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

Deadline for manuscript submissions: closed (15 March 2023) | Viewed by 49343

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Special Issue Editor

Dr. Eleonora Cella

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Guest Editor

Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, USA
Interests: molecular epidemiology; genomic epidemiology; phylogenomics; microbiology; virology; phylogeny; bioinformatics; molecular microbiology; infectious diseases; public health
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

In recent years, a significant increase in the emergence of infectious diseases has been observed. Several of these pathogens, such as different betacoronaviruses, arboviruses (Dengue Chikungunya and Zika virus), and Ebola viruses, have important public health implications. This increased incidence of infectious diseases is a complex interface of host–pathogen–environment and is influenced by international trade and the changing distribution of disease vectors.

Zoonotic viral diseases are maintained in complex life cycles in nature through biological transmission between reservoir species and susceptible vertebrate hosts. These cycles usually remain undetected until humans encroach on a natural focus or the virus escapes this focus via a secondary vector or vertebrate host as a result of some ecologic change. Diseases then emerge in the human population or naïve animal population, from areas where they never have been observed before, suddenly appearing with a newly described pathogenesis (emerging disease), or already known diseases and their pathogens suddenly reappear in areas where they were not recorded for a long period of time, sometimes with a known epidemic pattern or in a larger proportion or increased pathogenicity (reemerging disease).

Emerging and reemerging zoonotic diseases caused by betacoronaviruses (e.g., SARS-CoV-2, MERS, SARS), arboviruses (e.g., yellow fever, dengue, and chikungunya), and filoviruses (e.g., Ebola and Marburg) altogether represent an enormous challenge and growing public health worldwide, given the increasing mobility of the population (travel and trade) and the pathogen genetic plasticity and evolution.

Etiological agents of zoonotic viral diseases generally incubate asymptomatically in wild reservoirs and then follow different and often complex transmission mechanisms to reach human populations and other permissive animal hosts. Reservoirs and host vertebrates often have vast ranges, which pose especially big challenges to the developing world where their study and related public health programs are often limited. During the worldwide pandemic of SARS-CoV-2 with the emergence of VoCs (variants of concern), the repetitive Ebola outbreaks in Africa and Zika virus outbreaks in South America, and their pandemic extensions, biosurveillance and preparedness are implemented worldwide, demonstrating the global concern and growing awareness of the need for research and intervention in zoonotic diseases.

Authors are invited to submit original research articles, clinical studies, and review articles in areas of viral zoonotic diseases.

Potential topics include, but are not limited to:

Biosurveillance of pathogen wildlife, One Health approach;
Spatial and temporal epidemiology: unveiling hazard and vulnerability;
Virus genetics (phylogenetics, next-generation sequencing), multiple infection: understanding the molecular basis of the pathogen complex;
Genetics and ecology of reservoirs and vectors: the host–pathogen complex;
Pathogenesis: infection patterns (natural, chronic, subclinical, etc.) and mechanism of transmission (direct, indirect, etc.).

Dr. Eleonora Cella
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 2200 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

epidemiology
molecular epidemiology
viruses
outbreak
viral genetics
biosurvelliance
infectious diseases

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Published Papers (14 papers)

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Research

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18 pages, 3157 KiB

Open AccessArticle

Evolution of Rabies Virus Isolates: Virulence Signatures and Effects of Modulation by Neutralizing Antibodies

by Juliana Amorim Conselheiro, Gisely Toledo Barone, Sueli Akemi Taniwaki Miyagi, Sheila Oliveira de Souza Silva, Washington Carlos Agostinho, Joana Aguiar and Paulo Eduardo Brandão

Pathogens 2022, 11(12), 1556; https://doi.org/10.3390/pathogens11121556 - 19 Dec 2022

