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3.
J Med Virol ; 2022 Jun 26.
Article in English | MEDLINE | ID: covidwho-1905894

ABSTRACT

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.

4.
Front Public Health ; 10: 823047, 2022.
Article in English | MEDLINE | ID: covidwho-1903199

ABSTRACT

Objective: The study aimed to evaluate the knowledge, attitude, and practices toward the prevention of coronavirus disease 2019 (COVID-19) among the public in Malaysia. Methods: A cross-sectional study was conducted online among the general public in Malaysia from June 2020 to August 2020 between the second and third wave (Phase 3 of the Recovery Movement Control Order). Participants were conveniently recruited through multiple social media platforms to encourage nationwide participation. A patient-administered questionnaire was used to assess their knowledge, attitude, and practice toward the prevention of COVID-19. For descriptive analysis, percentage, mean, and standard deviation (SD) were used to report demographic characteristics and knowledge, attitude, and practice scores. For inferential analysis, t-test, ANOVA, Pearson's correlation, Spearman's correlation, Chi-square test, and Binary Logistic Regression was used to analyze the study variables' differentiation, association, and correlations. The confidence interval selected for this study was 95%. Results: A total of 420 respondents participated in this survey. The majority of the participants (n = 412, 98%) were aware of COVID-19. Most participants (60%) learned about the pandemic through social media. About half of the participants had poor knowledge (45.5%) and a negative attitude (43.3%). Participants residing in urban areas showed good preventive practices as compared to those residing in rural areas (P < 0.05). There was a significant association between participants' attitudes and preventive practices toward COVID-19, where the majority of the participants (57.4%) who showed negative attitudes were more likely to follow poor preventive practices. Conclusion: Despite having good knowledge, participants with a negative attitude toward COVID-19 were less likely to follow the preventive practices of COVID-19. People's mindset and willingness may play an important role to influence their practices. Thus, these are the vulnerable groups, and strategies should be made to change their mindset through proper counseling and education.


Subject(s)
COVID-19 , COVID-19/epidemiology , COVID-19/prevention & control , Cross-Sectional Studies , Health Knowledge, Attitudes, Practice , Humans , Pandemics/prevention & control , SARS-CoV-2
5.
Antibiotics (Basel) ; 11(6)2022 Jun 09.
Article in English | MEDLINE | ID: covidwho-1883976

ABSTRACT

BACKGROUND: COVID-19 patients are typically prescribed antibiotics empirically despite concerns. There is a need to evaluate antibiotic use among hospitalized COVID-19 patients during successive pandemic waves in Pakistan alongside co-infection rates. METHODS: A retrospective review of patient records among five tertiary care hospitals during successive waves was conducted. Data were collected from confirmed COVID-19 patients during the first five waves. RESULTS: 3221 patients were included. The majority were male (51.53%), residents from urban areas (56.35%) and aged >50 years (52.06%). Cough, fever and a sore throat were the clinical symptoms in 20.39%, 12.97% and 9.50% of patients, respectively. A total of 23.62% of COVID-19 patients presented with typically mild disease and 45.48% presented with moderate disease. A high prevalence of antibiotic prescribing (89.69%), averaging 1.66 antibiotics per patient despite there only being 1.14% bacterial co-infections and 3.14% secondary infections, was found. Antibiotic use significantly increased with increasing severity, elevated WBCs and CRP levels, a need for oxygen and admittance to the ICU; however, this decreased significantly after the second wave (p < 0.001). Commonly prescribed antibiotics were piperacillin plus an enzyme inhibitor (20.66%), azithromycin (17.37%) and meropenem (15.45%). Common pathogens were Staphylococcus aureus (24.19%) and Streptococcus pneumoniae (20.96%). The majority of the prescribed antibiotics (93.35%) were from the WHO's "Watch" category. CONCLUSIONS: Excessive prescribing of antibiotics is still occurring among COVID-19 patients in Pakistan; however, rates are reducing. Urgent measures are needed for further reductions.

