Research

Jump to: Review

16 pages, 1306 KiB

Open AccessArticle

Association of Ambient Temperature and Absolute Humidity with the Effective Reproduction Number of COVID-19 in Japan

by Keita Wagatsuma

Pathogens 2023, 12(11), 1307; https://doi.org/10.3390/pathogens12111307 - 01 Nov 2023

Viewed by 912

This study aimed to quantify the exposure-lag-response relationship between short-term changes in ambient temperature and absolute humidity and the transmission dynamics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Japan. The prefecture-specific daily time-series of newly confirmed cases, meteorological variables, retail and [...] Read more.

This study aimed to quantify the exposure-lag-response relationship between short-term changes in ambient temperature and absolute humidity and the transmission dynamics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Japan. The prefecture-specific daily time-series of newly confirmed cases, meteorological variables, retail and recreation mobility, and Government Stringency Index were collected for all 47 prefectures of Japan for the study period from 15 February 2020 to 15 October 2022. Generalized conditional Gamma regression models were formulated with distributed lag nonlinear models by adopting the case-time-series design to assess the independent and interactive effects of ambient temperature and absolute humidity on the relative risk (RR) of the time-varying effective reproductive number (R_t). With reference to 17.8 °C, the corresponding cumulative RRs (95% confidence interval) at a mean ambient temperatures of 5.1 °C and 27.9 °C were 1.027 (1.016–1.038) and 0.982 (0.974–0.989), respectively, whereas those at an absolute humidity of 4.2 m/g³ and 20.6 m/g³ were 1.026 (1.017–1.036) and 0.995 (0.985–1.006), respectively, with reference to 10.6 m/g³. Both extremely hot and humid conditions synergistically and slightly reduced the R_t. Our findings provide a better understanding of how meteorological drivers shape the complex heterogeneous dynamics of SARS-CoV-2 in Japan. Full article

(This article belongs to the Special Issue Epidemiology of Emerging Infectious Disease: Importance of Surveillance and Detection in Public Health Initiatives)

► Show Figures

Figure 1

13 pages, 1642 KiB

Open AccessCommunication

Identification of Potential Hazards Associated with South Korean Prawns and Monitoring Results Targeting Fishing Bait

by Gyoungsik Kang, Won-Sik Woo, Kyung-Ho Kim, Ha-Jeong Son, Min-Young Sohn, Hee Jeong Kong, Young-Ok Kim, Dong-Gyun Kim, Eun Mi Kim, Eun Soo Noh and Chan-Il Park

Pathogens 2023, 12(10), 1228; https://doi.org/10.3390/pathogens12101228 - 10 Oct 2023

Viewed by 1101

Abstract

This study detected two potential pathogens, Vibro parahaemolyticus, which causes acute hepatopancreatic necrosis disease (AHPND), and white spot syndrome virus (WSSV), in fishing bait in South Korea. However, their infectious nature was not confirmed, possibly due to the degradation caused by freezing/thawing [...] Read more.

This study detected two potential pathogens, Vibro parahaemolyticus, which causes acute hepatopancreatic necrosis disease (AHPND), and white spot syndrome virus (WSSV), in fishing bait in South Korea. However, their infectious nature was not confirmed, possibly due to the degradation caused by freezing/thawing or prolonged storage under frozen conditions. While infectivity was not confirmed in this study, there is still a significant risk of exposure to these aquatic products. Furthermore, fishing bait and feed should be handled with caution as they are directly exposed to water, increasing the risk of disease transmission. In Australia, cases of WSSV infection caused by imported shrimp intended for human consumption have occurred, highlighting the need for preventive measures. While freezing/thawing is a method for inactivating pathogens, there are still regulatory and realistic issues to be addressed. Full article

(This article belongs to the Special Issue Epidemiology of Emerging Infectious Disease: Importance of Surveillance and Detection in Public Health Initiatives)

