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Impact of Pandemic Measures on the Epidemiology and Seasonality of Other Viruses

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A special issue of Viruses (ISSN 1999-4915). This special issue belongs to the section "Human Virology and Viral Diseases".

Deadline for manuscript submissions: 31 December 2024 | Viewed by 12913

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Dr. Julian Tang

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Department of Respiratory Sciences, University of Leicester, Leicester LE1 7RH, UK
Interests: respiratory viruses; diagnosis; treatment; aerosol transmission; infection control; pathogenesis; epidemiology; bloodborne viruses; congenital viral infections; viral infections of the immunocompromised
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Since the COVID-19 pandemic restrictions have been lifted in many countries, reports are being published about how the pandemic measures have impacted on the normal seasonal epidemiology of other viruses, such as influenza, RSV, parainfluenza, rhinoviruses, enteroviruses, adenoviruses, etc.

These changes have often manifested as viral rebounds in case numbers after social distancing measures were removed.

This has had the potential to cause more severe disease in children caught in this viral rebound, where children were less exposed to circulating viruses, due to reduced socialising with school friends, and not being able to develop immunity to these agents. One example may be the global outbreaks of severe hepatitis that were linked to adenoviruses in many cases in 2022.

This Special Issue will capture some of these reports and assess their impact on related populations. Such studies will prepare us for the possible consequences of such prolonged non-pharmaceutical measures being taken during any next pandemic.

Dr. Julian Tang
Guest Editor

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Keywords

epidemiology
pandemic measures
changing pattern
seasonality
COVID-19
impact
lockdown
viral circulation
host immunity

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Published Papers (9 papers)

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Research

16 pages, 1748 KiB

Open AccessArticle

Influenza Virus Surveillance from the 1918 Influenza Pandemic to the 2020 Coronavirus Pandemic in New York State, USA

by Kay L. Escuyer, Donna L. Gowie and Kirsten St. George

Viruses 2024, 16(12), 1952; https://doi.org/10.3390/v16121952 - 20 Dec 2024

Viewed by 409

Abstract

A historical perspective of more than one hundred years of influenza surveillance in New York State demonstrates the progression from anecdotes and case counts to next-generation sequencing and electronic database management, greatly improving pandemic preparedness and response. Here, we determined if influenza virologic surveillance at the New York State public health laboratory (NYS PHL) tests sufficient specimen numbers within preferred confidence limits to assess situational awareness and detect novel viruses that pose a pandemic risk. To this end, we analyzed retrospective electronic data on laboratory test results for the influenza seasons 1997–1998 to 2021–2022 according to sample sizes recommended in the Influenza Virologic Surveillance Right Size Roadmap issued by the Association of Public Health Laboratories and Centers for Disease Control and Prevention. Although data solely from specimens submitted to the NYS PHL were insufficient to meet surveillance goals, when supplemented with testing data from clinical laboratories participating in surveillance programs, the recommended surveillance goals were achieved. Despite the sudden decline in influenza cases in 2020–2021, impacted by the COVID-19 mitigation measures, the dramatic increases in influenza cases surrounding the coronavirus pandemic reveal that influenza remains a national and international public health threat. Sample submissions to public health laboratories must be encouraged to facilitate monitoring for emerging viruses and preparedness for another pandemic. Full article

(This article belongs to the Special Issue Impact of Pandemic Measures on the Epidemiology and Seasonality of Other Viruses)

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13 pages, 301 KiB

Open AccessArticle

The Clinical Effectiveness and Tolerability of Oseltamivir in Unvaccinated Pediatric Influenza Patients during Two Influenza Seasons after the COVID-19 Pandemic: The Impact of Comorbidities on Hospitalization for Influenza in Children

by Gheorghiță Jugulete, Mihaela Cristina Olariu, Raluca Stanescu, Monica Luminita Luminos, Daniela Pacurar, Carmen Pavelescu and Mădălina-Maria Merișescu

