Diagnostic Virology during the COVID-19 Pandemic - Business as Usual

A special issue of Viruses (ISSN 1999-4915). This special issue belongs to the section "SARS-CoV-2 and COVID-19".

Deadline for manuscript submissions: closed (31 December 2022) | Viewed by 23795

Special Issue Editor

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,

We are interested in highlighting your work on other viruses during the COVID-19 pandemic, including how the pandemic may have impacted on these other virus infections in terms of diagnostics, surveillance, epidemiology, clinical management, infection control, etc.

Has the pandemic changed and improved the way you address other viruses—or not—in the laboratory or wards, including infection control?

Original papers, reviews and commentaries are welcome.

Prof. Dr. Julian Tang
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. Viruses 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 2600 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

  • Virus
  • Diagnostics
  • Surveillance
  • HIV
  • RSV
  • SARS-COV-2
  • Enteroviruses

Published Papers (11 papers)

Order results
Result details
Select all
Export citation of selected articles as:

Research

Jump to: Other

16 pages, 4585 KiB  
Article
Whole-Genome Analysis of Influenza A(H3N2) and B/Victoria Viruses Detected in Myanmar during the COVID-19 Pandemic in 2021
by Irina Chon, Reiko Saito, Yadanar Kyaw, Moe Myat Aye, Swe Setk, Wint Wint Phyu, Keita Wagatsuma, Jiaming Li, Yuyang Sun, Teruhime Otoguro, Su Mon Kyaw Win, Sayaka Yoshioka, Nay Chi Win, Lasham Di Ja, Htay Htay Tin and Hisami Watanabe
Viruses 2023, 15(2), 583; https://0-doi-org.brum.beds.ac.uk/10.3390/v15020583 - 20 Feb 2023
Cited by 1 | Viewed by 2367
Abstract
An influenza circulation was observed in Myanmar between October and November in 2021. Patients with symptoms of influenza-like illness were screened using rapid diagnostic test (RDT) kits, and 147/414 (35.5%) upper respiratory tract specimens presented positive results. All RDT-positive samples were screened by [...] Read more.
An influenza circulation was observed in Myanmar between October and November in 2021. Patients with symptoms of influenza-like illness were screened using rapid diagnostic test (RDT) kits, and 147/414 (35.5%) upper respiratory tract specimens presented positive results. All RDT-positive samples were screened by a commercial multiplex real-time polymerase chain reaction (RT-PCR) assay, and 30 samples positive for influenza A(H3N2) or B underwent further typing/subtyping for cycle threshold (Ct) value determination based on cycling probe RT-PCR. The majority of subtyped samples (n = 13) were influenza A(H3N2), while only three were B/Victoria. Clinical samples with low Ct values obtained by RT-PCR were used for whole-genome sequencing via next-generation sequencing technology. All collected viruses were distinct from the Southern Hemisphere vaccine strains of the corresponding season but matched with vaccines of the following season. Influenza A(H3N2) strains from Myanmar belonged to clade 2a.3 and shared the highest genetic proximity with Bahraini strains. B/Victoria viruses belonged to clade V1A.3a.2 and were genetically similar to Bangladeshi strains. This study highlights the importance of performing influenza virus surveillance with genetic characterization of the influenza virus in Myanmar, to contribute to global influenza surveillance during the COVID-19 pandemic. Full article
(This article belongs to the Special Issue Diagnostic Virology during the COVID-19 Pandemic - Business as Usual)
Show Figures