► Show Figures

Figure 1

15 pages, 3044 KiB

Open AccessArticle

Molecular Epidemiology and Genetic Diversity of Human Respiratory Syncytial Virus in Sicily during Pre- and Post-COVID-19 Surveillance Seasons

by Fabio Tramuto, Carmelo Massimo Maida, Walter Mazzucco, Claudio Costantino, Emanuele Amodio, Giuseppe Sferlazza, Adriana Previti, Palmira Immordino and Francesco Vitale

Pathogens 2023, 12(9), 1099; https://doi.org/10.3390/pathogens12091099 - 28 Aug 2023

Cited by 2 | Viewed by 898

Abstract

Human respiratory syncytial virus (hRSV) is an important pathogen of acute respiratory tract infection of global significance. In this study, we investigated the molecular epidemiology and the genetic variability of hRSV over seven surveillance seasons between 2015 and 2023 in Sicily, Italy. hRSV [...] Read more.

Human respiratory syncytial virus (hRSV) is an important pathogen of acute respiratory tract infection of global significance. In this study, we investigated the molecular epidemiology and the genetic variability of hRSV over seven surveillance seasons between 2015 and 2023 in Sicily, Italy. hRSV subgroups co-circulated through every season, although hRSV-B mostly prevailed. After the considerable reduction in the circulation of hRSV due to the widespread implementation of non-pharmaceutical preventive measures during the COVID-19 pandemic, hRSV rapidly re-emerged at a high intensity in 2022–2023. The G gene was sequenced for genotyping and analysis of deduced amino acids. A total of 128 hRSV-A and 179 hRSV-B G gene sequences were obtained. The phylogenetic analysis revealed that the GA2.3.5a (ON1) and GB5.0.5a (BA9) genotypes were responsible for the hRSV epidemics in Sicily.; only one strain belonged to the genotype GB5.0.4a. No differences were observed in the circulating genotypes during pre- and post-pandemic years. Amino acid sequence alignment revealed the continuous evolution of the G gene, with a combination of amino acid changes specifically appearing in 2022–2023. The predicted N-glycosylation sites were relatively conserved in ON1 and BA9 genotype strains. Our findings augment the understanding and prediction of the seasonal evolution of hRSV at the local level and its implication in the monitoring of novel variants worth considering in better design of candidate vaccines. Full article

(This article belongs to the Special Issue Epidemiology of Emerging Infectious Disease: Importance of Surveillance and Detection in Public Health Initiatives)

► Show Figures

Figure 1

17 pages, 3102 KiB

Open AccessArticle

Timeline of SARS-CoV-2 Transmission in Sabah, Malaysia: Tracking the Molecular Evolution

by Krishnan Nair Balakrishnan, Chee Wei Yew, Eric Tzyy Jiann Chong, Sylvia Daim, Nurul Elyani Mohamad, Kenneth Rodrigues and Ping-Chin Lee

Pathogens 2023, 12(8), 1047; https://doi.org/10.3390/pathogens12081047 - 15 Aug 2023

Cited by 2 | Viewed by 1131

Abstract

Background: The COVID-19 pandemic poses an unprecedented public health challenge in Malaysia. The impact of COVID-19 varies between countries, including geographically divided states within a country. The deadly transmission of COVID-19 has taken a heavy toll in Sabah, Malaysia’s third most populous state, [...] Read more.