Cited by 4 | Viewed by 3560

Abstract

Lyssavirus rabies (RABV) is an RNA virus and, therefore, is subject to mutations due to low RNA polymerase replication fidelity, forming a population structure known as a viral quasispecies, which is the core of RNA viruses’ adaptive strategy. Under new microenvironmental conditions, the fittest populations are selected, and the study of this process on the molecular level can help determine molecular signatures related to virulence. Our aim was to survey gene signatures on nucleoprotein and glycoprotein genes that might be involved in virulence modulation during the in vitro evolution of RABV lineages after serial passages in a neuronal cell system with or without the presence of neutralizing antibodies based on replicative fitness, in vivo neurotropism and protein structure and dynamics. The experiments revealed that amino acids at positions 186 and 188 of the glycoprotein are virulence factors of Lyssavirus rabies, and site 186 specifically might allow the attachment to heparan as a secondary cell receptor, while polymorphism at position 333 might allow the selection of escape mutants under suboptimal neutralizing antibodies titers. Full article

(This article belongs to the Special Issue Emerging and Re-emerging Viral Infectious Diseases)

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15 pages, 1428 KiB

Open AccessArticle

Intestinal Fatty Acid Binding Protein (I-FABP) as a Prognostic Marker in Critically Ill COVID-19 Patients

by Maciej Tyszko, Małgorzata Lipińska-Gediga, Anna Lemańska-Perek, Katarzyna Kobylińska, Waldemar Gozdzik and Barbara Adamik

Pathogens 2022, 11(12), 1526; https://doi.org/10.3390/pathogens11121526 - 13 Dec 2022

Cited by 14 | Viewed by 3781

Abstract

Gastrointestinal symptoms are common in critically ill COVID-19 patients. There is currently no generally recognized method of assessing gastrointestinal injury in unconscious or sedated intensive care unit (ICU) patients. I-FABP (intestinal fatty acid binding protein) and citrulline have previously been studied as potential biomarkers of enterocyte damage in various gastrointestinal tract diseases, and changes in the levels of these markers may reflect intestinal wall damage in COVID-19. Patients with critical COVID-19, with diagnosed sepsis, or septic shock requiring ICU treatment were included in the study. Blood samples for citrulline and I-FABP were taken daily from day 1 to 5. I-FABP levels were significantly higher in patients who eventually died from COVID-19 than in survivors, and the optimal I-FABP cut-off point for predicting 28-day mortality was 668.57 pg/mL (sensitivity 0.739, specificity 0.765). Plasma levels of I-FABP, but not citrulline, were associated with significantly higher mortality and appeared to be a predictor of poor outcome in multivariate logistic regression analysis. In conclusion, I-FABP seems to be an effective prognostic marker in critically ill COVID-19 patients. Assessing mortality risk based on intestinal markers may be helpful in making clinical decisions regarding the management of intestinal injury, imaging diagnostics, and potential surgical interventions. Full article

(This article belongs to the Special Issue Emerging and Re-emerging Viral Infectious Diseases)

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15 pages, 1161 KiB

Open AccessArticle

Tomography and Prognostic Indices in the State of the Art of Evaluation in Hospitalized Patients with COVID-19 Pneumonia

by Sergio Críales-Vera, Huitzilihuitl Saucedo-Orozco, Pedro Iturralde-Torres, Gustavo Martínez-Mota, Estefanía Dávila-Medina, Verónica Guarner-Lans, Linaloe Manzano-Pech, Israel Pérez-Torres and María Elena Soto

Pathogens 2022, 11(11), 1281; https://doi.org/10.3390/pathogens11111281 - 1 Nov 2022

Cited by 1 | Viewed by 1887

Abstract

Evaluation in medical emergencies of COVID-19 patients represents a challenge to regulate preventive and timely management. There are key imaging and laboratory tools to classify the severity. The aim of the study was to evaluate the chest CT score performance and prognostic indices in COVID-19 patients to predict the progression to critical illness. This was a retrospective study between run between April and December 2020, in which 109 patients were included. Patients of any age and gender and who required hospitalization due to a confirmed COVID-19 diagnosis by RT-PCR and chest CT and laboratory were analyzed. In 75% of them, there was at least one comorbidity, and 30% developed critical illness, and the average mortality was 10%. In 49.5%, there was a CORADS-5 on admission, and in 50%, there was a peripheral distribution of the interstitial infiltrate in the left lower lobe. The risk factors were FiO₂, CT score > 18, and the NRL index. The combination of the high-risk Quick COVID-19 Severity Index (qCSI) plus CT score > 18 indices was the best prediction index for the development of a critical condition. The combined use of indices in infected COVID-19 patients showed diagnostic accuracy and predicted severity. Imaging and the laboratory tests are key tools independent of the wave of recurrence. Full article

