Research

14 pages, 2583 KiB

Open AccessArticle

Pandemic Risk Assessment for Swine Influenza A Virus in Comparative In Vitro and In Vivo Models

by Ian Padykula, Lambodhar Damodaran, Kelsey T. Young, Madelyn Krunkosky, Emily F. Griffin, James F. North, Peter J. Neasham, Vasilis C. Pliasas, Chris L. Siepker, James B. Stanton, Elizabeth W. Howerth, Justin Bahl, Constantinos S. Kyriakis and Stephen Mark Tompkins

Viruses 2024, 16(4), 548; https://doi.org/10.3390/v16040548 - 31 Mar 2024

Viewed by 655

Abstract

Swine influenza A viruses pose a public health concern as novel and circulating strains occasionally spill over into human hosts, with the potential to cause disease. Crucial to preempting these events is the use of a threat assessment framework for human populations. However, [...] Read more.

Swine influenza A viruses pose a public health concern as novel and circulating strains occasionally spill over into human hosts, with the potential to cause disease. Crucial to preempting these events is the use of a threat assessment framework for human populations. However, established guidelines do not specify which animal models or in vitro substrates should be used. We completed an assessment of a contemporary swine influenza isolate, A/swine/GA/A27480/2019 (H1N2), using animal models and human cell substrates. Infection studies in vivo revealed high replicative ability and a pathogenic phenotype in the swine host, with replication corresponding to a complementary study performed in swine primary respiratory epithelial cells. However, replication was limited in human primary cell substrates. This contrasted with our findings in the Calu-3 cell line, which demonstrated a replication profile on par with the 2009 pandemic H1N1 virus. These data suggest that the selection of models is important for meaningful risk assessment. Full article

(This article belongs to the Special Issue Animal and Human Respiratory Viruses - Causes of the Next Pandemic?)

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12 pages, 904 KiB

Open AccessArticle

Respiratory Syncytial Virus Reinfections in Children in Western Australia

by David A. Foley, Cara A. Minney-Smith, Wei Hao Lee, Daniel B. Oakes, Briony Hazelton, Timothy J. Ford, Ushma Wadia, Chisha Sikazwe, Hannah C. Moore, Mark P. Nicol, Avram Levy and Christopher C. Blyth

Viruses 2023, 15(12), 2417; https://doi.org/10.3390/v15122417 - 13 Dec 2023

Viewed by 1222

Abstract

Respiratory syncytial virus (RSV) reinfection in children is poorly understood. We examined the incidence, characteristics, and outcomes of hospital-attended RSV reinfections in children <16 years in Western Australia between 2012 and 2022. Individuals with repeat RSV detections ≥56 days apart were identified using [...] Read more.

Respiratory syncytial virus (RSV) reinfection in children is poorly understood. We examined the incidence, characteristics, and outcomes of hospital-attended RSV reinfections in children <16 years in Western Australia between 2012 and 2022. Individuals with repeat RSV detections ≥56 days apart were identified using laboratory data. The incidence of reinfection in the first five years of life was estimated using the total birth population from 2012 to 2017. Clinical data on a subset of reinfection episodes were obtained from two metropolitan pediatric centers. A total of 466 children with hospital-attended reinfections were identified. The median interval between RSV detections was 460 days (interquartile range: 324, 812), with a reinfection rate of 95 per 100,000 individuals (95% confidence interval: 82, 109). Reinfection was most common in children who experienced their first RSV detection <6 months of age. Predisposing factors were identified in 56% of children; children with predisposing factors were older at first and second detections, were more likely to be admitted, and had a longer length of stay. This study highlights the significant burden of hospital-attended RSV reinfections in children with and without predisposing factors. Expanded surveillance with in-depth clinical data is required to further characterize the impact of RSV reinfection. Full article

(This article belongs to the Special Issue Animal and Human Respiratory Viruses - Causes of the Next Pandemic?)

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14 pages, 3283 KiB

Open AccessArticle

Global Prevalence and Hemagglutinin Evolution of H7N9 Avian Influenza Viruses from 2013 to 2022

by Qianshuo Liu, Haowen Zeng, Xinghui Wu, Xuelian Yang and Guiqin Wang

Viruses 2023, 15(11), 2214; https://doi.org/10.3390/v15112214 - 04 Nov 2023

Cited by 1 | Viewed by 1329

Abstract

H7N9 avian influenza viruses have caused severe harm to the global aquaculture industry and human health. For further understanding of the characteristics of prevalence and hemagglutinin evolution of H7N9 avian influenza viruses, we generated the global epidemic map of H7N9 viruses from 2013 [...] Read more.