Viruses 2024, 16(10), 1576; https://doi.org/10.3390/v16101576 - 7 Oct 2024

Viewed by 919

Abstract

Antiviral therapy such as oseltamivir has been recommended for hospitalized children with suspected and confirmed influenza for almost 20 years. The therapy is officially authorized for newborns two weeks of age or older, however, questions about its safety and effectiveness still surround it. Our goals were to assess the epidemiological features of two consecutive seasonal influenza cases in children following the COVID-19 pandemic; to observe the clinical effectiveness and tolerability of oseltamivir in hospitalized children who were not vaccinated against influenza and had different influenza subtypes, including A(H1N1), A(H3N2), and B; and to identify specific comorbidities associated with influenza in children. We performed an observational study on 1300 children, enrolled between 1 October 2022 and 30 May 2023 and between 1 October 2023 and 4 May 2024, to the IX Pediatric Infectious Diseases Clinical Section of the National Institute of Infectious Diseases “Prof. Dr. Matei Balș”. During the 2022–2023 influenza season, 791 pediatric patients tested positive for influenza and received oseltamivir. Of these, 89% (704/791) had influenza A, with 86.4% having subtype A(H1N1) and 13.6% of cases having A(H3N2), and for influenza B, 11% (87/791) of the pediatric patients. Of the total group, 59% were male, and the median age was 2.4 years (1.02–9.28). For the 2023–2024 influenza season, 509 pediatric patients tested positive for influenza, with 56.9% being of the male gender and who were treated with oseltamivir. Of these patients, 81.6% had influenza A and 18.4% had influenza B. Treatment with neuraminidase inhibitors, specifically oseltamivir, 2 mg/kg/dose administered twice daily for 5 days, was well tolerated by the children, and we recorded no deaths. The duration of hospitalization for patients with a fever after the oseltamivir administration was significantly longer for patients with A(H1N1) infection than A(H3N2), during both seasons. We identified more complications in the 2022–2023 season and a decreasing number of influenza B for the 2023–2024 season. Among children with comorbidities, the most common were asthma, gastrointestinal diseases, and metabolic and endocrine diseases. In terms of effectiveness, oseltamivir significantly reduced the intensity of influenza symptoms, thus reducing the number of days of hospitalization (p = 0.001) as well as post-infection complications (p = 0.005) in both groups. In this study, we evaluated the clinical effectiveness of oseltamivir therapy for all influenza types/subtypes in children, and the length of hospitalization. We identified comorbidities associated with the prolonged duration of hospitalization. Influenza vaccination should be the main tool in the prevention of influenza and its complications in children, especially those with comorbidities. Full article

(This article belongs to the Special Issue Impact of Pandemic Measures on the Epidemiology and Seasonality of Other Viruses)

15 pages, 2615 KiB

Open AccessArticle

Prevalence and Seasonal Patterns of 16 Common Viral Respiratory Pathogens during the COVID-19 Pandemic in Gauteng Province, South Africa, 2020–2021

by Bhaveshan Reddy, Andiswa Simane, Hloniphile Mthiyane, Bonolo Mashishi, Nonhlanhla Mbenenge and Florette K. Treurnicht

Viruses 2024, 16(8), 1325; https://doi.org/10.3390/v16081325 - 19 Aug 2024

Viewed by 863

Abstract

Coronavirus disease 2019 (COVID-19) is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The COVID-19 pandemic resulted in widespread morbidity and mortality, but generally, the diagnosis of other respiratory viruses was limited. This study aimed to assess the prevalence of other respiratory viruses during the 2020/2021 pandemic among patients of all ages who accessed care at public healthcare facilities in Gauteng Province, South Africa. Laboratory diagnosis for respiratory viruses, with or without SARS-CoV-2, was conducted via multiplex real-time polymerase chain reactions using respiratory specimens. A total of 1776 patients were included from 1 April 2020 to 31 March 2021, of which 766 (43.1%) were positive for respiratory viruses other than SARS-CoV-2. RV (368/1776; 20.7%) was the most prevalent, followed by RSV (304/1776; 17.1%), AdV (112/1776; 6.3%) and EV (105/1776; 5.9%). hCoV-OC43 (39/1776; 2.2%) was the most prevalent common coronavirus. SARS-CoV-2 co-infections were detected in 4.8% (24/500) of patients. Only 27.1% (482/1776) of patients were admitted to high-care or intensive care units. A decrease in respiratory virus detections was observed, except for RSV, EV and hCoV-OC43. RSV prevalence increased in 2021, while influenza A/B viruses remained undetected. Full article

(This article belongs to the Special Issue Impact of Pandemic Measures on the Epidemiology and Seasonality of Other Viruses)