Figure 1

10 pages, 1777 KiB  
Article
Development and Validation of a Rapid Screening Test for HTLV-I IgG Antibodies
by Bobby Brooke Herrera, Rafaela Mayoral and Carlos Brites
Viruses 2023, 15(1), 129; https://0-doi-org.brum.beds.ac.uk/10.3390/v15010129 - 31 Dec 2022
Cited by 1 | Viewed by 2139
Abstract
Initial diagnosis of human T cell lymphotropic virus (HTLV) infections is mainly based by detecting antibodies in plasma or serum using laboratory-based methods. The aim of this study was to develop and evaluate a rapid screening test for HTLV-I antibodies. Our rapid screening [...] Read more.
Initial diagnosis of human T cell lymphotropic virus (HTLV) infections is mainly based by detecting antibodies in plasma or serum using laboratory-based methods. The aim of this study was to develop and evaluate a rapid screening test for HTLV-I antibodies. Our rapid screening test uses HTLV-I p24 antigen conjugated to gold nanoparticles and an anti-human IgG antibody immobilized to a nitrocellulose strip to detect human HTLV-I p24-specific IgG antibodies via immunochromatography. Performance of the rapid screening test for HTLV-I was conducted on a total of 118 serum specimens collected in Salvador, Bahia, the epicenter for HTLV-1 infection in Brazil. Using a Western blot test as the comparator, 55 serum specimens were HTLV-I positive, 5 were HTLV-I and HTLV-II positive, and 58 were negative. The sensitivity of the rapid screening test for HTLV-1 was 96.7% and the specificity was 100%. The rapid screening test did not show cross-reaction with serum specimens from individuals with potentially interfering infections including those caused by HTLV-II, HIV-I, HIV-II, hepatitis A virus, hepatitis B virus, hepatitis C virus, herpes simplex virus, Epstein–Barr virus, SARS-CoV-2, Chlamydia trachomatis, Neisseria gonorrhoeae, Treponema pallidum, Toxoplasma gondii, and Plasmodium falciparum. The rapid screening test also did not show cross-reaction with potentially interfering substances. Strategies for HTLV diagnosis in non- and high-endemic areas can be improved with low-cost, rapid screening tests. Full article
(This article belongs to the Special Issue Diagnostic Virology during the COVID-19 Pandemic - Business as Usual)
Show Figures

Figure 1

16 pages, 2031 KiB  
Article
Towards Next-Generation Sequencing for HIV-1 Drug Resistance Testing in a Clinical Setting
by Calesta Hui Yi Teo, Nurul Hannah Binte Norhisham, Ogestelli Fabia Lee, Siyu Png, Chean Nee Chai, Gabriel Yan, Julian Wei-Tze Tang and Chun Kiat Lee
Viruses 2022, 14(10), 2208; https://0-doi-org.brum.beds.ac.uk/10.3390/v14102208 - 07 Oct 2022
Cited by 1 | Viewed by 2074
Abstract
The HIV genotypic resistance test (GRT) is a standard of care for the clinical management of HIV/AIDS patients. In recent decades, population or Sanger sequencing has been the foundation for drug resistance monitoring in clinical settings. However, the advent of high-throughput or next-generation [...] Read more.
The HIV genotypic resistance test (GRT) is a standard of care for the clinical management of HIV/AIDS patients. In recent decades, population or Sanger sequencing has been the foundation for drug resistance monitoring in clinical settings. However, the advent of high-throughput or next-generation sequencing has caused a paradigm shift towards the detection and characterization of low-abundance covert mutations that would otherwise be missed by population sequencing. This is clinically significant, as these mutations can potentially compromise the efficacy of antiretroviral therapy, causing poor virologic suppression. Therefore, it is important to develop a more sensitive method so as to reliably detect clinically actionable drug-resistant mutations (DRMs). Here, we evaluated the diagnostic performance of a laboratory-developed, high-throughput, sequencing-based GRT using 103 archived clinical samples that were previously tested for drug resistance using population sequencing. As expected, high-throughput sequencing found all the DRMs that were detectable by population sequencing. Significantly, 78 additional DRMs were identified only by high-throughput sequencing, which is statistically significant based on McNemar’s test. Overall, our results complement previous studies, supporting the notion that the two methods are well correlated, and the high-throughput sequencing method appears to be an excellent alternative for drug resistance testing in a clinical setting. Full article
(This article belongs to the Special Issue Diagnostic Virology during the COVID-19 Pandemic - Business as Usual)
Show Figures