H7N9 avian influenza viruses have caused severe harm to the global aquaculture industry and human health. For further understanding of the characteristics of prevalence and hemagglutinin evolution of H7N9 avian influenza viruses, we generated the global epidemic map of H7N9 viruses from 2013 to 2022, constructed a phylogenetic tree, predicted the glycosylation sites and compared the selection pressure of the hemagglutinin. The results showed that although H7N9 avian influenza appeared sporadically in other regions worldwide, China had concentrated outbreaks from 2013 to 2017. The hemagglutinin genes were classified into six distinct lineages: A, B, C, D, E and F. After 2019, H7N9 viruses from the lineages B, E and F persisted, with the lineage B being the dominant. The hemagglutinin of highly pathogenic viruses in the B lineage has an additional predicted glycosylation site, which may account for their persistent pandemic, and is under more positive selection pressure. The most recent ancestor of the H7N9 avian influenza viruses originated in September 1991. The continuous evolution of hemagglutinin has led to an increase in virus pathogenicity in both poultry and humans, and sustained human-to-human transmission. This study provides a theoretical basis for better prediction and control of H7N9 avian influenza. Full article

(This article belongs to the Special Issue Animal and Human Respiratory Viruses - Causes of the Next Pandemic?)

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11 pages, 1045 KiB

Open AccessArticle

Influenza A and B Viruses in Fine Aerosols of Exhaled Breath Samples from Patients in Tropical Singapore

by Vincent T. K. Chow, Douglas Jie Wen Tay, Mark I. C. Chen, Julian W. Tang, Donald K. Milton and Kwok Wai Tham

Viruses 2023, 15(10), 2033; https://doi.org/10.3390/v15102033 - 30 Sep 2023

Viewed by 1060

Abstract

Influenza is a highly contagious respiratory illness that commonly causes outbreaks among human communities. Details about the exact nature of the droplets produced by human respiratory activities such as breathing, and their potential to carry and transmit influenza A and B viruses is [...] Read more.

Influenza is a highly contagious respiratory illness that commonly causes outbreaks among human communities. Details about the exact nature of the droplets produced by human respiratory activities such as breathing, and their potential to carry and transmit influenza A and B viruses is still not fully understood. The objective of our study was to characterize and quantify influenza viral shedding in exhaled aerosols from natural patient breath, and to determine their viral infectivity among participants in a university cohort in tropical Singapore. Using the Gesundheit-II exhaled breath sampling apparatus, samples of exhaled breath of two aerosol size fractions (“coarse” > 5 µm and “fine” ≤ 5 µm) were collected and analyzed from 31 study participants, i.e., 24 with influenza A (including H1N1 and H3N2 subtypes) and 7 with influenza B (including Victoria and Yamagata lineages). Influenza viral copy number was quantified using reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Infectivity of influenza virus in the fine particle fraction was determined by culturing in Madin–Darby canine kidney cells. Exhaled influenza virus RNA generation rates ranged from 9 to 1.67 × 10⁵ and 10 to 1.24 × 10⁴ influenza virus RNA copies per minute for the fine and coarse aerosol fractions, respectively. Compared to the coarse aerosol fractions, influenza A and B viruses were detected more frequently in the fine aerosol fractions that harbored 12-fold higher viral loads. Culturable virus was recovered from the fine aerosol fractions from 9 of the 31 subjects (29%). These findings constitute additional evidence to reiterate the important role of fine aerosols in influenza transmission and provide a baseline range of influenza virus RNA generation rates. Full article

(This article belongs to the Special Issue Animal and Human Respiratory Viruses - Causes of the Next Pandemic?)

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17 pages, 722 KiB

Open AccessArticle

Nonlinear and Multidelayed Effects of Meteorological Drivers on Human Respiratory Syncytial Virus Infection in Japan

by Keita Wagatsuma, Iain S. Koolhof and Reiko Saito

Viruses 2023, 15(9), 1914; https://doi.org/10.3390/v15091914 - 12 Sep 2023

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Abstract

In this study, we aimed to characterize the nonlinear and multidelayed effects of multiple meteorological drivers on human respiratory syncytial virus (HRSV) infection epidemics in Japan. The prefecture-specific weekly time-series of the number of newly confirmed HRSV infection cases and multiple meteorological variables [...] Read more.