Background: The COVID-19 pandemic poses an unprecedented public health challenge in Malaysia. The impact of COVID-19 varies between countries, including geographically divided states within a country. The deadly transmission of COVID-19 has taken a heavy toll in Sabah, Malaysia’s third most populous state, contributing nearly 10% to the recorded national death toll as of 31 December 2022. Although several SARS-CoV-2 genome sequences have been analysed in Malaysia, molecular epidemiology data from Sabah focusing on the diversity and evolution of SARS-CoV-2 variants are still lacking. This study examines the major SARS-CoV-2 variants and emerging mutations from Sabah, the Malaysian Borneo, which is geographically divided from West Malaysia by the South China Sea. Methods: A total of 583 COVID-19 samples were subjected to whole genome sequencing and analysed with an additional 1123 Sabah COVID-19 sequences retrieved from the GISAID EpiCoV consortium. Nextclade and Pangolin were used to classify these sequences according to the clades and lineages. To determine the molecular evolutionary characteristics, Bayesian time-scaled phylogenetic analysis employing the maximum likelihood algorithm was performed on selected SARS-CoV-2 genome sequences, using the Wuhan-Hu-1 sequence as a reference. Results: Sabah was affected starting from the second COVID-19 wave in Malaysia, and the early sequences were classified under the O clade. The clade was gradually replaced during subsequent waves by G, GH, GK and GRA, with the latter being dominant as of December 2022. Phylogenetically, the Delta isolates in this study belong to the three main subclades 21A, 21J and 21I, while Omicron isolates belong to 21M, 21L and 22B. The time-scaled phylogeny suggested that SARS-CoV-2 introduced into Sabah originated from Peninsular Malaysia in early March 2020, and phylodynamic analysis indicated that increased viral spread was observed in early March and declined in late April, followed by an evolutionary stationary phase in June 2020. Conclusion: Continuous molecular epidemiology of SARS-CoV-2 in Sabah will provide a deeper understanding of the emergence and dominance of each variant in the locality, thus facilitating public health intervention measures. Full article

(This article belongs to the Special Issue Epidemiology of Emerging Infectious Disease: Importance of Surveillance and Detection in Public Health Initiatives)

► Show Figures

Figure 1

17 pages, 3176 KiB

Open AccessArticle

Enhancing Insights into Australia’s Gonococcal Surveillance Programme through Stochastic Modelling

by Phu Cong Do, Yibeltal Assefa Alemu and Simon Andrew Reid

Pathogens 2023, 12(7), 907; https://doi.org/10.3390/pathogens12070907 - 04 Jul 2023

Viewed by 714

Abstract

Continued surveillance of antimicrobial resistance is critical as a feedback mechanism for the generation of concerted public health action. A characteristic of importance in evaluating disease surveillance systems is representativeness. Scenario tree modelling offers an approach to quantify system representativeness. This paper utilises [...] Read more.

Continued surveillance of antimicrobial resistance is critical as a feedback mechanism for the generation of concerted public health action. A characteristic of importance in evaluating disease surveillance systems is representativeness. Scenario tree modelling offers an approach to quantify system representativeness. This paper utilises the modelling approach to assess the Australian Gonococcal Surveillance Programme’s representativeness as a case study. The model was built by identifying the sequence of events necessary for surveillance output generation through expert consultation and literature review. A scenario tree model was developed encompassing 16 dichotomous branches representing individual system sub-components. Key classifications included biological sex, clinical symptom status, and location of healthcare service access. The expected sensitivities for gonococcal detection and antibiotic status ascertainment were 0.624 (95% CI; 0.524, 0.736) and 0.144 (95% CI; 0.106, 0.189), respectively. Detection capacity of the system was observed to be high overall. The stochastic modelling approach has highlighted the need to consider differential risk factors such as sex, health-seeking behaviours, and clinical behaviour in sample generation. Actionable points generated by this study include modification of clinician behaviour and supplementary systems to achieve a greater contextual understanding of the surveillance data generation process. Full article

(This article belongs to the Special Issue Epidemiology of Emerging Infectious Disease: Importance of Surveillance and Detection in Public Health Initiatives)

► Show Figures

Figure 1

13 pages, 1087 KiB

Open AccessArticle

Wastewater-Based Epidemiology as a Tool to Detect SARS-CoV-2 Circulation at the Community Level: Findings from a One-Year Wastewater Investigation Conducted in Sicily, Italy

by Carmelo Massimo Maida, Fabio Tramuto, Giovanni Maurizio Giammanco, Roberta Palermo, Walter Priano, Simona De Grazia, Giuseppa Purpari, Giuseppina La Rosa, Elisabetta Suffredini, Luca Lucentini, Mario Palermo, Walter Pollina Addario, Giorgio Graziano, Palmira Immordino, Francesco Vitale, SARI Collaboration Group and Walter Mazzucco

Pathogens 2023, 12(6), 748; https://doi.org/10.3390/pathogens12060748 - 23 May 2023

Cited by 2 | Viewed by 1335

Abstract

Wastewater-based epidemiology is a well-established tool for detecting and monitoring the spread of enteric pathogens and the use of illegal drugs in communities in real time. Since only a few studies in Italy have investigated the correlation between SARS-CoV-2 in wastewater and the [...] Read more.