6.
PLoS One ; 17(4): e0267139, 2022.
Article in English | MEDLINE | ID: covidwho-1883691

ABSTRACT

PURPOSE: COVID-19 infection resulting from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) began to spread across the globe in early 2020. Patients with hematologic malignancies are supposed to have an increased risk of mortality from coronavirus disease of 2019 (COVID-19) infection. From Pakistan, we report the analysis of the outcome and interaction between patient demographics and tumor subtype and COVID-19 infection and hematological malignancy. PATIENTS AND METHODS: This multicenter, retrospective study included adult patients with a history of histologically proven hematological malignancies who were tested positive for COVID-19 via PCR presented at the oncology department of 5 tertiary care hospitals in Pakistan from February to August 2020. A patient with any known hematological malignancy who was positive for COVID-19 on RT-PCR, was included in the study. Chi-square test and Cox-regression hazard regression model was applied considering p ≤ 0.05 significant. RESULTS: A total of 107 patients with hematological malignancies were diagnosed with COVID-19, out of which 82 (76.64%) were alive, and 25 (23.36%) were dead. The significant hematological malignancy was B-cell Lymphoma in dead 4 (16.00%) and alive group 21 (25.61%), respectively. The majority of the patients in both the dead and alive group were on active treatment for hematological malignancy while they came positive for COVID-19 [21 (84.00%) & 48 (58.54%) p 0.020]. All patients in the dead group were admitted to the hospital 25 (100.00%), and among these, 14 (56.00%) were admitted in ICU with a median 11 (6-16.5) number of days. Among those who had contact exposure, the hazard of survival or death in patients with hematological malignancies and COVID-19 positive was 2.18 (CI: 1.90-4.44) times and 3.10 (CI: 2.73-4.60) times in patients with travel history compared to no exposure history (p 0.001). CONCLUSION: Taken together, this data supports the emerging consensus that patients with hematologic malignancies experience significant morbidity and mortality resulting from COVID-19 infection.


Subject(s)
COVID-19 , Hematologic Neoplasms , Adult , Hematologic Neoplasms/therapy , Humans , Pakistan/epidemiology , Retrospective Studies , SARS-CoV-2
9.
J Med Virol ; 2021 Nov 02.
Article in English | MEDLINE | ID: covidwho-1718378

ABSTRACT

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.

10.
EuropePMC; 2022.
Preprint in English | EuropePMC | ID: ppcovidwho-329264

ABSTRACT

The Omicron variant of SARS-CoV-2 has rapidly replace previous variants of SARS CoV2 around the globe and is now a major variant of concern. The genomic surveillance of Omicron variant also reveals spread of its subvariant BA.2 which has differing transmissibility in comparison to its other subvariant BA.1. BA.1 and BA.2 harbors different mutational profile. One of the important change in both the subvariants is the presence of 69-70 deletion in BA.1 and absence of this deletion in BA.2. This deletion can be used as tool for the detection of omicron sub variants using real time PCR. In the current study we have used the TaqPath COVID-19 PCR kit for the detection of 69-70 deletion followed by genotyping using SNPsig® SARS-CoV-2 (EscapePLEX) kit (PrimerDesign, UK) that target K417N, E484K, and P681R mutations. The samples with the amplification of spike gene and K417N were termed as probable BA.2 cases. A subset of samples (n=13) were further subjected to whole genome sequencing. The results showed all the 13 samples were of BA.2. Hence, this assay can be used as a cost effective method for the detection of omicron BA.2 variant using real time PCR in resource limiting settings. Moreover, the detection of BA.2 with highly transmissible mutations in Islamabad, Pakistan may potentially increase the number of positive cases. In that scenario, there has to be stringent genomic surveillance to understand the circulating lineages in the country.

11.
EuropePMC;
Preprint in English | EuropePMC | ID: ppcovidwho-327734

ABSTRACT

Since the start of COVID-19 pandemic, Pakistan has experienced four waves of pandemic. The fourth wave ended in October, 2021 while the fifth wave of pandemic starts in January, 2022. The data regarding the circulating strains after the fourth wave of pandemic from Pakistan is not available. The current study explore the genomic diversity of SARS-CoV-2 after fourth wave and before fifth wave of pandemic through whole genome sequencing. The results showed the circulation of different strains of SARS-CoV-2 during November-December, 2021. We have Omicron BA.1 (n=4), Lineage A (n=2) and delta AY.27 (n=1) variants of SARS-CoV-2 in the population of Islamabad. All the isolates harbors characteristics mutations of omicron and delta variant in the genome. The lineage A isolate harbors a nine amino acid (68-76) and a ten amino acid (679-688) deletion in the genome. The circulation of omicron in the population before the fifth wave of pandemic and subsequent upsurges of COVID-19 positive cases in Pakistan highlights the importance of genomic surveillance.