In this study, we aimed to characterize the nonlinear and multidelayed effects of multiple meteorological drivers on human respiratory syncytial virus (HRSV) infection epidemics in Japan. The prefecture-specific weekly time-series of the number of newly confirmed HRSV infection cases and multiple meteorological variables were collected for 47 Japanese prefectures from 1 January 2014 to 31 December 2019. We combined standard time-series generalized linear models with distributed lag nonlinear models to determine the exposure–lag–response association between the incidence relative risks (IRRs) of HRSV infection and its meteorological drivers. Pooling the 2-week cumulative estimates showed that overall high ambient temperatures (22.7 °C at the 75th percentile compared to 16.3 °C) and high relative humidity (76.4% at the 75th percentile compared to 70.4%) were associated with higher HRSV infection incidence (IRR for ambient temperature 1.068, 95% confidence interval [CI], 1.056–1.079; IRR for relative humidity 1.045, 95% CI, 1.032–1.059). Precipitation revealed a positive association trend, and for wind speed, clear evidence of a negative association was found. Our findings provide a basic picture of the seasonality of HRSV transmission and its nonlinear association with multiple meteorological drivers in the pre-HRSV-vaccination and pre-coronavirus disease 2019 (COVID-19) era in Japan. Full article

(This article belongs to the Special Issue Animal and Human Respiratory Viruses - Causes of the Next Pandemic?)

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18 pages, 555 KiB

Open AccessArticle

The Experience of Testing for Coronavirus Disease (COVID-19) at a Single Diagnostic Center in Paraguay before the Introduction of Vaccination

by Florencia del-Puerto, Leticia E. Rojas, Chyntia C. Díaz Acosta, Laura X. Franco, Fátima Cardozo, María E. Galeano, Adriana Valenzuela, Alejandra Rojas, Magaly Martínez, Ana Ayala-Lugo, Laura Mendoza, Fátima S. Ovando, Mario F. Martínez, Hyun J. Chung, Richard Webby, Eva Nara and Miguela A. Caniza

Viruses 2023, 15(5), 1136; https://doi.org/10.3390/v15051136 - 10 May 2023

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Abstract

Soon after the declaration of the COVID-19 pandemic, the Institute for Health Sciences Research (IICS) of the National University of Asunción, Paraguay became a testing laboratory (COVID-Lab) for SARS-CoV-2. The COVID-Lab testing performance was assessed from 1 April 2020 to 12 May 2021. [...] Read more.

Soon after the declaration of the COVID-19 pandemic, the Institute for Health Sciences Research (IICS) of the National University of Asunción, Paraguay became a testing laboratory (COVID-Lab) for SARS-CoV-2. The COVID-Lab testing performance was assessed from 1 April 2020 to 12 May 2021. The effect of the pandemic on the IICS and how the COVID-Lab contributed to the academic and research activities of the institute were also assessed. IICS researchers and staff adjusted their work schedules to support the COVID-Lab. Of the 13,082 nasopharyngeal/oropharyngeal swabs processed, 2704 (20.7%) tested positive for SARS-CoV-2 by RT-PCR. Of the individuals testing positive, 55.4% were female and 48.3% were aged 21–40 years. Challenges faced by the COVID-Lab were unstable reagent access and insufficient staff; shifting obligations regarding research, academic instruction, and grantsmanship; and the continuous demands from the public for information on COVID-19. The IICS provided essential testing and reported on the progress of the pandemic. IICS researchers gained better laboratory equipment and expertise in molecular SARS-CoV-2 testing but struggled to manage their conflicting educational and additional research obligations during the pandemic, which affected their productivity. Therefore, policies protecting the time and resources of the faculty and staff engaged in pandemic-related work or research are necessary components of healthcare emergency preparedness. Full article

(This article belongs to the Special Issue Animal and Human Respiratory Viruses - Causes of the Next Pandemic?)

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Review

Jump to: Research, Other

35 pages, 522 KiB

Open AccessReview

Evolution of SARS-CoV-2 Variants: Implications on Immune Escape, Vaccination, Therapeutic and Diagnostic Strategies

by Nur Zawanah Zabidi, Hern Liang Liew, Isra Ahmad Farouk, Ashwini Puniyamurti, Ashley Jia Wen Yip, Vindya Nilakshi Wijesinghe, Zheng Yao Low, Julian W. Tang, Vincent T. K. Chow and Sunil K. Lal

Viruses 2023, 15(4), 944; https://doi.org/10.3390/v15040944 - 10 Apr 2023

Cited by 17 | Viewed by 3468

Abstract

The COVID-19 pandemic caused by SARS-CoV-2 is associated with a lower fatality rate than its SARS and MERS counterparts. However, the rapid evolution of SARS-CoV-2 has given rise to multiple variants with varying pathogenicity and transmissibility, such as the Delta and Omicron variants. [...] Read more.