Figure 1

14 pages, 2874 KiB  
Article
An Unusual Resurgence of Human Metapneumovirus in Western Australia Following the Reduction of Non-Pharmaceutical Interventions to Prevent SARS-CoV-2 Transmission
by David Anthony Foley, Chisha T. Sikazwe, Cara A. Minney-Smith, Timo Ernst, Hannah C. Moore, Mark P. Nicol, David W. Smith, Avram Levy and Christopher C. Blyth
Viruses 2022, 14(10), 2135; https://0-doi-org.brum.beds.ac.uk/10.3390/v14102135 - 28 Sep 2022
Cited by 10 | Viewed by 2300
Abstract
Non-pharmaceutical interventions (NPIs) to reduce SARS-CoV-2 transmission disrupted respiratory virus seasonality. We examined the unusual return of human metapneumovirus (hMPV) in Western Australia following a period of absence in 2020. We analysed hMPV laboratory testing data from 1 January 2017 to 31 December [...] Read more.
Non-pharmaceutical interventions (NPIs) to reduce SARS-CoV-2 transmission disrupted respiratory virus seasonality. We examined the unusual return of human metapneumovirus (hMPV) in Western Australia following a period of absence in 2020. We analysed hMPV laboratory testing data from 1 January 2017 to 31 December 2021. Whole-genome sequencing of selected hMPV-positive samples was performed using a tiled-amplicon approach. Following an absence in spring 2020, an unusual hMPV surge was observed during the wet summer season in the tropical Northern region in late 2020. Following a six-month delay, an intense winter season occurred in the subtropical/temperate Southern and Metropolitan regions. Compared to 2017–2019, hMPV incidence in 2021 increased by 3-fold, with a greater than 4-fold increase in children aged 1–4 years. There was a collapse in hMPV diversity in 2020, with the emergence of a single subtype. NPIs contributed to an absent 2020 season and a clonal hMPV resurgence. The summer surge and delayed winter season suggest that prevailing temperature and humidity are keys determinant of hMPV transmission. The increased incidence in 2021 was linked to an expanded cohort of hMPV-naïve 1–4-year-old children and waning population immunity. Further intense and unusual respiratory virus seasons are expected as COVID-19 associated NPIs are removed. Full article
(This article belongs to the Special Issue Diagnostic Virology during the COVID-19 Pandemic - Business as Usual)
Show Figures

Figure 1

12 pages, 983 KiB  
Article
Emerging Genotype IV Japanese Encephalitis Virus Outbreak in New South Wales, Australia
by Annaleise R. Howard-Jones, David Pham, Neisha Jeoffreys, John-Sebastian Eden, Linda Hueston, Alison M. Kesson, Vanathi Nagendra, Harsha Samarasekara, Peter Newton, Sharon C.-A. Chen, Matthew V. O’Sullivan, Susan Maddocks, Dominic E. Dwyer and Jen Kok
Viruses 2022, 14(9), 1853; https://0-doi-org.brum.beds.ac.uk/10.3390/v14091853 - 24 Aug 2022
Cited by 11 | Viewed by 3815
Abstract
The detection of a new and unexpected Japanese encephalitis virus (JEV) outbreak in March 2022 in Australia, where JEV is not endemic, demanded the rapid development of a robust diagnostic framework to facilitate the testing of suspected patients across the state of New [...] Read more.
The detection of a new and unexpected Japanese encephalitis virus (JEV) outbreak in March 2022 in Australia, where JEV is not endemic, demanded the rapid development of a robust diagnostic framework to facilitate the testing of suspected patients across the state of New South Wales (NSW). This nascent but comprehensive JEV diagnostic service encompassed serological, molecular and metagenomics testing within a centralised reference laboratory. Over the first three months of the outbreak (4 March 2022 to 31 May 2022), 1,061 prospective samples were received from 878 NSW residents for JEV testing. Twelve confirmed cases of Japanese encephalitis (JE) were identified, including ten cases diagnosed by serology alone, one case by metagenomic next generation sequencing and real-time polymerase chain reaction (RT-PCR) of brain tissue and serology, and one case by RT-PCR of cerebrospinal fluid, providing an incidence of JE over this period of 0.15/100,000 persons in NSW. As encephalitis manifests in <1% of cases of JEV infection, the population-wide prevalence of JEV infection is likely to be substantially higher. Close collaboration with referring laboratories and clinicians was pivotal to establishing successful JEV case ascertainment for this new outbreak. Sustained and coordinated animal, human and environmental surveillance within a OneHealth framework is critical to monitor the evolution of the current outbreak, understand its origins and optimise preparedness for future JEV and arbovirus outbreaks. Full article
(This article belongs to the Special Issue Diagnostic Virology during the COVID-19 Pandemic - Business as Usual)
Show Figures