(This article belongs to the Special Issue Emerging and Re-emerging Viral Infectious Diseases)

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7 pages, 660 KiB

Open AccessArticle

Reemerging Influenza Virus Infections during the Dominance of the Omicron SARS-CoV-2 Variant in Mexico

by Mónica Ríos-Silva, Xóchitl Trujillo, Miguel Huerta, Verónica Benites-Godínez, José Guzmán-Esquivel, Jaime Alberto Bricio-Barrios, Oliver Mendoza-Cano, Agustín Lugo-Radillo and Efrén Murillo-Zamora

Pathogens 2022, 11(10), 1181; https://doi.org/10.3390/pathogens11101181 - 13 Oct 2022

Cited by 4 | Viewed by 2559

Abstract

The burden of influenza in Mexico has been high. We aimed to characterize its epidemiological patterns before and during the coronavirus disease 2019 (COVID-19) pandemic. A retrospective cohort study was conducted and 5652 PCR-confirmed cases of influenza (October 2019–April 2022) were analyzed. The highest incidence (144 per million) was observed in December 2019 and rapidly decreased right before the start of the pandemic (February 2020). No cases were documented in the 2020–2021 season, and infections reemerged at a low level (8 per million) in December 2021. The case-fatality rates were around 5% in both seasons (p = 0.591). The dominant strains were AH1N1 and AH3N2 in the 2019–2020 and 2021–2022 seasons, respectively. In multiple analysis, males and older patients were at increased risk of a fatal outcome. Flu vaccination and infection by B lineages (vs. AH1N1) showed a protective effect. Our results suggest that the spread of the influenza virus reemerged in the 2021–2022 season when the SARS-CoV-2 Omicron variant (B.1.1.529) was dominant. Efforts focusing on the prevention of transmission of respiratory viral pathogens, together with flu vaccination, may be useful to reduce the risk of an influenza outbreak. Full article

(This article belongs to the Special Issue Emerging and Re-emerging Viral Infectious Diseases)

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11 pages, 2158 KiB

Open AccessArticle

Downregulation of sCD40 and sCTLA4 in Recovered COVID-19 Patients with Comorbidities

by Gwendolyne Méndez-Frausto, Susana Godina-González, César E. Rivas-Santiago, Edna Nungaray-Anguiano, Gretel Mendoza-Almanza, Bruno Rivas-Santiago, Carlos E. Galván-Tejada and Irma E. Gonzalez-Curiel

Pathogens 2022, 11(10), 1128; https://doi.org/10.3390/pathogens11101128 - 30 Sep 2022

Viewed by 1919

Abstract

The aim of this study was to analyze molecules associated with regulatory immune response in unvaccinated, recovered COVID-19 patients with and without diabetes mellitus (DM) and hypertension (HTN). We determined anti-SARS-CoV-2 nucleocapsid IgG in plasma by electrochemiluminescence immunoassay. The levels of sCD40, TGF-ß, IL-10, and sCTLA-4 were assessed by ELISA in the serum of the subjects, as well as in healthy donors. We observed that only half of the subjects in the non-comorbid group produced antibodies, whereas all subjects in comorbid groups were IgG-positive for the anti-SARS-CoV-2 nucleocapsid. High levels of sCTL-4 were observed in the non-comorbid group, and the level of IL-10 was observed to increase in seropositive subjects without comorbidities. TGF-ß concentration was similar in all groups studied. Finally, sCD40 decreased in the comorbid group. In conclusion, our results suggest that comorbidities such as DM and HTN alter the production of co-stimulatory inhibitory molecules sCTLA-4 and sCD40 in subjects recovering from mild COVID-19. The alterations observed here were independent of seropositivity, suggesting an effective humoral immune response against COVID-19 separate from the levels of co-stimulatory inhibitory molecules. Full article