Wastewater-based epidemiology is a well-established tool for detecting and monitoring the spread of enteric pathogens and the use of illegal drugs in communities in real time. Since only a few studies in Italy have investigated the correlation between SARS-CoV-2 in wastewater and the prevalence of COVID-19 cases from clinical testing, we conducted a one-year wastewater surveillance study in Sicily to correlate the load of SARS-CoV-2 RNA in wastewater and the reported cumulative prevalence of COVID-19 in 14 cities from October 2021 to September 2022. Furthermore, we investigated the role of SARS-CoV-2 variants and subvariants in the increase in the number of SARS-CoV-2 infections. Our findings showed a significant correlation between SARS-CoV-2 RNA load in wastewater and the number of active cases reported by syndromic surveillance in the population. Moreover, the correlation between SARS-CoV-2 in wastewater and the active cases remained high when a lag of 7 or 14 days was considered. Finally, we attributed the epidemic waves observed to the rapid emergence of the Omicron variant and the BA.4 and BA.5 subvariants. We confirmed the effectiveness of wastewater monitoring as a powerful epidemiological proxy for viral variant spread and an efficient complementary method for surveillance. Full article

(This article belongs to the Special Issue Epidemiology of Emerging Infectious Disease: Importance of Surveillance and Detection in Public Health Initiatives)

► Show Figures

Graphical abstract

8 pages, 509 KiB

Open AccessArticle

Campylobacter spp. Prevalence in Santiago, Chile: A Study Based on Molecular Detection in Clinical Stool Samples from 2014 to 2019

by Lorena Porte, Caricia Pérez, Mario Barbé, Carmen Varela, Valeska Vollrath, Paulette Legarraga and Thomas Weitzel

Pathogens 2023, 12(3), 504; https://doi.org/10.3390/pathogens12030504 - 22 Mar 2023

Cited by 2 | Viewed by 1169

Abstract

Campylobacter spp. is an emerging cause of infectious diarrhea worldwide. In South American countries such as Chile, its prevalence is underestimated due to inadequate detection methods. Gastrointestinal multiplex PCR panels (GMP) permit rapid and sensitive detection of bacterial pathogens and provide important epidemiological [...] Read more.

Campylobacter spp. is an emerging cause of infectious diarrhea worldwide. In South American countries such as Chile, its prevalence is underestimated due to inadequate detection methods. Gastrointestinal multiplex PCR panels (GMP) permit rapid and sensitive detection of bacterial pathogens and provide important epidemiological information. This study aimed to analyze Campylobacter epidemiology using the results of molecular methods and to compare molecular detection results to those of culture methods. We performed a retrospective, descriptive analysis of Campylobacter spp. detected in clinical stool samples between 2014–2019 by GMP and culture. Within 16,582 specimens examined by GMP, Campylobacter was the most prevalent enteropathogenic bacteria (8.5%), followed by Salmonella spp. (3.9%), Shigella spp./enteroinvasive Escherichia coli (EIEC) (1.9%), and Yersinia enterocolitica (0.8%). The highest Campylobacter prevalence occurred in 2014/2015. Campylobacteriosis affected more males (57.2%) and adults from 19–65 years (47.9%) and showed a bimodal seasonality with summer and winter peaks. In 11,251 routine stool cultures, Campylobacter spp. was detected in 4.6%, mostly C. jejuni (89.6%). Among 4533 samples tested by GMP and culture in parallel, GMP showed a superior sensitivity (99.1% versus 50%, respectively). The study suggests that Campylobacter spp. is the most frequent bacterial enteropathogen in Chile. Full article