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15 pages, 1818 KiB

Open AccessArticle

Whole-Genome Analysis of the Influenza A(H1N1)pdm09 Viruses Isolated from Influenza-like Illness Outpatients in Myanmar and Community-Acquired Oseltamivir-Resistant Strains Present from 2015 to 2019

by Irina Chon, Su Mon Kyaw Win, Wint Wint Phyu, Reiko Saito, Yadanar Kyaw, Nay Chi Win, Di Ja Lasham, Htay Htay Tin, Tsutomu Tamura, Teruhime Otoguro, Keita Wagatsuma, Yuyang Sun, Jiaming Li and Hisami Watanabe

Viruses 2024, 16(8), 1300; https://doi.org/10.3390/v16081300 - 15 Aug 2024

Viewed by 1106

Abstract

In this study, we describe the genetic characteristics of influenza A(H1N1)pdm09 strains detected in Myanmar from 2015 to 2019. Whole genomes from 60 A(H1N1)pdm09 virus isolates were amplified using real-time polymerase chain reaction and successfully sequenced using the Illumina iSeq100 platforms. Eight individual phylogenetic trees were retrieved for each segment along with those of the World Health Organization (WHO)-recommended Southern Hemisphere vaccine strains for the respective years. A(H1N1)pdm09 viruses from 2015 were found to belong to clade 6B, those from 2016 to 6B.1, 2017 to 6B.1A, and 2019 to 6B.1A.5a, and were genetically distinct from the Southern Hemisphere vaccine strains for the respective seasons, A/California/7/2009 and A/Michigan/45/2015. We observed one virus with intra-subtype reassortment, collected in the 2015 season. Importantly, three viruses possessed the H275Y substitution in the neuraminidase protein, appearing to be community-acquired without the prior administration of neuraminidase inhibitors. These viruses exhibited highly reduced susceptibility to oseltamivir and peramivir. This study demonstrates the importance of monitoring genetic variations in influenza viruses that will contribute to the selection of global influenza vaccines. Full article

(This article belongs to the Special Issue Impact of Pandemic Measures on the Epidemiology and Seasonality of Other Viruses)

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13 pages, 2142 KiB

Open AccessArticle

Impact of COVID-19 Pandemic Restrictions on Respiratory Virus Patterns: Insights from RSV Surveillance in Gwangju, South Korea

by Sun-Ju Cho, Sun-Hee Kim, Jeongeun Mun, Ji-eun Yun, Sujung Park, Jungwook Park, Yeong-Un Lee, Ji-su Park, Haebi Yun, Cheong-mi Lee, Jong-Pil Kim and Jung-Mi Seo

Viruses 2024, 16(6), 850; https://doi.org/10.3390/v16060850 - 26 May 2024

Cited by 1 | Viewed by 1201

Abstract

The social restriction measures implemented due to the COVID-19 pandemic have impacted the pattern of occurrences of respiratory viruses. According to surveillance results in the Gwangju region of South Korea, respiratory syncytial virus (RSV) did not occur during the 2020/2021 season. However, there was a delayed resurgence in the 2021/2022 season, peaking until January 2022. To analyze this, a total of 474 RSV positive samples were investigated before and after the COVID-19 pandemic. Among them, 73 samples were selected for whole-genome sequencing. The incidence rate of RSV in the 2021/2022 season after COVID-19 was found to be approximately three-fold higher compared to before the pandemic, with a significant increase observed in the age group from under 2 years old to under 5 years old. Phylogenetic analysis revealed that, for RSV-A, whereas four lineages were observed before COVID-19, only the A.D.3.1 lineage was observed during the 2021/2022 season post-pandemic. Additionally, during the 2022/2023 season, the A.D.1, A.D.3, and A.D.3.1 lineages co-circulated. For RSV-B, while the B.D.4.1.1 lineage existed before COVID-19, both the B.D.4.1.1 and B.D.E.1 lineages circulated after the pandemic. Although atypical RSV occurrences were not due to new lineages, there was an increase in the frequency of mutations in the F protein of RSV after COVID-19. These findings highlight the need to continue monitoring changes in RSV occurrence patterns in the aftermath of the COVID-19 pandemic to develop and manage strategies in response. Full article