(This article belongs to the Special Issue Emerging and Re-emerging Viral Infectious Diseases)

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11 pages, 527 KiB

Open AccessArticle

Prevalence and Genotyping of HPV in Oral Squamous Cell Carcinoma in Northern Brazil

by Silvio Augusto Fernandes de Menezes, Yasmim Marçal Soares Miranda, Yngrid Monteiro da Silva, Tábata Resque Beckmann Carvalho, Flávia Rayane Souza Alves, Rodrigo Vellasco Duarte Silvestre, Aldemir Branco Oliveira-Filho, Tatiany Oliveira de Alencar Menezes, Ricardo Roberto de Souza Fonseca, Rogério Valois Laurentino and Luiz Fernando Almeida Machado

Pathogens 2022, 11(10), 1106; https://doi.org/10.3390/pathogens11101106 - 27 Sep 2022

Cited by 2 | Viewed by 2156

Abstract

Highly oncogenic human papillomavirus (HPV) is well known to be associated with and a risk factor for various types of oral carcinomas such as oral squamous cell carcinoma (OSCC). The aim of this study was to evaluate and describe the HPV-induced OSCC prevalence and genotyping in the city of Belém, northern Brazil. This cross-sectional study features 101 participants who attended an oral pathology referral center in a dental college looking for diagnoses of oral lesions (OL). After signing the consent term and meeting the inclusion criteria, all participants went through a sociodemographic and epidemiological questionnaire. Then, OL were collected by excisional or incisional biopsy depending on OL size; after that, OL tissues were preserved in paraffin blocks to histopathological diagnoses. Afterwards, paraffin blocks were divided into benign and malignant/premalignant lesions based on the classification of potentially malignant disorders of the oral and oropharyngeal mucosa. Then, the paraffin blocks had DNA extraction performed by the ReliaPrep FFPE gDNA Miniprep method in order to identify HPV DNA of high oncogenic risk and low oncogenic risk. Then, the viral DNA was amplified and typed using the Inno-Lipa genotyping Extra II method, and the collected data were analyzed by Chi-square and G-tests. In total, 59/101 (58.4%) OL were malignant/premalignant lesions, of which OSCC was the most prevalent with 40/59 (67.7%) and 42/101 (41.6%) benign lesions. The most common area of OL incidence was upper gingiva 46/101 (45.5%). Regarding HPV DNA detection, approximately 27/101 (26.7%) had positive results; of these, 17/59 (28.8%) were malignant/premalignant lesions, and the most prevalent genotypes detected were 16, 18, 52 and 58, while among benign lesions, 10/42 (66.6%) had HPV-positive results, and the most prevalent genotypes detected were 6, 11 and 42. Age range was the only risk factor with a significant association between HPV and OSCC presence (p-value: 0.0004). A correlation between OSCC and oral HPV among analyzed samples could not be demonstrated in our small cohort. Full article

(This article belongs to the Special Issue Emerging and Re-emerging Viral Infectious Diseases)

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12 pages, 1701 KiB

Open AccessArticle

IgA-Based Secretory Response in Tears of COVID-19 Patients: A Potential Biomarker of Pro-Inflammatory State in Course of SARS-CoV-2 Infection

by Anna Niedźwiedź, Ewa Pius-Sadowska, Miłosz Kawa, Agnieszka Kuligowska, Miłosz Parczewski, Krzysztof Safranow, Krzysztof Kozłowski, Bogusław Machaliński and Anna Machalińska

Pathogens 2022, 11(10), 1098; https://doi.org/10.3390/pathogens11101098 - 25 Sep 2022