Figure 1

10 pages, 572 KiB  
Article
Evaluation of Two Broadly Used Commercial Methods for Detection of Respiratory Viruses with a Recently Added New Target for Detection of SARS-CoV-2
by Monika Jevšnik Virant, Tina Uršič, Rok Kogoj, Miša Korva, Miroslav Petrovec and Tatjana Avšič-Županc
Viruses 2022, 14(7), 1530; https://0-doi-org.brum.beds.ac.uk/10.3390/v14071530 - 13 Jul 2022
Cited by 4 | Viewed by 1263
Abstract
The clinical symptoms caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are nonspecific and can be associated with most other respiratory viruses that cause acute respiratory tract infections (ARI). Because the clinical differentiation of COVID-19 patients from those with other respiratory [...] Read more.
The clinical symptoms caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are nonspecific and can be associated with most other respiratory viruses that cause acute respiratory tract infections (ARI). Because the clinical differentiation of COVID-19 patients from those with other respiratory viruses is difficult, the evaluation of automated methods to detect important respiratory viruses together with SARS-CoV-2 seems necessary. Therefore, this study compares two molecular assays for the detection of respiratory viruses, including SARS-CoV-2: the Respiratory Viruses 16-Well Assay (AusDiagnostics, Pty Ltd., Mascot, Australia) and the Allplex™ RV Essential Assay coupled with the Allplex™-nCoV Assay (Seegene Inc., Seoul, Korea). The two methods (AusDiagnostics and AlplexTM-nCoV Assay SARS-CoV-2) had 98.6% agreement with the reference method, cobas 6800, for the detection of SARS-CoV-2. Agreement between the AusDiagnostics assay and the AlplexTM RV Essential Assay for the detection of seven respiratory viruses was 99%. In our experience, the Respiratory Viruses 16-Well Assay proved to be the most valuable and useful medium-throughput method for simultaneous detection of important respiratory viruses and SARS-CoV-2. The main advantages of the method are high specificity for all targets included and their simultaneous detection and medium throughput with the option of having multiple instruments provide a constant run. Full article
(This article belongs to the Special Issue Diagnostic Virology during the COVID-19 Pandemic - Business as Usual)
Show Figures

Figure 1

18 pages, 998 KiB  
Article
Was the Reduction in Seasonal Influenza Transmission during 2020 Attributable to Non-Pharmaceutical Interventions to Contain Coronavirus Disease 2019 (COVID-19) in Japan?
by Keita Wagatsuma, Iain S. Koolhof and Reiko Saito
Viruses 2022, 14(7), 1417; https://0-doi-org.brum.beds.ac.uk/10.3390/v14071417 - 28 Jun 2022
Cited by 8 | Viewed by 2052
Abstract
We quantified the effects of adherence to various non-pharmaceutical interventions (NPIs) on the seasonal influenza epidemic dynamics in Japan during 2020. The total monthly number of seasonal influenza cases per sentinel site (seasonal influenza activity) reported to the National Epidemiological Surveillance of Infectious [...] Read more.
We quantified the effects of adherence to various non-pharmaceutical interventions (NPIs) on the seasonal influenza epidemic dynamics in Japan during 2020. The total monthly number of seasonal influenza cases per sentinel site (seasonal influenza activity) reported to the National Epidemiological Surveillance of Infectious Diseases and alternative NPI indicators (retail sales of hand hygiene products and number of airline passenger arrivals) from 2014–2020 were collected. The average number of monthly seasonal influenza cases in 2020 had decreased by approximately 66.0% (p < 0.001) compared to those in the preceding six years. An increase in retail sales of hand hygiene products of ¥1 billion over a 3-month period led to a 15.5% (95% confidence interval [CI]: 10.9–20.0%; p < 0.001) reduction in seasonal influenza activity. An increase in the average of one million domestic and international airline passenger arrivals had a significant association with seasonal influenza activity by 11.6% at lag 0–2 months (95% CI: 6.70–16.5%; p < 0.001) and 30.9% at lag 0–2 months (95% CI: 20.9–40.9%; p < 0.001). NPI adherence was associated with decreased seasonal influenza activity during the COVID-19 pandemic in Japan, which has crucial implications for planning public health interventions to minimize the health consequences of adverse seasonal influenza epidemics. Full article
(This article belongs to the Special Issue Diagnostic Virology during the COVID-19 Pandemic - Business as Usual)
Show Figures