(This article belongs to the Special Issue Impact of Pandemic Measures on the Epidemiology and Seasonality of Other Viruses)

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13 pages, 785 KiB

Open AccessArticle

Presence and Significance of Multiple Respiratory Viral Infections in Children Admitted to a Tertiary Pediatric Hospital in Italy

by Velia Chiara Di Maio, Rossana Scutari, Lorena Forqué, Luna Colagrossi, Luana Coltella, Stefania Ranno, Giulia Linardos, Leonarda Gentile, Eugenia Galeno, Anna Chiara Vittucci, Mara Pisani, Sebastian Cristaldi, Alberto Villani, Massimiliano Raponi, Paola Bernaschi, Cristina Russo and Carlo Federico Perno

Viruses 2024, 16(5), 750; https://doi.org/10.3390/v16050750 - 9 May 2024

Viewed by 1320

Abstract

Viral co-infections are frequently observed among children, but whether specific viral interactions enhance or diminish the severity of respiratory disease is still controversial. This study aimed to investigate the type of viral mono- and co-infections by also evaluating viral correlations in 3525 respiratory samples from 3525 pediatric in/outpatients screened by the Allplex Respiratory Panel Assays and with a Severe Acute Respiratory Syndrome-COronaVirus 2 (SARS-CoV-2) test available. Overall, viral co-infections were detected in 37.8% of patients and were more frequently observed in specimens from children with lower respiratory tract infections compared to those with upper respiratory tract infections (47.1% vs. 36.0%, p = 0.003). SARS-CoV-2 and influenza A were more commonly detected in mono-infections, whereas human bocavirus showed the highest co-infection rate (87.8% in co-infection). After analyzing viral pairings using Spearman’s correlation test, it was noted that SARS-CoV-2 was negatively associated with all other respiratory viruses, whereas a markedly significant positive correlation (p < 0.001) was observed for five viral pairings (involving adenovirus/human bocavirus/human enterovirus/metapneumoviruses/rhinovirus). The correlation between co-infection and clinical outcome may be linked to the type of virus(es) involved in the co-infection rather than simple co-presence. Further studies dedicated to this important point are needed, since it has obvious implications from a diagnostic and clinical point of view. Full article

(This article belongs to the Special Issue Impact of Pandemic Measures on the Epidemiology and Seasonality of Other Viruses)

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13 pages, 1061 KiB

Open AccessArticle

The Changing Detection Rate of Respiratory Syncytial Virus in Adults in Western Australia between 2017 and 2023

by David A. Foley, Cara A. Minney-Smith, Andrew Tjea, Mark P. Nicol, Avram Levy, Hannah C. Moore and Christopher C. Blyth

Viruses 2024, 16(5), 656; https://doi.org/10.3390/v16050656 - 23 Apr 2024

Viewed by 1695

Abstract

The incidence of respiratory syncytial virus (RSV) in adults is inadequately defined and the impact of SARS-CoV-2-related non-pharmaceutical interventions (NPIs) is underexplored. Using laboratory data, we described the detection rate of RSV in adults ≥16 years in Western Australia (WA) between 2017 and 2023. With the exception of 2020, RSV detections rose annually between 2017 and 2023, reaching 50.7 per 100,000 in 2023 (95% confidence interval [CI], 47.9–53.8). RSV testing expanded considerably across the study period, with the testing in 2023 more than five times the 2017 total. The detection rate was highest in adults ≥60 years between 2017 and 2019, particularly those ≥75 years. Following 2020, the detections in all age groups increased, with the highest detection rate in 2023 in those ≥75-years (199.5 per 100,000; 95% CI, 180.5–220). NPIs significantly impacted RSV seasonality; the preceding winter pattern was disrupted, resulting in an absent 2020 winter season and two major summer seasons in 2020/21 and 2021/22. The RSV season began to realign in 2022, reverting to a winter seasonal pattern in 2023 and the largest season in the study period. Ongoing surveillance will be required to understand the stability of these increases and to delineate the impact of new immunisation strategies. Full article

(This article belongs to the Special Issue Impact of Pandemic Measures on the Epidemiology and Seasonality of Other Viruses)

