Frequency and survival of Covid associated mucormycosis patients at tertiary care hospitals in Pakistan: A retrospective observational study.

Background: Mucormycosis is a serious fungal infection associated with uncontrolled diabetes and immunocompromised patients. This angioinvasive infection emerged as a post-covid complication worldwide especially in developing countries. Due to the common socio-demographic status of South Asian countries, we expected a surge in mucormycosis cases in Pakistan. This study aims to observe the frequency and survival of Covid associated mucormycosis patients at tertiary care hospitals in Pakistan during the third wave of Covid-19 in 2021. Materials and Methods: In this retrospective study, we collected the data of clinically and histopathologically confirmed cases of rhino-occipito-cerebral mucormycosis from three tertiary care hospitals of Lahore. These cases were analysed for history of Covid-19 and other associated comorbidities using SPSS28. History of steroid medication was also taken. Data were retrieved from May to July 2021 after the approval from the ethical review board. Results: Out of the total 43 reported patients of mucormycosis in the set time frame only 22 cases had a history of Covid-19. The mean age was 50 ± 13.27 years with slight male predilection (60%). Diabetes mellitus was the most common comorbidity (88.4%) and all the patients with covid associated mucormycosis (CAM) had taken corticosteroid regimen for covid management (p < 0.0001). The survival of the patient was not significantly different between CAM and non-CAM patients of Mucormycosis (p = 0.747). Conclusion: Covid-19 and mucormycosis make a lethal duo against the weakened health system of Pakistan. This problem can be prevented by avoiding nonjudicial use of corticosteroids and proper diabetes control program following Covid-19 infection. Furthermore, large-scale epidemiological studies should be carried out to evaluate the true burden of Mucormycosis in the population.

Frequency and survival of Covid associated mucormycosis patients at tertiary care hospitals in Pakistan: A retrospective observational study

Background Mucormycosis is a serious fungal infection associated with uncontrolled diabetes and immunocompromised patients. This angioinvasive infection emerged as a post‐covid complication worldwide especially in developing countries. Due to the common socio‐demographic status of South Asian countries, we expected a surge in mucormycosis cases in Pakistan. This study aims to observe the frequency and survival of Covid associated mucormycosis patients at tertiary care hospitals in Pakistan during the third wave of Covid‐19 in 2021. Materials and Methods In this retrospective study, we collected the data of clinically and histopathologically confirmed cases of rhino‐occipito‐cerebral mucormycosis from three tertiary care hospitals of Lahore. These cases were analysed for history of Covid‐19 and other associated comorbidities using SPSS28. History of steroid medication was also taken. Data were retrieved from May to July 2021 after the approval from the ethical review board. Results Out of the total 43 reported patients of mucormycosis in the set time frame only 22 cases had a history of Covid‐19. The mean age was 50 ± 13.27 years with slight male predilection (60%). Diabetes mellitus was the most common comorbidity (88.4%) and all the patients with covid associated mucormycosis (CAM) had taken corticosteroid regimen for covid management (p < 0.0001). The survival of the patient was not significantly different between CAM and non‐CAM patients of Mucormycosis (p = 0.747). Conclusion Covid‐19 and mucormycosis make a lethal duo against the weakened health system of Pakistan. This problem can be prevented by avoiding nonjudicial use of corticosteroids and proper diabetes control program following Covid‐19 infection. Furthermore, large‐scale epidemiological studies should be carried out to evaluate the true burden of Mucormycosis in the population.

Breakthrough cases of Omicron and Delta variants of SARS-CoV-2 during the fifth wave in Pakistan.

COVID-19 pandemic has severely affected Pakistan with 1,557,134 cases as of August 4, 2022. However, the data regarding breakthrough infections in Pakistan is scant. Hence, the objective was to analyze SARS-CoV-2 breakthrough infections with respect to vaccines and variants during the fifth wave in Pakistan. Therefore, the Department of Virology (NIH, Pakistan) genotyped 2,467 randomly selected individuals between November 2021 and February 2022 using the SNPsig® SARS-CoV-2 (EscapePLEX) kit (PrimerDesign, UK). P681R and K417N mutations were used to distinguish delta and omicron. Data on the patient's age, gender, date of collection, variant, and vaccination status were analyzed using Statistical Package for Social Sciences (SPSS) software. Among 2,467 genotyped samples, Omicron was detected in 58.6% (n = 1445), Delta in 40.4% (n = 998) and undetermined/wildtype variant in 24 samples. The vaccination status of omicron-positive patients showed (49.7%; n = 718/1445) and Delta-positive patients (39.67%; n = 396/998) to be fully vaccinated. Of note, a high percentage 85% of breakthrough cases (n = 947) were identified among fully vaccinated individuals (n = 1114). Among them, 85.9% (n = 617/718) belonged to omicron and 83.3% (n = 330/396) to delta. Moreover, 76.7% (n = 855) of vaccinated individuals (n = 1114) received Sinopharm (n = 432) and Sinovac (n = 423) vaccines. The majority of breakthrough subjects who contracted Omicron were vaccinated with Sinopharm (93.0%, n = 256) and delta with Cansino (100%, n = 44). Individuals vaccinated with Sinovac showed the most frequent breakthrough cases for both Omicron and Delta variant between the 4th and 6th months (n = 278) after primary vaccination as compared to the 7th to 9th months (n = 24) category. While in case of Sinopharm, maximum breakthrough cases occurred between 7th to 9th months (n = 234) as compared to the 4th to 6th months (n = 120) after primary vaccination. Omicron and Delta breakthrough cases in men (n = 364 and 193) are more frequently seen than women (n = 253 and 138) respectively and breakthrough majority cases (n = 392) occurred in individuals aged 18-33 years. Breakthrough cases limiting monitoring in Pakistan impose a substantial constraint on policymakers' ability to take timely effective decisions. Since the current study consists of only a 2,467-genotyped sample, comprehensive data should be analyzed.