Cited by 4 | Viewed by 2339

Abstract

Mucosal immunity, including secretory IgA (sIgA), plays an important role in the early defence against SARS-CoV-2 infection. However, a comprehensive evaluation of the local immune response in tears in relation to blood antibody reservoirs has not yet been conducted. A total of 179 symptomatic laboratory-confirmed COVID-19 patients were included in this single-centre study. Conjunctival swabs were analysed by a reverse transcription polymerase chain reaction for the detection of SARS-CoV-2 RNA. In parallel, tear samples collected by Schirmer test strips and plasma samples were analysed by ELISA to detect anti-S1 IgA levels. The concentrations of selected inflammatory cytokines in tears were determined by a magnetic bead assay. Anti-SARS-CoV-2 sIgA was present in the tears of 81 (45.25%) confirmed COVID-19 patients, and the tear IgA levels were correlated with the plasma IgA levels (Rs = +0.29, p = 0.0003). SARS-CoV-2 RNA in the conjunctival sac was identified in 18 COVID-19 patients (10%). Positive correlations between the tear IgA level and the concentrations of several cytokines TNF-α (Rs = +0.23, p = 0.002), IL-1β (Rs = +0.25, p < 0.001), IL-2 (Rs = +0.20, p = 0.007), IL-4 (Rs = +0.16, p = 0.04), IL-5 (Rs = +0.36, p < 0.001), IL-6 (Rs = +0.32, p < 0.001), IL-8 (Rs = +0.31, p < 0.001), VEGF (Rs = +0.25, p < 0.001) and GM-CSF (Rs = +0.27, p < 0.001) were also found. Quantitative tear film-based sIgA could potentially serve as a rapid and easily accessible biomarker of external mucosal immunity to SARS-CoV-2. The concentration of sIgA is directly related to individual host immune responses to SARS-CoV-2 infection. Full article

(This article belongs to the Special Issue Emerging and Re-emerging Viral Infectious Diseases)

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11 pages, 298 KiB

Open AccessArticle

Prevalence, Diversity, and Risk Factors for Cervical HPV Infection in Women Screened for Cervical Cancer in Belém, Pará, Northern Brazil

by Jacqueline Cortinhas Monteiro, Mihoko Yamamoto Tsutsumi, Deivid Oliveira de Carvalho, Elenice do Carmo da Silva Costa, Rosimar Neris Martins Feitosa, Rogério Valois Laurentino, Ricardo Roberto de Souza Fonseca, Rodrigo Vellasco Duarte Silvestre, Aldemir Branco Oliveira-Filho and Luiz Fernando Almeida Machado

Pathogens 2022, 11(9), 960; https://doi.org/10.3390/pathogens11090960 - 24 Aug 2022

Cited by 4 | Viewed by 2703

Abstract

Background: Human papillomavirus (HPV) is the most common viral sexually transmitted infection of the reproductive tract, and cervical cancer is the most common HPV-related disease. This study estimated the prevalence, diversity of HPV genotypes, and associated risk factors in women screened for cervical cancer in northern Brazil. Methods: The cross-sectional study was conducted in Belém, Pará, in the Amazon region of Brazil, and it included 162 women who were spontaneously undergoing a Pap-smear routine. Epidemiological, sexual, and health-related information was collected by interviews, and cervical samples were collected for cytological examination and HPV-DNA detection. HPV genotypes were classified as low risk (LR) and high risk (HR) by nucleotide sequencing. Results: In total, 17.3% (28/162) of the participants had HPV-DNA, and LR-HPV was the most prevalent (71.4%). Among the 13 different types of HPV detected, HPV-11 was found most frequently (12/28; 42.9%), followed by HPV-31 (3/28; 10.7%). Of the participants with cytological alterations, HPV infection was detected in only four: two were diagnosed with low-grade squamous intraepithelial lesions (15.4%), one with atypical squamous cells of undetermined significance (7.7%), and one with atypical squamous cells, cannot exclude high-grade squamous intraepithelial lesions (7.7%). Of the 61 women who presented a normal cytology, 13 (21.3%) had positive tests for HPV infection, 4 (8.2%) of which were positive for a high-risk genotype. Conclusion: The prevalence of HPV was high in Belém, Pará, and especially in women who had normal cytology results, which suggests the need for greater screening for HPV infection in women’s primary health care. Full article