(This article belongs to the Special Issue Epidemiology of Emerging Infectious Disease: Importance of Surveillance and Detection in Public Health Initiatives)

► Show Figures

Figure 1

9 pages, 591 KiB

Open AccessArticle

Value of Verbal Autopsy in a Fragile Setting: Reported versus Estimated Community Deaths Associated with COVID-19, Banadir, Somalia

by Tahlil Abdi Afrah, Lilly M. Nyagah, Asma Swaleh Ali, Mary Karanja, Hassan W. Nor, Solomon Abera, Ali Sh Mohamed, Mohamed Ahmed Yusuf Guled, Mohamed Mohamud Hassan Biday, Majdouline Obtel and Sk Md Mamunur Rahman Malik

Pathogens 2023, 12(2), 328; https://doi.org/10.3390/pathogens12020328 - 15 Feb 2023

Cited by 1 | Viewed by 1317

Abstract

Background: Accurate mortality data associated with infectious diseases such as coronavirus disease 2019 (COVID-19) are often unavailable in countries with fragile health systems such as Somalia. We compared officially reported COVID-19 deaths in Somalia with COVID-19 deaths estimated using verbal autopsy. Methods: We [...] Read more.

Background: Accurate mortality data associated with infectious diseases such as coronavirus disease 2019 (COVID-19) are often unavailable in countries with fragile health systems such as Somalia. We compared officially reported COVID-19 deaths in Somalia with COVID-19 deaths estimated using verbal autopsy. Methods: We interviewed relatives of deceased persons to collect information on symptoms, cause, and place of death. We compared these data with officially reported data and estimated the positive and negative predictive values of verbal autopsy. Results: We identified 530 deaths during March–October 2020. We classified 176 (33.2%) as probable COVID-19 deaths. Most deaths (78.5%; 416/530) occurred at home and 144 (34.6%) of these were attributed to COVID-19. The positive predictive value of verbal autopsy was lower for home deaths (22.3%; 95% CI: 15.7–30.1%) than for hospital deaths (32.3%; 95% CI: 16.7–51.4%). The negative predictive value was higher: 97.8% (95% CI: 95.0–99.3%) for home deaths and 98.4% (95% CI: 91.5–100%) for hospital deaths. Conclusions Verbal autopsy has acceptable predictive value to estimate COVID-19 deaths where disease prevalence is high and can provide data on the COVID-19 burden in countries with low testing and weak mortality surveillance where home deaths may be missed. Full article

(This article belongs to the Special Issue Epidemiology of Emerging Infectious Disease: Importance of Surveillance and Detection in Public Health Initiatives)

► Show Figures

Figure 1

10 pages, 597 KiB

Open AccessArticle

Using Zoos as Sentinels for Re-Emerging Arboviruses: Vector Surveillance during an Outbreak of Epizootic Hemorrhagic Disease at the Minnesota Zoo

by Bethany L. McGregor, Lindsey M. Reister-Hendricks, Cale Nordmeyer, Seth Stapleton, Travis M. Davis and Barbara S. Drolet

Pathogens 2023, 12(1), 140; https://doi.org/10.3390/pathogens12010140 - 14 Jan 2023

Cited by 2 | Viewed by 1859

Abstract

Vector-borne disease prevalence is increasing at a time when surveillance capacity in the United States is decreasing. One way to address this surveillance deficiency is to utilize established infrastructure, such as zoological parks, to investigate animal disease outbreaks and improve our epidemiological understanding [...] Read more.

