Identification of a Novel Pathogen Using Family-Wide PCR: Initial Confirmation of COVID-19 in Thailand

Wacharapluesadee, Supaporn; Buathong, Rome; Iamsirithawon, Sopon; Chaifoo, Walairat; Ponpinit, Teerada; Ruchisrisarod, Chanida; Sonpee, Chanikarn; Katasrila, Panticha; Yomrat, Siriporn; Ghai, Siriporn; Sirivichayakul, Sunee; Okada, Pilailuk Akkapaiboon; Mekha, Nanthawan; Karnkawinpong, Opart; Uttayamakul, Sumonmal; Vachiraphan, Apichart; Plipat, Tanarak; Hemachudha, Thiravat

doi:10.3389/fpubh.2020.555013

Cited by 6 publications

(5 citation statements)

References 17 publications

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“…At a low copy number of SARS-CoV-2 (Ct > 30) in wastewater specimens, the X-CoV PCR showed a higher sensitivity than the Q-CoV PCR assay (Table S3), which is hypothesized to be due to the number of primer mismatches. The W-CoV PCR could not detect SARS-CoV-2 in clinical samples and laboratory strains due to eight primer mismatches within the reverse primers [19,25], as confirmed in our study.…”

Section: Discussionsupporting

confidence: 80%

“…The Q-CoV PCR primers were designed in 2010 to detect bat SARS-like CoV using degenerate primers [ 26 ]. Despite 2–4 primer mismatches to SARS-CoV-2 ( Table S6 ), this protocol successfully detected the first COVID-19 case in Thailand [ 25 ], while the X-CoV PCR primers were newly designed in 2020 and have a 0–1 primer mismatch to SARS-CoV-2. Both assays have equal sensitivity at PCR Ct values less than 31 in human specimens ( Table S2 ).…”

Section: Discussionmentioning

confidence: 99%

“…MERS-CoV was first detected from an uncharacterized viral isolate with cytopathic effects using family wide CoV PCR [ 11 , 23 , 24 ]. The first COVID-19 case outside China was detected in Thailand [ 25 ], using two pan-CoV PCR assays developed by Quan et al [ 26 ] and Corman VM et al [ 27 ]. Coronavirus diversity was studied in multiple host taxa from twenty countries during the USAID PREDICT project to explore the factors driving viral diversity at a global scale [ 28 ].…”

Section: Introductionmentioning

confidence: 99%

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Comparative Performance in the Detection of Four Coronavirus Genera from Human, Animal, and Environmental Specimens

Wacharapluesadee,

Thippamom,

Hirunpatrawong

et al. 2024

Viruses

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Emerging coronaviruses (CoVs) are understood to cause critical human and domestic animal diseases; the spillover from wildlife reservoirs can result in mild and severe respiratory illness in humans and domestic animals and can spread more readily in these naïve hosts. A low-cost CoV molecular method that can detect a variety of CoVs from humans, animals, and environmental specimens is an initial step to ensure the early identification of known and new viruses. We examine a collection of 50 human, 46 wastewater, 28 bat, and 17 avian archived specimens using 3 published pan-CoV PCR assays called Q-, W-, and X-CoV PCR, to compare the performance of each assay against four CoV genera. X-CoV PCR can detect all four CoV genera, but Q- and W-CoV PCR failed to detect δ-CoV. In total, 21 (42.0%), 9 (18.0%), and 21 (42.0%) of 50 human specimens and 30 (65.22%), 6 (13.04%), and 27 (58.70%) of 46 wastewater specimens were detected using Q-, W-, and X-CoV PCR assays, respectively. The X-CoV PCR assay has a comparable sensitivity to Q-CoV PCR in bat CoV detection. Combining Q- and X-CoV PCR assays can increase sensitivity and avoid false negative results in the early detection of novel CoVs.

