one of the top priorities. Continuing access to new personal protective equipment (PPE) was not guaranteed; thus, disinfecting and reusing PPE was considered as a potential alternative. Here, we describe part of a local program intended to test and implement a system to disinfect PPE for potential reuse in New Zealand. We used filtering facepiece respirator (FFR) coupons inoculated with SARS-CoV-2 or clinically relevant multidrug-resistant pathogens (Acinetobacter baumannii Ab5075, methicillin-resistant Staphylococcus aureus USA300 LAC and cystic-fibrosis isolate Pseudomonas aeruginosa LESB58), to evaluate the potential use of ultraviolet-C germicidal irradiation (UV-C) or dry heat treatment to disinfect PPE. An applied UV-C dose of 1000 mJ/cm² was sufficient to completely inactivate high doses of SARS-CoV-2; however, irregularities in the FFR coupons hindered the efficacy of UV-C to fully inactivate the virus, even at higher UV-C doses (2000 mJ/cm²). Conversely, incubating contaminated FFR coupons at 65 °C for 30 min or 70 °C for 15 min, was sufficient to block SARS-CoV-2 replication, even in the presence of mucin or a soil load (mimicking salivary or respiratory secretions, respectively). Dry heat (90 min at 75 °C to 80 °C) effectively killed 10⁶ planktonic bacteria; however, even extending the incubation time up to two hours at 80 °C did not completely kill bacteria when grown in colony biofilms. Importantly, we also showed that FFR material can harbor replication-competent SARS-CoV-2 for up to 35 days at room temperature in the presence of a soil load. We are currently using these findings to optimize and establish a robust process for decontaminating, reusing, and reducing wastage of PPE in New Zealand. Full article

(This article belongs to the Special Issue 10th Anniversary of Pathogens—Emerging and Re-emerging Viral Pathogens in a Pandemic World)

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Review

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15 pages, 977 KiB

Open AccessReview

Clinical Outcome of Coronavirus Disease 2019 in Patients with Primary Antibody Deficiencies

by Tomas Milota, Jitka Smetanova and Jirina Bartunkova

Pathogens 2023, 12(1), 109; https://doi.org/10.3390/pathogens12010109 - 09 Jan 2023

Cited by 3 | Viewed by 2212

Abstract

In 2019, the novel coronavirus, SARS-CoV-2, caused a worldwide pandemic, affecting more than 630 million individuals and causing 6.5 million deaths. In the general population, poorer outcomes have been associated with older age, chronic lung and cardiovascular diseases, and lymphopenia, highlighting the important role of cellular immunity in the immune response against SARS-CoV-2. Moreover, SARS-CoV-2 variants may have a significant impact on disease severity. There is a significant overlap with complications commonly found in inborn errors of immunity (IEI), such as primary antibody deficiencies. The results of various studies have provided ambiguous findings. Several studies identified risk factors in the general population with a minor impact on SARS-CoV-2 infection. However, other studies have found a significant contribution of underlying immunodeficiency and immune-system dysregulation to the disease course. This ambiguity probably reflects the demographic differences and viral evolution. Impaired antibody production was associated with prolonged viral shedding, suggesting a critical role of humoral immunity in controlling SARS-CoV-2 infection. This may explain the poorer outcomes in primary antibody deficiencies compared to other IEIs. Understanding coronavirus disease 2019 (COVID-19) pathogenesis and identifying risk factors may help us identify patients at high risk of severe COVID-19 for whom preventive measures should be introduced. Full article

(This article belongs to the Special Issue 10th Anniversary of Pathogens—Emerging and Re-emerging Viral Pathogens in a Pandemic World)

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19 pages, 1587 KiB

Open AccessEditor’s ChoiceReview

Many Ways to Communicate—Crosstalk between the HBV-Infected Cell and Its Environment

by Annika Jasmin Walter, Maarten A. van de Klundert and Stephanie Jung

Pathogens 2023, 12(1), 29; https://doi.org/10.3390/pathogens12010029 - 24 Dec 2022