Vector-borne disease prevalence is increasing at a time when surveillance capacity in the United States is decreasing. One way to address this surveillance deficiency is to utilize established infrastructure, such as zoological parks, to investigate animal disease outbreaks and improve our epidemiological understanding of vector-borne pathogens. During fall 2020, an outbreak of epizootic hemorrhagic disease (EHD) at the Minnesota Zoo resulted in morbidity and seroconversion of several collection animals. In response to this outbreak, insect surveillance was conducted, and the collected insects were tested for the presence of epizootic hemorrhagic disease virus (EHDV) by RT-qPCR to better understand the local transmitting vector populations responsible for the outbreak. Six pools of Culicoides biting midges were positive for EHDV, including three pools of Culicoides sonorensis, two pools of Culicoides variipennis, and a pool of degraded C. variipennis complex midges. All three endemic serotypes of EHDV (1, 2, and 6) were detected in both animals and midge pools from the premises. Despite this outbreak, no EHDV cases had been reported in wild animals near the zoo. This highlights the importance and utility of using animal holding facilities, such as zoos, as sentinels to better understand the spatio-temporal dynamics of pathogen transmission. Full article

(This article belongs to the Special Issue Epidemiology of Emerging Infectious Disease: Importance of Surveillance and Detection in Public Health Initiatives)

► Show Figures

Figure 1

10 pages, 433 KiB

Open AccessArticle

Changes in the Epidemiology of Respiratory Pathogens in Children during the COVID-19 Pandemic

by Asmae Lamrani Hanchi, Morad Guennouni, Toufik Ben Houmich, Mohamed Echchakery, Ghizlane Draiss, Noureddine Rada, Said Younous, Mohamed Bouskraoui and Nabila Soraa

Pathogens 2022, 11(12), 1542; https://doi.org/10.3390/pathogens11121542 - 15 Dec 2022

Cited by 9 | Viewed by 1697

Abstract

Since the outbreak of the COVID-19 pandemic, a significant decrease in non-COVID-19 respiratory illnesses were observed, suggesting that the implementation of measures against COVID-19 affected the transmission of other respiratory pathogens. The aim of this study was to highlight the changes in the [...] Read more.

Since the outbreak of the COVID-19 pandemic, a significant decrease in non-COVID-19 respiratory illnesses were observed, suggesting that the implementation of measures against COVID-19 affected the transmission of other respiratory pathogens. The aim of this study was to highlight the changes in the epidemiology of respiratory pathogens in children during the COVID-19 pandemic. All children with Severe Acute respiratory illness admitted to the pediatric departments between January 2018 and December 2021 with negative COVID-19 PCR, were enrolled. The detection of respiratory pathogens was made by the Film Array Respiratory Panel. A total of 902 respiratory specimens were tested. A significantly lower positivity rate during the COVID-19 period was found (p = 0.006), especially in infants under 6 months (p = 0.008). There was a substantial absence of detection of Respiratory Syncytial Virus and Influenza A during the winter season following the outbreak of the pandemic (p < 0.05; p = 0.002 respectively). An inter-seasonal resurgence of Respiratory Syncytial Virus was noted. Human Rhinovirus was detected throughout the year, and more prevalent in winter during COVID-19 (p = 0.0002). These changes could be explained by the impact of the implementation of preventive measures related to the COVID-19 pandemic on the transmission of respiratory pathogens in children. Full article

(This article belongs to the Special Issue Epidemiology of Emerging Infectious Disease: Importance of Surveillance and Detection in Public Health Initiatives)

► Show Figures

Figure 1

9 pages, 275 KiB

Open AccessArticle

Comparison of Three Real-Time PCR Assays for the Detection of Cyclospora cayetanensis in Stool Samples Targeting the 18S rRNA Gene and the hsp70 Gene

by Felix Weinreich, Andreas Hahn, Kirsten Alexandra Eberhardt, Torsten Feldt, Fred Stephen Sarfo, Veronica Di Cristanziano, Hagen Frickmann and Ulrike Loderstädt

Pathogens 2022, 11(2), 165; https://doi.org/10.3390/pathogens11020165 - 26 Jan 2022

Cited by 5 | Viewed by 2302

Abstract

Diagnostic real-time PCR for the detection of Cyclospora cayetanensis in human stool samples has been applied for two decades. However, recent comparative assessments between in-house and commercial assays suggested room for improvement regarding the agreement of positive signals of the applied real-time PCRs. [...] Read more.

