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1. Coinfection of severe acute respiratory syndrome coronavirus 2 and polyomavirus in a patient with coronavirus disease 2019 detected by enrichment next-generation sequencing: a case report

Author

Gunadi, Esensi Tarian Geometri, Pramana Adhityo, Ali Zainal Abidin, Marcellus, Dyah Ayu Puspitarani, Fadila Dyah Trie Utami, Kristy Iskandar, Hendra Wibawa, and Mohamad Saifudin Hakim

Subjects
SARS-CoV-2, Polyomavirus, Coinfection, Next, Generation sequencing, Whole, Medicine
Abstract

Abstract Background Severe acute respiratory syndrome coronavirus 2 was found first in Wuhan and declared a pandemic by the World Health Organization. Coinfection with other respiratory viruses may occur, complicating the diagnosis and treatment of coronavirus disease 2019 . Herein, we identified a Karolinska Institute polyomavirus Stockholm 60 present in a nasopharyngeal swab of a patient with severe acute respiratory syndrome coronavirus 2 infection using next-generation sequencing with an enrichment method. Case presentation A 24-year-old Indonesian woman was admitted to our institution due to a cough, cold, and sore throat. She had no family history of hypertension and diabetes mellitus, and she was well. Her vital signs were as follows: heart rate, 84 beats per minute; respiratory rate, 22 breaths per minute; temperature, 39 °C; and pulse oximetry, 96% on room air. She had runny nose and slightly inflamed pharynx. Her nasopharyngeal swab and real-time polymerase chain reaction were positive for the coronavirus disease 2019 nucleocapsid and open reading frame genes, with cycle threshold values of 32.33 and 33.74, respectively. Whole-genome sequencing of severe acute respiratory syndrome coronavirus 2 was performed using the Nextera DNA Flex for Enrichment using the Respiratory Virus Oligos Panel, Illumina MiSeq instruments, and Illumina MiSeq reagent v3 150 cycles (2 × 75 cycles). The full genomes were aligned to the reference genome (NC_045512.2) by the Burrow–Wheeler aligner algorithm. The whole-genome sequencing showed coinfection of Karolinska Institute polyomavirus Stockholm 60 (NC_009238.1) with an overall coverage of 3561x. The patient was given acetaminophen, vitamin C, vitamin D, and zinc for the treatment and discharged uneventfully from the hospital 4 days after admission. Then, 2 weeks after discharge, she visited the outpatient clinic without any further concerns. Conclusion This report presents a case of Karolinska Institute polyomavirus and severe acute respiratory syndrome coronavirus 2 coinfection in a patient with nonspecific clinical manifestation. Further studies with a larger sample size are mandatory to clarify the association between severe acute respiratory syndrome coronavirus 2 and Karolinska Institute polyomavirus coinfection, particularly on patient outcomes. Moreover, the results propose the usefulness of enrichment-based next-generation sequencing in detecting viral coinfection in patients with severe acute respiratory syndrome coronavirus 2.

Published
2024
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2. Is the Infection of the SARS-CoV-2 Delta Variant Associated With the Outcomes of COVID-19 Patients?

Author

Gunadi, Mohamad Saifudin Hakim, Hendra Wibawa, Marcellus, Vivi Setiawaty, Slamet, Ika Trisnawati, Endah Supriyati, Riat El Khair, Kristy Iskandar, Afiahayati, Siswanto, Irene, Nungki Anggorowati, Edwin Widyanto Daniwijaya, Dwi Aris Agung Nugrahaningsih, Yunika Puspadewi, Dyah Ayu Puspitarani, Irene Tania, Khanza Adzkia Vujira, Muhammad Buston Ardlyamustaqim, Gita Christy Gabriela, Laudria Stella Eryvinka, Bunga Citta Nirmala, Esensi Tarian Geometri, Abirafdi Amajida Darutama, Anisa Adityarini Kuswandani, Lestari, Sri Handayani Irianingsih, Siti Khoiriyah, Ina Lestari, Nur Rahmi Ananda, Eggi Arguni, Titik Nuryastuti, and Tri Wibawa