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18 pages, 909 KiB

Open AccessArticle

Changes in Prevalence and Seasonality of Pathogens Identified in Acute Respiratory Tract Infections in Hospitalised Individuals in Rural and Urban Settings in South Africa; 2018–2022

by Michaela Davids, Siobhan Johnstone, Adriano Mendes, Gadean Brecht, Theunis Avenant, Nicolette du Plessis, Maryke de Villiers, Nicola Page and Marietjie Venter

Viruses 2024, 16(3), 404; https://doi.org/10.3390/v16030404 - 5 Mar 2024

Cited by 2 | Viewed by 2017

Abstract

Severe acute respiratory tract infections (SARIs) has been well described in South Africa with seasonal patterns described for influenza and respiratory syncytial virus (RSV), while others occur year-round (rhinovirus and adenovirus). This prospective syndromic hospital-based surveillance study describes the prevalence and impact of public interventions on the seasonality of other respiratory pathogens during the coronavirus disease-19 (COVID-19) pandemic. This occurred from August 2018 to April 2022, with 2595 patients who met the SARS case definition and 442 controls, from three sentinel urban and rural hospital sites in South Africa. Naso/oro-pharyngeal (NP/OP) swabs were tested using the FastTrack Diagnostics^® Respiratory pathogens 33 (RUO) kit. Descriptive statistics, odds ratios, and univariate/multivariate analyses were used. Rhinovirus (14.80%, 228/1540) and Streptococcus pneumoniae (28.50%, 439/1540) were most frequently detected in NP/OP swabs and in children <1 years old (35%, 648/1876). Among others, pathogens associated with SARI cases causing disease were influenza A&B, HRV, RSV, hCoV 229e, Haemophilus influenzae, Staphylococcus aureus, and Streptococcus pneumoniae. Pre-COVID-19, seasonal trends of these pathogens correlated with previous years, with RSV and influenza A seasons only resuming after the national lockdown (2021). It is evident that stringent lockdown conditions have severe impacts on the prevalence of respiratory tract infections. Full article

(This article belongs to the Special Issue Impact of Pandemic Measures on the Epidemiology and Seasonality of Other Viruses)

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19 pages, 3777 KiB

Open AccessArticle

Molecular Epidemiology of Respiratory Syncytial Virus during 2019–2022 and Surviving Genotypes after the COVID-19 Pandemic in Japan

by Sayaka Yoshioka, Wint Wint Phyu, Keita Wagatsuma, Takao Nagai, Yasuko Sano, Kiyosu Taniguchi, Nobuo Nagata, Kazuhiko Tomimoto, Isamu Sato, Harumi Kaji, Ken Sugata, Katsumi Sugiura, Naruo Saito, Satoshi Aoki, Eitaro Suzuki, Yasushi Shimada, Hirotsune Hamabata, Irina Chon, Teruhime Otoguro, Hisami Watanabe and Reiko Saito Show full author list Hide full author list

Viruses 2023, 15(12), 2382; https://doi.org/10.3390/v15122382 - 4 Dec 2023

Cited by 2 | Viewed by 2281

Abstract

To evaluate the changes in respiratory syncytial virus (RSV) collected between 2019 and 2022, we analyzed RSV-A and RSV-B strains from various prefectures in Japan before and after the COVID-19 pandemic. RT-PCR-positive samples collected from children with rapid test positivity at outpatient clinics in 11 prefectures in Japan were sequenced for the ectodomain of the G gene to determine the genotype. Time-aware phylogeographic analyses were performed using the second hypervariable region (HVR) of the G gene from 2012 to 2022. Of 967 samples, 739 (76.4%) were found to be RSV-positive using RT-PCR. RSV peaked in September 2019 but was not detected in 2020, except in Okinawa. Nationwide epidemics occurred with peaks in July 2021 and 2022. The genotype remained the same, ON1 for RSV-A and BA9 for RSV-B during 2019–2022. Phylogeographic analysis of HVR revealed that at least seven clusters of RSV-A had circulated previously but decreased to two clusters after the pandemic, whereas RSV-B had a single monophyletic cluster over the 10 years. Both RSV-A and RSV-B were transferred from Okinawa into other prefectures after the pandemic. The RSV epidemic was suppressed due to pandemic restrictions; however, pre-pandemic genotypes spread nationwide after the pandemic. Full article

(This article belongs to the Special Issue Impact of Pandemic Measures on the Epidemiology and Seasonality of Other Viruses)

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