Diagnostic real-time PCR for the detection of Cyclospora cayetanensis in human stool samples has been applied for two decades. However, recent comparative assessments between in-house and commercial assays suggested room for improvement regarding the agreement of positive signals of the applied real-time PCRs. In order to assess the effect of the choice of the target sequence, 3 inhouse real time PCR assays targeting the 18S rRNA gene (n = 2, one of them later referred to as SSU rRNA gene assay to avoid confusion) and the hsp70 gene of C. cayetanensis were compared in a head-to-head comparison with 905 samples with high pretest probability for C. cayetanensis infections from Ghanaian HIV patients in a test comparison without a reference standard. Only slight agreement kappa of 0.095 was observed. In the assays targeting the SSU rRNA gene, the 18S rRNA gene, and hsp70, positive signals were recorded in 63, 45, and 0 instances, respectively, with latent class analysis-based estimation of sensitivity of 32.2%, 23.3%, 0% as well as of specificity of 99.7%, 99.9% and 100%, respectively. High cycle threshold values with an average of about 35 indicated low quantities of target DNA in the samples with similar Ct values in concordantly and discordantly positive samples. In conclusion, the study suggested target-gene-specific differences in the diagnostic accuracy of real-time PCR-based diagnosis of C. cayetanensis as well as an ongoing need for further standardization of this diagnostic approach. Full article

(This article belongs to the Special Issue Epidemiology of Emerging Infectious Disease: Importance of Surveillance and Detection in Public Health Initiatives)

9 pages, 520 KiB

Open AccessArticle

Comparative Diagnostic Performance of a Novel Reverse Transcription Loop-Mediated Isothermal Amplification (RT-LAMP) Kit for the Rapid Detection of SARS-CoV-2

by Alexander Domnich, Andrea Orsi, Donatella Panatto, Vanessa De Pace, Valentina Ricucci, Patrizia Caligiuri, Giulia Guarona, Valerio Chessa, Diego Ferone, Simona Boccotti, Bianca Bruzzone and Giancarlo Icardi

Pathogens 2021, 10(12), 1629; https://doi.org/10.3390/pathogens10121629 - 15 Dec 2021

Cited by 2 | Viewed by 2662

Abstract

Although the reverse transcription-polymerase chain reaction (RT-PCR) is considered a standard-of-care assay for the laboratory diagnosis of SARS-CoV-2, several limitations of this method have been described. Reverse transcription loop-mediated isothermal amplification (RT-LAMP) is an alternative molecular assay and is potentially able to overcome [...] Read more.

Although the reverse transcription-polymerase chain reaction (RT-PCR) is considered a standard-of-care assay for the laboratory diagnosis of SARS-CoV-2, several limitations of this method have been described. Reverse transcription loop-mediated isothermal amplification (RT-LAMP) is an alternative molecular assay and is potentially able to overcome some intrinsic shortcomings of RT-PCR. In this study, we evaluated the diagnostic performance of the novel HG COVID-19 RT-LAMP assay. In this retrospective analysis, a total of 400 routinely collected leftover nasopharyngeal samples with a known RT-PCR result were tested by means of the HG COVID-19 RT-LAMP assay. The overall sensitivity and specificity values of HG COVID-19 RT-LAMP versus RT-PCR were 97.0% (95% CI: 93.6–98.9%) and 98.5% (95% CI: 95.7–99.7%), respectively. Inter-assay agreement was almost perfect (κ = 0.96). Concordance was perfect in samples with high viral loads (cycle threshold < 30). The average time to a positive result on RT-LAMP was 17 min. HG COVID-19 RT-LAMP is a reliable molecular diagnostic kit for detecting SARS-CoV-2, and its performance is comparable to that of RT-PCR. Shorter turnaround times and the possibility of performing molecular diagnostics in the point-of-care setting make it a valuable option for facilities without sophisticated laboratory equipment. Full article