Figure 1

9 pages, 1319 KiB  
Communication
Variation in Thermal Stability among Respiratory Syncytial Virus Clinical Isolates under Non-Freezing Conditions
by Yuki Kitai, Ko Sato, Kazuya Shirato, Suguru Ohmiya, Oshi Watanabe, Tomoko Kisu, Reiko Ota, Makoto Takeda, Kazuyoshi Kawakami and Hidekazu Nishimura
Viruses 2022, 14(4), 679; https://0-doi-org.brum.beds.ac.uk/10.3390/v14040679 - 25 Mar 2022
Cited by 2 | Viewed by 2425
Abstract
Virus isolates are not only useful for diagnosing infections, e.g., respiratory syncytial virus (RSV), but can also facilitate many aspects of practical viral studies such as analyses of antigenicity and the action mechanisms of antivirals, among others. We have been isolating RSV from [...] Read more.
Virus isolates are not only useful for diagnosing infections, e.g., respiratory syncytial virus (RSV), but can also facilitate many aspects of practical viral studies such as analyses of antigenicity and the action mechanisms of antivirals, among others. We have been isolating RSV from clinical specimens from patients with respiratory symptoms every year since our first isolation of RSV in 1964, and isolation rates have varied considerably over the years. As collected clinical specimens are conventionally stored in a refrigerator from collection to inoculation into cells, we hypothesized that certain storage conditions or associated factors might account for these differences. Hence, we evaluated the thermal stability of a total of 64 viruses isolated from 1998 to 2018 upon storage at 4 °C and 20 °C for a defined duration. Interestingly, and contrary to our current understanding, 22 strains (34%) showed a greater loss of viability upon short-term storage at 4 °C than at 20 °C. Thirty-seven strains (57%) showed an almost equal loss, and only five strains (8%) were more stable at 4 °C than at 20 °C. This finding warrants reconsideration of the temperature for the temporary storage of clinical samples for RSV isolation. Full article
(This article belongs to the Special Issue Diagnostic Virology during the COVID-19 Pandemic - Business as Usual)
Show Figures