(This article belongs to the Special Issue Emerging and Re-emerging Viral Infectious Diseases)

10 pages, 1938 KiB

Open AccessArticle

WO₃ Photocatalyst Containing Copper Inactivates SARS-CoV-2 Pango Lineage A and Omicron BA.2 Variant in Visible Light and in Darkness

by Ryosuke Matsuura, Ken Maeda, Kyoji Hagiwara, Yosuke Mori, Toru Kitamura, Yasunobu Matsumoto and Yoko Aida

Pathogens 2022, 11(8), 922; https://doi.org/10.3390/pathogens11080922 - 16 Aug 2022

Cited by 6 | Viewed by 2224

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of coronavirus disease 2019, which has been a global pandemic. Since SARS-CoV-2 is transmitted through contaminated surfaces and aerosols, environmental disinfection is important to block the spread of the virus. Photocatalysts are attractive tools for virus inactivation and are widely used as air purifiers and coating materials. However, photocatalysts are inactive in the dark, and some of them need to be excited with light of a specific wavelength. Therefore, photocatalysts that can effectively inactivate SARS-CoV-2 in indoor environments are needed. Here, we show that a WO₃ photocatalyst containing copper inactivated the SARS-CoV-2 WK-521 strain (Pango lineage A) upon irradiation with white light in a time- and concentration-dependent manner. Additionally, this photocatalyst also inactivated SARS-CoV-2 in dark conditions due to the antiviral effect of copper. Furthermore, this photocatalyst inactivated not only the WK-521 strain but also the Omicron variant BA.2. These results indicate that the WO₃ photocatalyst containing copper can inactivate indoor SARS-CoV-2 regardless of the variant, in visible light or darkness, making it an effective tool for controlling the spread of SARS-CoV-2. Full article

(This article belongs to the Special Issue Emerging and Re-emerging Viral Infectious Diseases)

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12 pages, 287 KiB

Open AccessArticle

Prevalence of Transfusion-Transmitted Infections (HCV, HIV, Syphilis and Malaria) in Blood Donors: A Large-Scale Cross-Sectional Study

by Talal Alharazi, Tawfique K. Alzubiery, Jerold C. Alcantara, Husam Qanash, Abdulrahman S. Bazaid, Malik A. Altayar and Abdu Aldarhami

Pathogens 2022, 11(7), 726; https://doi.org/10.3390/pathogens11070726 - 26 Jun 2022

Cited by 11 | Viewed by 5915

Abstract

Blood plays a major role in transmitting infectious diseases such as hepatitis C virus (HCV), human immunodeficiency virus (HIV), hepatitis B virus (HBV), syphilis, malaria, and many others. Thus, this study sought to evaluate the distribution of HCV, HIV, syphilis, and malaria among blood donors in Yemen. This is a cross-sectional study, conducted on blood donors at the national center in Yemen. Blood donors’ specimens were serologically tested for the presence of anti-HCV and anti-HIV antibodies, as well as anti-Treponema pallidum, anti-Plasmodium falciparum, and anti-Plasmodium vivax. A total of 16,367 donors were included in this study. Based on the donor’s occupation, the study showed that the relative seroprevalence of anti-HCV Ab among the donors was statistically significant, and relatively high prevalence was found among military donors (2.8%). Positive HIV antibody tests were only reported in 33 male donors (0.2%), who were mostly manual workers. A remarkably high prevalence of anti-Treponema pallidum was observed among manual workers (3.1%). There was a statistically significant difference in the distribution of anti-malaria Ab based on residency and age groups. This study revealed that the prevalence of HCV, HIV, syphilis, and malaria among donors was 2.0%, 0.2%, 2.4%, and 0.7%, respectively. Further genotyping studies are necessary to provide a complete picture of the prevalence of transfusion-transmitted infections (TTIs). Full article