Subjects
comorbidity, Ct value, delta variant, hospitalization, mortality, SARS-CoV-2, Medicine (General), R5-920
Abstract

Background: Severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) Delta variant (B.1.617.2) has been responsible for the current increase in Coronavirus disease 2019 (COVID-19) infectivity rate worldwide. We compared the impact of the Delta variant and non-Delta variant on the COVID-19 outcomes in patients from Yogyakarta and Central Java provinces, Indonesia.Methods: In this cross-sectional study, we ascertained 161 patients, 69 with the Delta variant and 92 with the non-Delta variant. The Illumina MiSeq next-generation sequencer was used to perform the whole-genome sequences of SARS-CoV-2.Results: The mean age of patients with the Delta variant and the non-Delta variant was 27.3 ± 20.0 and 43.0 ± 20.9 (p = 3 × 10−6). The patients with Delta variant consisted of 23 males and 46 females, while the patients with the non-Delta variant involved 56 males and 36 females (p = 0.001). The Ct value of the Delta variant (18.4 ± 2.9) was significantly lower than that of the non-Delta variant (19.5 ± 3.8) (p = 0.043). There was no significant difference in the hospitalization and mortality of patients with Delta and non-Delta variants (p = 0.80 and 0.29, respectively). None of the prognostic factors were associated with the hospitalization, except diabetes with an OR of 3.6 (95% CI = 1.02–12.5; p = 0.036). Moreover, the patients with the following factors have been associated with higher mortality rate than the patients without the factors: age ≥65 years, obesity, diabetes, hypertension, and cardiovascular disease with the OR of 11 (95% CI = 3.4–36; p = 8 × 10−5), 27 (95% CI = 6.1–118; p = 1 × 10−5), 15.6 (95% CI = 5.3–46; p = 6 × 10−7), 12 (95% CI = 4–35.3; p = 1.2 × 10−5), and 6.8 (95% CI = 2.1–22.1; p = 0.003), respectively. Multivariate analysis showed that age ≥65 years, obesity, diabetes, and hypertension were the strong prognostic factors for the mortality of COVID-19 patients with the OR of 3.6 (95% CI = 0.58–21.9; p = 0.028), 16.6 (95% CI = 2.5–107.1; p = 0.003), 5.5 (95% CI = 1.3–23.7; p = 0.021), and 5.8 (95% CI = 1.02–32.8; p = 0.047), respectively.Conclusions: We show that the patients infected by the SARS-CoV-2 Delta variant have a lower Ct value than the patients infected by the non-Delta variant, implying that the Delta variant has a higher viral load, which might cause a more transmissible virus among humans. However, the Delta variant does not affect the COVID-19 outcomes in our patients. Our study also confirms that older age and comorbidity increase the mortality rate of patients with COVID-19.

Published
2021
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3. Comparative analysis of the outcomes of COVID-19 between patients infected with SARS-CoV-2 Omicron and Delta variants: a retrospective cohort study

Author

null Gunadi, Mohamad Saifudin Hakim, Hendra Wibawa, Khanza Adzkia Vujira, Dyah Ayu Puspitarani, Endah Supriyati, Ika Trisnawati, Kristy Iskandar, Riat El Khair, null Afiahayati, null Siswanto, Yunika Puspadewi, null Irene, Sri Handayani Irianingsih, Edwin Widyanto Daniwijaya, Dwi Aris Agung Nugrahaningsih, Gita Christy Gabriela, Esensi Tarian Geometri, Laudria Stella Eryvinka, Fadila Dyah Trie Utami, Edita Mayda Devana, Lanang Aditama, Nathania Christi Putri Kinasih, Verrell Christopher Amadeus, Yekti Hediningsih, Nur Rahmi Ananda, Eggi Arguni, Titik Nuryastuti, and Tri Wibawa