The COVID-19 pandemic caused by SARS-CoV-2 is associated with a lower fatality rate than its SARS and MERS counterparts. However, the rapid evolution of SARS-CoV-2 has given rise to multiple variants with varying pathogenicity and transmissibility, such as the Delta and Omicron variants. Individuals with advanced age or underlying comorbidities, including hypertension, diabetes and cardiovascular diseases, are at a higher risk of increased disease severity. Hence, this has resulted in an urgent need for the development of better therapeutic and preventive approaches. This review describes the origin and evolution of human coronaviruses, particularly SARS-CoV-2 and its variants as well as sub-variants. Risk factors that contribute to disease severity and the implications of co-infections are also considered. In addition, various antiviral strategies against COVID-19, including novel and repurposed antiviral drugs targeting viral and host proteins, as well as immunotherapeutic strategies, are discussed. We critically evaluate strategies of current and emerging vaccines against SARS-CoV-2 and their efficacy, including immune evasion by new variants and sub-variants. The impact of SARS-CoV-2 evolution on COVID-19 diagnostic testing is also examined. Collectively, global research and public health authorities, along with all sectors of society, need to better prepare against upcoming variants and future coronavirus outbreaks. Full article

(This article belongs to the Special Issue Animal and Human Respiratory Viruses - Causes of the Next Pandemic?)

27 pages, 4185 KiB

Open AccessReview

Avian Influenza Virus Tropism in Humans

by Umarqayum AbuBakar, Lina Amrani, Farah Ayuni Kamarulzaman, Saiful Anuar Karsani, Pouya Hassandarvish and Jasmine Elanie Khairat

Viruses 2023, 15(4), 833; https://doi.org/10.3390/v15040833 - 24 Mar 2023

Cited by 6 | Viewed by 7462

Abstract

An influenza pandemic happens when a novel influenza A virus is able to infect and transmit efficiently to a new, distinct host species. Although the exact timing of pandemics is uncertain, it is known that both viral and host factors play a role [...] Read more.

An influenza pandemic happens when a novel influenza A virus is able to infect and transmit efficiently to a new, distinct host species. Although the exact timing of pandemics is uncertain, it is known that both viral and host factors play a role in their emergence. Species-specific interactions between the virus and the host cell determine the virus tropism, including binding and entering cells, replicating the viral RNA genome within the host cell nucleus, assembling, maturing and releasing the virus to neighboring cells, tissues or organs before transmitting it between individuals. The influenza A virus has a vast and antigenically varied reservoir. In wild aquatic birds, the infection is typically asymptomatic. Avian influenza virus (AIV) can cross into new species, and occasionally it can acquire the ability to transmit from human to human. A pandemic might occur if a new influenza virus acquires enough adaptive mutations to maintain transmission between people. This review highlights the key determinants AIV must achieve to initiate a human pandemic and describes how AIV mutates to establish tropism and stable human adaptation. Understanding the tropism of AIV may be crucial in preventing virus transmission in humans and may help the design of vaccines, antivirals and therapeutic agents against the virus. Full article

(This article belongs to the Special Issue Animal and Human Respiratory Viruses - Causes of the Next Pandemic?)

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Other

Jump to: Research, Review

19 pages, 1322 KiB

Open AccessSystematic Review

Prevalence and Molecular Epidemiology of Human Coronaviruses in Africa Prior to the SARS-CoV-2 Outbreak: A Systematic Review

by Lisa Arrah Mbang Tambe, Phindulo Mathobo, Mukhethwa Munzhedzi, Pascal Obong Bessong and Lufuno Grace Mavhandu-Ramarumo

Viruses 2023, 15(11), 2146; https://doi.org/10.3390/v15112146 - 25 Oct 2023

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Abstract

Coronaviruses, re-emerging in human populations, cause mild or severe acute respiratory diseases, and occasionally epidemics. This study systematically reviewed human coronavirus (HCoVs) infections in Africa prior to the SARS-CoV-2 outbreak. Forty studies on the prevalence or molecular epidemiology of HCoVs were available from [...] Read more.

Coronaviruses, re-emerging in human populations, cause mild or severe acute respiratory diseases, and occasionally epidemics. This study systematically reviewed human coronavirus (HCoVs) infections in Africa prior to the SARS-CoV-2 outbreak. Forty studies on the prevalence or molecular epidemiology of HCoVs were available from 13/54 African countries (24%). The first published data on HCoV was from South Africa in 2008. Eight studies (20%) reported on HCoV molecular epidemiology. Endemic HCoV prevalence ranged from 0.0% to 18.2%. The prevalence of zoonotic MERS-CoV ranged from 0.0% to 83.5%. Two studies investigated SARS-CoV infection, for which a prevalence of 0.0% was reported. There was heterogeneity in the type of tests used in determining HCoV prevalence. Two studies reported that risk factors for HCoV include exposure to infected animals or humans. The quantity of virologic investigations on HCoV on the African continent was scant, and Africa was not prepared for SARS-CoV-2. Full article

(This article belongs to the Special Issue Animal and Human Respiratory Viruses - Causes of the Next Pandemic?)

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