(This article belongs to the Special Issue Emerging and Re-emerging Viral Infectious Diseases)

15 pages, 2050 KiB

Open AccessArticle

What Is the Impact of Early and Subsequent Epidemic Characteristics on the Pre-delta COVID-19 Epidemic Size in the United States?

by Hao Lai, Yusha Tao, Mingwang Shen, Rui Li, Maosheng Zou, Leilei Zhang and Lei Zhang

Pathogens 2022, 11(5), 576; https://doi.org/10.3390/pathogens11050576 - 13 May 2022

Viewed by 2531

Abstract

It is still uncertain how the epidemic characteristics of COVID-19 in its early phase and subsequent waves contributed to the pre-delta epidemic size in the United States. We identified the early and subsequent characteristics of the COVID-19 epidemic and the correlation between these characteristics and the pre-delta epidemic size. Most (96.1% (49/51)) of the states entered a fast-growing phase before the accumulative number of cases reached (30). The days required for the number of confirmed cases to increase from 30 to 100 was 5.6 (5.1–6.1) days. As of 31 March 2021, all 51 states experienced at least 2 waves of COVID-19 outbreaks, 23.5% (12/51) experienced 3 waves, and 15.7% (8/51) experienced 4 waves, the epidemic size of COVID-19 was 19,275–3,669,048 cases across the states. The pre-delta epidemic size was significantly correlated with the duration from 30 to 100 cases (p = 0.003, r = −0.405), the growth rate of the fast-growing phase (p = 0.012, r = 0.351), and the peak cases in the subsequent waves (K₁ (p < 0.001, r = 0.794), K₂ (p < 0.001, r = 0.595), K₃ (p < 0.001, r = 0.977), and K₄ (p = 0.002, r = 0.905)). We observed that both early and subsequent epidemic characteristics contribute to the pre-delta epidemic size of COVID-19. This identification is important to the prediction of the emerging viral infectious diseases in the primary stage. Full article

(This article belongs to the Special Issue Emerging and Re-emerging Viral Infectious Diseases)

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8 pages, 536 KiB

Open AccessArticle

Non-SARS Non-MERS Human Coronaviruses: Clinical Characteristics and Outcome

by Israa Saib, Saud Aleisa, Husam Ardah, Ebrahim Mahmoud, Ahmad O. Alharbi, Abdulrahman Alsaedy, Sameera Aljohani, Ahmed Alshehri, Naif Khalaf Alharbi and Mohammad Bosaeed

Pathogens 2021, 10(12), 1549; https://doi.org/10.3390/pathogens10121549 - 27 Nov 2021

Cited by 5 | Viewed by 2536

Abstract

Human coronaviruses (HCoVs) have become evident sources of human respiratory infections with new emerging HCoVs as a significant cause of morbidity and mortality. The common four coronaviruses (229E, HKU1, NL63, and OC43) are known to cause respiratory illness in humans, but their clinical impact is poorly described in the literature. We analyzed the data of all patients who tested positive for at least one of the four HCoVs from October 2015 to January 2020 in a tertiary care center. HCoVs were detected in 1062 specimens, with an incidence rate of 1.01%, out of all documented respiratory illnesses. Detection of these viruses was reported sporadically throughout the years, with a peak of occurrence during winter seasons. OC43 had the highest incidence (53.7%), followed by NL63 (21.9%), HKU1 (12.6%), and 229E (11.8%). Most of these infections were community-acquired, with symptoms of both upper and lower respiratory tract. Co-detection with other viruses were observed, mostly with rhinovirus. 229E was the most frequent (26.4%) HCoV in patients requiring intensive care, while NL63 and 229E were the most common in patients requiring invasive ventilation. The highest 30-day mortality rate was observed in patients infected with 229E (6.4%). HCoVs are common circulating pathogens that have been present for decades, with 229E being the most virulent in this study cohort. Full article