Figure 1

10 pages, 4538 KiB  
Communication
Clinical, Laboratory, and Molecular Epidemiology of an Outbreak of Aseptic Meningitis Due to a Triple-Recombinant Echovirus in Ashburton, New Zealand
by Meik Dilcher, Julia C. Howard, Simon C. Dalton, Trevor Anderson, Richard T. Clinghan and Anja M. Werno
Viruses 2022, 14(4), 658; https://0-doi-org.brum.beds.ac.uk/10.3390/v14040658 - 22 Mar 2022
Cited by 3 | Viewed by 1778
Abstract
Here, we describe a small enterovirus outbreak including nine cases of aseptic meningitis in a New Zealand hospital in 2017. Most patients had a lymphocytic predominance in the CSF, their length of stay was short, and there were no paediatric cases or ICU [...] Read more.
Here, we describe a small enterovirus outbreak including nine cases of aseptic meningitis in a New Zealand hospital in 2017. Most patients had a lymphocytic predominance in the CSF, their length of stay was short, and there were no paediatric cases or ICU admissions. VP1 genotyping revealed that the outbreak was caused by an echovirus E30 strain closely related to strains reported from the US, UK, Brazil, and Denmark. They all form a separate cluster within lineage “h”, which leads to the proposal of establishing a new lineage tentatively named “j” for this group of echovirus E30 strains. However, whole genome sequencing and reference mapping to echovirus E30 sequences showed very poor mapping of reads to the 3′ half of the genome. Further bioinformatic analysis indicated that the causative agent of this outbreak might be a mosaic triple-recombinant enterovirus composed of echovirus E6, echovirus E11, and echovirus E30 genome segments. Full article
(This article belongs to the Special Issue Diagnostic Virology during the COVID-19 Pandemic - Business as Usual)
Show Figures

Figure 1

Other

Jump to: Research

4 pages, 330 KiB  
Brief Report
Influenza A Outbreaks in Two Professional Ice Hockey Teams during COVID-19 Epidemic
by Niklas Lindblad, Timo Hänninen, Maarit Valtonen, Olli J. Heinonen, Matti Waris and Olli Ruuskanen
Viruses 2022, 14(12), 2730; https://0-doi-org.brum.beds.ac.uk/10.3390/v14122730 - 07 Dec 2022
Cited by 1 | Viewed by 1151
Abstract
Influenza A outbreaks occurred in two professional hockey teams just after two games they played against each other. Thirteen players and two staff members fell ill during 17–20 April 2022, while COVID-19 was prevalent. Altogether, seven players missed an important game due to [...] Read more.
Influenza A outbreaks occurred in two professional hockey teams just after two games they played against each other. Thirteen players and two staff members fell ill during 17–20 April 2022, while COVID-19 was prevalent. Altogether, seven players missed an important game due to influenza. The rapid diagnosis permitted effective pharmaceutical and nonpharmaceutical control of the outbreaks. Full article
(This article belongs to the Special Issue Diagnostic Virology during the COVID-19 Pandemic - Business as Usual)
Show Figures

Figure 1

6 pages, 886 KiB  
Brief Report
Performing under Pressure: Insights into the Diagnostic Testing Burden at a UK National Health Service Clinical Virology Laboratory during the SARS-CoV-2 Pandemic
by Paul William Bird, Georgina Taylor, Jessica Cafferata, Judi Gardener, Claire L. McMurray, Oliver Fletcher, Oliver T. R. Toovey, Christopher W. Holmes and Julian W. Tang
Viruses 2022, 14(10), 2233; https://0-doi-org.brum.beds.ac.uk/10.3390/v14102233 - 12 Oct 2022
Viewed by 1131
Abstract
UK National Health Service (NHS) Clinical Virology Departments provide a repertoire of tests on clinical samples to detect the presence of viral genomic material or host immune responses to viral infection. In December 2019, a novel coronavirus (SARS-CoV-2) emerged which quickly developed into [...] Read more.
UK National Health Service (NHS) Clinical Virology Departments provide a repertoire of tests on clinical samples to detect the presence of viral genomic material or host immune responses to viral infection. In December 2019, a novel coronavirus (SARS-CoV-2) emerged which quickly developed into a global pandemic; NHS laboratories responded rapidly to upscale their testing capabilities. To date, there is little information on the impact of increased SARS-CoV-2 screening on non-SARS-CoV-2 testing within NHS laboratories. This report details the virology test requests received by the Leicester-based NHS Virology laboratory from January 2018 to May 2022. Data show that in spite of a dramatic increase in screening, along with multiple logistic and staffing issues, the Leicester Virology Department was mostly able to maintain the same level of service for non-respiratory virus testing while meeting the new increase in SARS-CoV-2 testing. Full article
(This article belongs to the Special Issue Diagnostic Virology during the COVID-19 Pandemic - Business as Usual)
Show Figures

Figure 1

Back to TopTop