Abstract

BackgroundThe SARS-CoV-2 Omicron variant has replaced the previously dominant Delta variant because of high transmissibility. It is responsible for the current increase in the COVID-19 infectivity rate worldwide. However, studies on the impact of the Omicron variant on the severity of COVID-19 are still limited in developing countries. Here, we compared the outcomes of patients infected with SARS-CoV-2 Omicron and Delta variants and associated with prognostic factors, including age, sex, comorbidities, and smoking.MethodsWe involved 352 patients, 139 with the Omicron variant and 213 with the Delta variant. The whole-genome sequences of SARS-CoV-2 were conducted using the Illumina MiSeq next-generation sequencer.ResultsCt value and mean age of COVID-19 patients were not significantly different between both groups (Delta: 20.35 ± 4.07 vs. Omicron: 20.62 ± 3.75; p=0.540; and Delta: 36.52 ± 21.24 vs. Omicron: 39.10 ± 21.24; p=0.266, respectively). Patients infected with Omicron and Delta variants showed similar hospitalization (p=0.433) and mortality rates (p=0.565). Multivariate analysis showed that older age (≥65 years) had higher risk for hospitalization (OR=3.67 [95% CI=1.22-10.94]; p=0.019) and fatalities (OR=3.93 [95% CI=1.35-11.42]; p=0.012). In addition, patients with cardiovascular disease had higher risk for hospitalization (OR=5.27 [95% CI=1.07-25.97]; p=0.041), whereas patients with diabetes revealed higher risk for fatalities (OR=9.39 [95% CI=3.30-26.72]; p=ConclusionsOur study shows that patients infected with Omicron and Delta variants reveal similar clinical outcomes, including hospitalization and mortality. In addition, our findings further confirm that older age, cardiovascular disease, and diabetes are strong prognostic factors for the outcomes of COVID-19 patients.

Published
2022
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4. Long-term growth outcomes in children with Hirschsprung disease after definitive surgery: A cross-sectional study

Author

Gita Christy Gabriela, Aditya Rifqi Fauzi, Janatin Hastuti, Griselda Elisse Santoso, Kemala Athollah, Gunadi, and Esensi Tarian Geometri

Subjects
Pediatrics, medicine.medical_specialty, Hirschsprung disease, Cross-sectional study, HAEC, Hirschsprung-associated enterocolitis, WAZ, weight-for-age z-score, Disease, Long-term growth outcomes, WHO, World Health Organization, Surgical methods, 03 medical and health sciences, 0302 clinical medicine, Nutritional status, BAZ, body mass index-for-age z-score, Transabdominal soave and duhamel surgeries, Definitive surgery, Medicine, Outpatient clinic, IQR, interquartile range, Original Research, Long term growth, business.industry, ICD10, The International Statistical Classification of Diseases and Related Health Problems, 10th Revision, TEPT, transanal endorectal pull-through, General Medicine, HSCR, Hirschsprung disease, Transanal endorectal pull-through, Sample size determination, 030220 oncology & carcinogenesis, 030211 gastroenterology & hepatology, Surgery, business
Abstract

Background The growth of children with Hirschsprung disease (HSCR) can be affected by many factors, including the environment, nutrient intake, and surgery. Our study compared the long-term (i.e., at least 3 years of follow-up) growth outcomes in HSCR children after transabdominal Soave and Duhamel and transanal endorectal pull-through (TEPT) surgeries. Methods A cross-sectional study was conducted in children, Highlights • The growth of children with Hirschsprung disease (HSCR) can be affected by many factors, such as the environment, nutrient intake, and pull-through surgery. • It is important to determine the long-term (i.e. at least 3 years of follow-up) growth outcomes in HSCR children after pull-through prospectively. • While some HSCR children show an improvement in their nutritional status after Soave and TEPT procedures, the overall nutritional status is similar among different pull-through procedures.

Published
2020
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5. Is the Infection of the SARS-CoV-2 Delta Variant Associated With the Outcomes of COVID-19 Patients?