(This article belongs to the Special Issue Epidemiology of Emerging Infectious Disease: Importance of Surveillance and Detection in Public Health Initiatives)

► Show Figures

Figure 1

Review

Jump to: Research

13 pages, 1297 KiB

Open AccessReview

Challenges in Direct Detection of Flaviviruses: A Review

by Bruna de Paula Dias, Camila Cavadas Barbosa, Cyntia Silva Ferreira, Samara Mayra Soares Alves dos Santos, Orlando Alfredo Pineda Arrieta, Wellington Carvalho Malta, Maria Laura Maximiano Dias Gomes, Mariela Alves e Silva, Júlia de Matos Fonseca, Lysandro Pinto Borges and Breno de Mello Silva

Pathogens 2023, 12(5), 643; https://doi.org/10.3390/pathogens12050643 - 26 Apr 2023

Cited by 4 | Viewed by 1630

Abstract

Arthropods transmit arboviruses via mosquito and tick bites to humans and other animals. The genus flavivirus, which causes diseases, sequelae, and thousands of deaths, mainly in developing and underdeveloped countries, is among the arboviruses of interest to public health. Given the importance of [...] Read more.

Arthropods transmit arboviruses via mosquito and tick bites to humans and other animals. The genus flavivirus, which causes diseases, sequelae, and thousands of deaths, mainly in developing and underdeveloped countries, is among the arboviruses of interest to public health. Given the importance of early and accurate diagnosis, this review analyzes the methods of direct detection of flaviviruses, such as reverse transcription loop-mediated isothermal amplification, microfluidics, localized surface plasmon resonance, and surface-enhanced Raman scattering, and presents the advantages, disadvantages, and detection limits identified in studies reported in the literature for each methodology. Among the different methods available, it is essential to balance four fundamental indicators to determine the ideal test: good sensitivity, high specificity, low false positive rate, and rapid results. Among the methods analyzed, reverse transcription loop-mediated isothermal amplification stands out, owing to result availability within a few minutes, with good sensitivity and specificity; in addition, it is the best-characterized methodology. Full article

(This article belongs to the Special Issue Epidemiology of Emerging Infectious Disease: Importance of Surveillance and Detection in Public Health Initiatives)

► Show Figures

Figure 1

14 pages, 3679 KiB

Open AccessReview

Placing Leishmaniasis in the Limelight through the Communicable Disease Surveillance System: An Experience from Sri Lanka

by Sonali Dinushika Gunasekara, Hasara Nuwangi, Nuwan Darshana Wickramasinghe, Kosala Weerakoon, Helen P. Price, Lisa Dikomitis and Suneth Buddhika Agampodi

Pathogens 2022, 11(6), 680; https://doi.org/10.3390/pathogens11060680 - 13 Jun 2022

Cited by 4 | Viewed by 2866

Abstract

Having an effective surveillance system is imperative to take timely and appropriate actions for disease control and prevention. In Sri Lanka, leishmaniasis was declared as a notifiable disease in 2008. This paper presents a comprehensive compilation of the up-to-date documents on the communicable [...] Read more.

Having an effective surveillance system is imperative to take timely and appropriate actions for disease control and prevention. In Sri Lanka, leishmaniasis was declared as a notifiable disease in 2008. This paper presents a comprehensive compilation of the up-to-date documents on the communicable disease and leishmaniasis surveillance in Sri Lanka in order to describe the importance of the existing leishmaniasis surveillance system and to identify gaps that need to be addressed. The documents perused included circulars, reports, manuals, guidelines, ordinances, presentations, and published articles. The disease trends reported were linked to important landmarks in leishmaniasis surveillance. The findings suggest that there is a well-established surveillance system in Sri Lanka having a massive impact on increased case detection, resulting in im-proved attention on leishmaniasis. However, the system is not without its short comings and there is room for further improvements. Full article

(This article belongs to the Special Issue Epidemiology of Emerging Infectious Disease: Importance of Surveillance and Detection in Public Health Initiatives)

► Show Figures