(This article belongs to the Special Issue Emerging and Re-emerging Viral Infectious Diseases)

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17 pages, 1183 KiB

Open AccessReview

Avian Influenza: Strategies to Manage an Outbreak

by Alison Simancas-Racines, Santiago Cadena-Ullauri, Patricia Guevara-Ramírez, Ana Karina Zambrano and Daniel Simancas-Racines

Pathogens 2023, 12(4), 610; https://doi.org/10.3390/pathogens12040610 - 17 Apr 2023

Cited by 16 | Viewed by 9861

Abstract

Avian influenza (AI) is a contagious disease among the poultry population with high avian mortality, which generates significant economic losses and elevated costs for disease control and outbreak eradication. AI is caused by an RNA virus part of the Orthomyxoviridae family; however, only Influenzavirus A is capable of infecting birds. AI pathogenicity is based on the lethality, signs, and molecular characteristics of the virus. Low pathogenic avian influenza (LPAI) virus has a low mortality rate and ability to infect, whereas the highly pathogenic avian influenza (HPAI) virus can cross respiratory and intestinal barriers, diffuse to the blood, damage all tissues of the bird, and has a high mortality rate. Nowadays, avian influenza is a global public health concern due to its zoonotic potential. Wild waterfowl is the natural reservoir of AI viruses, and the oral–fecal path is the main transmission route between birds. Similarly, transmission to other species generally occurs after virus circulation in densely populated infected avian species, indicating that AI viruses can adapt to promote the spread. Moreover, HPAI is a notifiable animal disease; therefore, all countries must report infections to the health authorities. Regarding laboratory diagnoses, the presence of influenza virus type A can be identified by agar gel immunodiffusion (AGID), enzyme immunoassay (EIA), immunofluorescence assays, and enzyme-linked immunoadsorption assay (ELISAs). Furthermore, reverse transcription polymerase chain reaction is used for viral RNA detection and is considered the gold standard for the management of suspect and confirmed cases of AI. If there is suspicion of a case, epidemiological surveillance protocols must be initiated until a definitive diagnosis is obtained. Moreover, if there is a confirmed case, containment actions should be prompt and strict precautions must be taken when handling infected poultry cases or infected materials. The containment measures for confirmed cases include the sanitary slaughter of infected poultry using methods such as environment saturation with CO₂, carbon dioxide foam, and cervical dislocation. For disposal, burial, and incineration, protocols should be followed. Lastly, disinfection of affected poultry farms must be carried out. The present review aims to provide an overview of the avian influenza virus, strategies for its management, the challenges an outbreak can generate, and recommendations for informed decision making. Full article

(This article belongs to the Special Issue Emerging and Re-emerging Viral Infectious Diseases)

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Complexities in Case Definition of SARS-CoV-2 Reinfection: Clinical Evidence and Implications in COVID-19 Surveillance and Diagnosis

by Lisa Yamasaki and Meng Ling Moi

Pathogens 2021, 10(10), 1262; https://doi.org/10.3390/pathogens10101262 - 29 Sep 2021

Cited by 1 | Viewed by 2789

Abstract

Reinfection cases have been reported in some countries with clinical symptoms ranging from mild to severe. In addition to clinical diagnosis, virus genome sequence from the first and second infection has to be confirmed to either belong to separate clades or had significant mutations for the confirmation of SARS-CoV-2 reinfection. While phylogenetic analysis with paired specimens offers the strongest evidence for reinfection, there remains concerns on the definition of SARS-CoV-2 reinfection, for reasons including accessibility to paired-samples and technical challenges in phylogenetic analysis. In light of the emergence of new SARS-CoV-2 variants that are associated with increased transmissibility and immune-escape further understanding of COVID-19 protective immunity, real-time surveillance directed at identifying COVID-19 transmission patterns, transmissibility of emerging variants and clinical implications of reinfection would be important in addressing the challenges in definition of COVID-19 reinfection and understanding the true disease burden. Full article

(This article belongs to the Special Issue Emerging and Re-emerging Viral Infectious Diseases)

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