Author

Esensi Tarian Geometri, Afiahayati, Hendra Wibawa, Muhammad Buston Ardlyamustaqim, Gunadi, Bunga Citta Nirmala, Slamet, Dwi Aris Agung Nugrahaningsih, Nungki Anggorowati, Nur Rahmi Ananda, Sri Handayani Irianingsih, Yunika Puspadewi, Siti Khoiriyah, Irene Tania, Irene, Gita Christy Gabriela, Kristy Iskandar, Lestari, Riat El Khair, Vivi Setiawaty, Ina Lestari, Siswanto, Dyah Ayu Puspitarani, Khanza Adzkia Vujira, Eggi Arguni, Abirafdi Amajida Darutama, Anisa Adityarini Kuswandani, Edwin Widyanto Daniwijaya, Ika Trisnawati, Marcellus, Tri Wibawa, Laudria Stella Eryvinka, Titik Nuryastuti, Mohamad S. Hakim, and Endah Supriyati

Subjects
Delta, medicine.medical_specialty, Medicine (General), Multivariate analysis, delta variant, Disease, Gastroenterology, Ct value, R5-920, Internal medicine, Diabetes mellitus, medicine, Original Research, whole genome sequencing, business.industry, SARS-CoV-2, Mortality rate, General Medicine, medicine.disease, Obesity, Comorbidity, mortality, viral load, comorbidity, Medicine, business, Viral load, hospitalization
Abstract

Background: Severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) Delta variant (B.1.617.2) has been responsible for the current increase in Coronavirus disease 2019 (COVID-19) infectivity rate worldwide. We compared the impact of the Delta variant and non-Delta variant on the COVID-19 outcomes in patients from Yogyakarta and Central Java provinces, Indonesia.Methods: In this cross-sectional study, we ascertained 161 patients, 69 with the Delta variant and 92 with the non-Delta variant. The Illumina MiSeq next-generation sequencer was used to perform the whole-genome sequences of SARS-CoV-2.Results: The mean age of patients with the Delta variant and the non-Delta variant was 27.3 ± 20.0 and 43.0 ± 20.9 (p = 3 × 10−6). The patients with Delta variant consisted of 23 males and 46 females, while the patients with the non-Delta variant involved 56 males and 36 females (p = 0.001). The Ct value of the Delta variant (18.4 ± 2.9) was significantly lower than that of the non-Delta variant (19.5 ± 3.8) (p = 0.043). There was no significant difference in the hospitalization and mortality of patients with Delta and non-Delta variants (p = 0.80 and 0.29, respectively). None of the prognostic factors were associated with the hospitalization, except diabetes with an OR of 3.6 (95% CI = 1.02–12.5; p = 0.036). Moreover, the patients with the following factors have been associated with higher mortality rate than the patients without the factors: age ≥65 years, obesity, diabetes, hypertension, and cardiovascular disease with the OR of 11 (95% CI = 3.4–36; p = 8 × 10−5), 27 (95% CI = 6.1–118; p = 1 × 10−5), 15.6 (95% CI = 5.3–46; p = 6 × 10−7), 12 (95% CI = 4–35.3; p = 1.2 × 10−5), and 6.8 (95% CI = 2.1–22.1; p = 0.003), respectively. Multivariate analysis showed that age ≥65 years, obesity, diabetes, and hypertension were the strong prognostic factors for the mortality of COVID-19 patients with the OR of 3.6 (95% CI = 0.58–21.9; p = 0.028), 16.6 (95% CI = 2.5–107.1; p = 0.003), 5.5 (95% CI = 1.3–23.7; p = 0.021), and 5.8 (95% CI = 1.02–32.8; p = 0.047), respectively.Conclusions: We show that the patients infected by the SARS-CoV-2 Delta variant have a lower Ct value than the patients infected by the non-Delta variant, implying that the Delta variant has a higher viral load, which might cause a more transmissible virus among humans. However, the Delta variant does not affect the COVID-19 outcomes in our patients. Our study also confirms that older age and comorbidity increase the mortality rate of patients with COVID-19.

Published
2021
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