Cited by 1 | Viewed by 2624

Abstract

Chronic infection with the hepatitis B virus (HBV) affects an estimated 257 million people worldwide and can lead to liver diseases such as cirrhosis and liver cancer. Viral replication is generally considered not to be cytopathic, and although some HBV proteins may have direct carcinogenic effects, the majority of HBV infection-related disease is related to chronic inflammation resulting from disrupted antiviral responses and aberrant innate immune reactions. Like all cells, healthy and HBV-infected cells communicate with each other, as well as with other cell types, such as innate and adaptive immune cells. They do so by both interacting directly and by secreting factors into their environment. Such factors may be small molecules, such as metabolites, single viral proteins or host proteins, but can also be more complex, such as virions, protein complexes, and extracellular vesicles. The latter are small, membrane-enclosed vesicles that are exchanged between cells, and have recently gained a lot of attention for their potential to mediate complex communication and their potential for therapeutic repurposing. Here, we review how HBV infection affects the communication between HBV-infected cells and cells in their environment. We discuss the impact of these interactions on viral persistence in chronic infection, as well as their relation to HBV infection-related pathology. Full article

(This article belongs to the Special Issue 10th Anniversary of Pathogens—Emerging and Re-emerging Viral Pathogens in a Pandemic World)

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Other

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7 pages, 1175 KiB

Open AccessBrief Report

Serological Evidence of Orthopoxvirus Infection in Neotropical Primates in Brazil

by Filipe Vieira Santos de Abreu, Kamila Lorene Soares Rocha, Ramon Silva-Oliveira, Mariana Viana Macedo, Thamires Gabriele Macedo Silva, Maria Eduarda Gonçalves-dos-Santos, Cirilo Henrique de Oliveira, Sandy Micaele Aquino-Teixeira, Vinícius de Oliveira Ottone, Alex Junio Jardim da Silva, Ronaldo Medeiros dos Santos, Aline Tátila-Ferreira, Marco Antônio Barreto de Almeida, Edmilson dos Santos, Jáder da Cruz Cardoso, Aline Alves Scarpellini Campos, George Rego Albuquerque, Anaiá da Paixão Sevá, Bergmann Morais Ribeiro, Danilo Simonini Teixeira, Fabrício Souza Campos, Ana Cláudia Franco, Paulo Michel Roehe, Giliane de Souza Trindade and Danilo Bretas de Oliveira Show full author list Hide full author list

Pathogens 2022, 11(10), 1167; https://doi.org/10.3390/pathogens11101167 - 10 Oct 2022

Cited by 2 | Viewed by 2069

Abstract

The genus Orthopoxvirus (OPXV) of the family Poxviridae comprises several viruses that are capable of infecting a wide range of hosts. One of the most widespread OPXVs is the Vaccinia virus (VACV), which circulates in zoonotic cycles in South America, especially in Brazil, infecting domestic and wild animals and humans and causing economic losses as well as impacting public health. Despite this, little is known about the presence and/or exposure of neotropical primates to orthopoxviruses in the country. In this study, we report the results of a search for evidence of OPVX infections in neotropical free-living primates in the state of Minas Gerais, southeast Brazil. The sera or liver tissues of 63 neotropical primates were examined through plaque reduction neutralization tests (PRNT) and real-time PCR. OPXV-specific neutralizing antibodies were detected in two sera (4.5%) from Callithrix penicillata, showing 55% and 85% reduction in plaque counts, evidencing their previous exposure to the virus. Both individuals were collected in urban areas. All real-time PCR assays were negative. This is the first time that evidence of OPXV exposure has been detected in C. penicillata, a species that usually lives at the interface between cities and forests, increasing risks of zoonotic transmissions through spillover/spillback events. In this way, studies on the circulation of OPXV in neotropical free-living primates are necessary, especially now, with the monkeypox virus being detected in new regions of the planet. Full article

(This article belongs to the Special Issue 10th Anniversary of Pathogens—Emerging and Re-emerging Viral Pathogens in a Pandemic World)

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