Genomic diversity of SARS-CoV-2 in Pakistan during the fourth wave of pandemic.

The emergence of different variants of concern of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in upsurges of coronavirus disease 2019 (COVID-19) cases around the globe. Pakistan faced the fourth wave of COVID-19 from July to August 2021 with 314,786 cases. To understand the genomic diversity of circulating SARS-CoV-2 strains during the fourth wave of the pandemic in Pakistan, this study was conducted. The samples from 140 COVID-19-positive patients were subjected to whole-genome sequencing using the iSeq Sequencer by Illumina. The results showed that 97% (n = 136) of isolates belonged to the delta variant while three isolates belonged to alpha and only one isolate belonged to the beta variant. Among delta variant cases, 20.5% (n = 28) isolates were showing B.1.617.2 while 23.5% (n = 25), 17.59% (n = 19), 14.81% (n = 16), and 13.89% (n = 15) of isolates were showing AY.108, AY.43 AY.127, and AY.125 lineages, respectively. Islamabad was found to be the most affected city with 65% (n = 89) of delta variant cases, followed by Karachi (17%, n = 23), and Rawalpindi (10%, n = 14). Apart from the characteristic spike mutations (T19R, L452R, T478K, P681R, and D950N) of the delta variant, the sublineages exhibited other spike mutations as E156del, G142D, T95I, A222V, G446V, K529N, N532S, Q613H, and V483A. The phylogenetic analysis revealed the introductions from Singapore, the United Kingdom, and Germany. This study highlights the circulation of delta variants (B.1.617.2 and sublineages) during the fourth wave of pandemic in Pakistan.

Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan.

SARS-CoV-2 variants of concern (VOCs) have emerged worldwide and gained significant importance due to their high transmissibility and global spread, thus meriting close monitoring. In Pakistan, limited information is available on circulation of these variants as the alpha variant has been reported the main circulating lineage. The current study was designed to detect and explore the genomic diversity of SARS-CoV-2 lineages circulating during the third wave of the pandemic in the indigenous population. From May 01 to June 09, 2021, a total of 16 689 samples were tested using TaqPath™ COVID-19 kit for the presence of SARS-CoV-2. Overall, 2562 samples (15.4%) were COVID-19 positive. Out of these positive samples, 2124 (12.7%) did not show the spike gene amplification (spike gene target failure ([SGTF]), whereas 438 (2.6%) showed spike gene amplification (non-SGTF). A subset (n = 58/438) of non-SGTF samples were randomly selected for whole-genome sequencing. Among VOCs, 45% (n = 26/58) were delta, 46% (n = 27/58) were beta, and one was gamma variant. The delta variant cases were reported mainly from Islamabad (n = 15; 58%) followed by Rawalpindi and Azad Kashmir (n = 1; 4% each). Beta variant cases originated mainly from Karachi (n = 8; 30%) and Islamabad (n = 11; 41%) and the gamma variant case was reported in a traveler from Italy. The delta, beta, and gamma variants possessed lineage-specific spike mutations. Notably, two rare mutations (E484Q and L5F) were found in the delta variant. Furthermore, in the beta variant, two significant rare non-synonymous spike mutations (A879S and K444R) were also reported. High prevalence of beta and delta variants in local population may increase the number of cases in the near future and provides an early warning to national health authorities to take timely decisions and devise suitable interventions to contain a possible fourth wave.

The Dilemma of Renal Involvement in COVID-19: A Systematic Review.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), now known as coronavirus disease 2019 (COVID-19), has posed a serious threat to global health since December 2019. It has spread worldwide and is consuming healthcare resources rapidly. Published literature suggests that people with advanced age and comorbidities are affected more severely. It is crucial to uncover the underlying pathogenesis of acute kidney insufficiency in COVID-19 patients to understand better the reasoning behind the grave outcomes in these patients. In this review, we have included articles stating the prevalence and specific mortality rates of COVID-19 patients with acute kidney insufficiency. Our study included 1098 COVID-19 positive patients, of whom 66 (6%) developed acute kidney insufficiency and 62 patients died, showing a mortality rate of 94%. Patients with acute kidney insufficiency showed a more severe disease course, and these patients ended up more in intensive care units. Particular attention should be paid to those with already established kidney disease, such as chronic kidney disease, or renal transplant recipients, as these patients are already on immunosuppressive therapy. Our review focuses on the prevalence of acute kidney insufficiency in COVID-19 patients and mortality rates in this subset of patients.