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Section: Discussionsupporting

confidence: 80%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Comparative Performance in the Detection of Four Coronavirus Genera from Human, Animal, and Environmental Specimens

Wacharapluesadee,

Thippamom,

Hirunpatrawong

et al. 2024

Viruses

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“…Expanding this comparison to four other studies that identified earlier cases, we inferred January 7, 2020 (95% CI December 22, 2019) as the most likely first case in Thailand. This is only 1 day after a case identified in a traveller to Thailand from Wuhan on January 8, 2020 [ 15 , 16 ]. However, the most likely first case in France was inferred as January 19, 2020 (95% CI January 4, 2020), while a retrospective review of medical records identified one patient as having COVID-19 from December 27 [ 6 ].…”

Section: Discussionmentioning

confidence: 99%

Dating first cases of COVID-19

2021

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Questions persist as to the origin of the COVID-19 pandemic. Evidence is building that its origin as a zoonotic spillover occurred prior to the officially accepted timing of early December, 2019. Here we provide novel methods to date the origin of COVID-19 cases. We show that six countries had exceptionally early cases, unlikely to represent part of their main case series. The model suggests a likely timing of the first case of COVID-19 in China as November 17 (95% CI October 4). Origination dates are discussed for the first five countries outside China and each continent. Results infer that SARS-CoV-2 emerged in China in early October to mid-November, and by January, had spread globally. This suggests an earlier and more rapid timeline of spread. Our study provides new approaches for estimating dates of the arrival of infectious diseases based on small samples that can be applied to many epidemiological situations.

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“…Secondly, HTS demonstrates superior sensitivity and speci city, enabling the identi cation of low-concentration pathogen nucleic acids and even offering effective detection for rare pathogens [11]. Additionally, this technology can uncover novel, previously unidenti ed pathogens [12]. By comparing and analyzing unknown sequences, it provides fresh insights for disease diagnosis and etiological research.…”

Section: Discussionmentioning

confidence: 99%

Leptospirosis-associated meningitis in a patient with Sjögren's Syndrome: a case report

Zhang,

Zheng

2023

Preprint

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Background Leptospirosis is a zoonotic disease that afflicts both humans and animals. It progresses from flu-like symptoms to more severe hepatic and renal failure, and may also lead to aseptic meningitis. Individuals with autoimmune diseases (ADs) are potentially more susceptible to Leptospirosis. Thus far, limited data has documented the association between Leptospirosis and autoimmune disorders.Case presentation The patient had a definitive pathological diagnosis of Sjögren's syndrome (SS). Due to recurrent headaches, the patient sought consultation with a neurologist. Lumbar puncture revealed elevated white blood cells and protein levels in the cerebrospinal fluid, along with decreased glucose. Tuberculous meningitis was suspected. Radiographic imaging exhibited meningeal enhancement, ventricular enlargement, and hydrocephalus. The patient commenced treatment with anti-tuberculosis therapy and corticosteroids. Subsequently, high-throughput sequencing (HTS) of cerebrospinal fluid identified the presence of Leptospira interrogans. The patient was ultimately diagnosed with Leptospiral meningitis, and underwent antimicrobial and immunosuppressive therapy, resulting in stabilization of the condition and gradual symptom recovery.Conclusions The case highlights the challenges in diagnosing and managing leptospirosis-related meningitis in the presence of ADs and emphasizes the importance of utilizing HTS for accurate pathogen detection. The potential correlation between leptospirosis and SS warrants further investigation, as does the need for multidisciplinary involvement in treatment strategies for such complex cases.

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Identification of a Novel Pathogen Using Family-Wide PCR: Initial Confirmation of COVID-19 in Thailand

Cited by 6 publications

References 17 publications

Comparative Performance in the Detection of Four Coronavirus Genera from Human, Animal, and Environmental Specimens

Comparative Performance in the Detection of Four Coronavirus Genera from Human, Animal, and Environmental Specimens

Dating first cases of COVID-19

Leptospirosis-associated meningitis in a patient with Sjögren's Syndrome: a case report

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