12.
O'Toole, Áine, Hill, Verity, Pybus, Oliver, Watts, Alexander, Bogoch, Issac, Khan, Kamran, Messina, Jane, Tegally, Houriiyah, Lessells, Richard, Giandhari, Jennifer, Pillay, Sureshnee, Tumedi, Kefentse Arnold, Nyepetsi, Gape, Kebabonye, Malebogo, Matsheka, Maitshwarelo, Mine, Madisa, Tokajian, Sima, Hassan, Hamad, Salloum, Tamara, Merhi, Georgi, Koweyes, Jad, Geoghegan, Jemma, de Ligt, Joep, Ren, Xiaoyun, Storey, Matthew, Freed, Nikki, Pattabiraman, Chitra, Prasad, Pramada, Desai, Anita, Vasanthapuram, Ravi, Schulz, Thomas, Steinbrück, Lars, Stadler, Tanja, Parisi, Antonio, Bianco, Angelica, García de Viedma, Darío, Buenestado-Serrano, Sergio, Borges, Vítor, Isidro, Joana, Duarte, Sílvia, Gomes, João Paulo, Zuckerman, Neta, Mandelboim, Michal, Mor, Orna, Seemann, Torsten, Arnott, Alicia, Draper, Jenny, Gall, Mailie, Rawlinson, William, Deveson, Ira, Schlebusch, Sanmarié, McMahon, Jamie, Leong, Lex, Lim, Chuan Kok, Chironna, Maria, Loconsole, Daniela, Bal, Antonin, Josset, Laurence, Holmes, Edward, St. George, Kirsten, Lasek-Nesselquist, Erica, Sikkema, Reina, Oude Munnink, Bas, Koopmans, Marion, Brytting, Mia, Sudha rani, V.; Pavani, S.; Smura, Teemu, Heim, Albert, Kurkela, Satu, Umair, Massab, Salman, Muhammad, Bartolini, Barbara, Rueca, Martina, Drosten, Christian, Wolff, Thorsten, Silander, Olin, Eggink, Dirk, Reusken, Chantal, Vennema, Harry, Park, Aekyung, Carrington, Christine, Sahadeo, Nikita, Carr, Michael, Gonzalez, Gabo, de Oliveira, Tulio, Faria, Nuno, Rambaut, Andrew, Kraemer, Moritz, The, Covid-Genomics U. K. consortium, Network for Genomic Surveillance in South, Africa, Brazil, U. K. Cadde Genomic Network, Swiss Viollier Sequencing, Consortium, Diego, Search Alliance San, National Virus Reference, Laboratory, Seq, Covid Spain, Danish Covid-19 Genome, Consortium, Communicable Diseases Genomic, Network, Dutch National, Sars-CoV-surveillance program, Division of Emerging Infectious, Diseases.
EuropePMC; 2021.
Preprint in English | EuropePMC | ID: ppcovidwho-318194

ABSTRACT

Late in 2020, two genetically-distinct clusters of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with mutations of biological concern were reported, one in the United Kingdom and one in South Africa. Using a combination of data from routine surveillance, genomic sequencing and international travel we track the international dispersal of lineages B.1.1.7 and B.1.351 (variant 501Y-V2). We account for potential biases in genomic surveillance efforts by including passenger volumes from location of where the lineage was first reported, London and South Africa respectively. Using the software tool grinch (global report investigating novel coronavirus haplotypes), we track the international spread of lineages of concern with automated daily reports, Further, we have built a custom tracking website (cov-lineages.org/global_report.html) which hosts this daily report and will continue to include novel SARS-CoV-2 lineages of concern as they are detected.

15.
Disaster Med Public Health Prep ; : 1-13, 2022 Jan 10.
Article in English | MEDLINE | ID: covidwho-1616880

ABSTRACT

OBJECTIVE: To ascertain the psychological impacts of COVID-19 among the Pakistani healthcare workers (HCWs) and their coping strategies. METHODS: This web-based, cross-sectional study was conducted among HCWs (N=398) from Punjab province of Pakistan. The generalized anxiety scale (GAD-7), patient health questionnaire (PHQ-9) and Brief-COPE were used to assess anxiety, depression and coping strategies, respectively. RESULTS: The average age of respondents was 28.67 years (SD=4.15), with the majority of medical doctors (52%). The prevalence of anxiety and depression were 21.4% and 21.9%, respectively. There was no significant difference in anxiety and depression scores among doctors, nurses and pharmacists. Females had significantly higher anxiety (p=0.003) and depression (p=0.001) scores than males. Moreover, frontline HCWs had significantly higher depression scores (p=0.010) than others. The depression, not anxiety, score were significantly higher among those who did not receive the infection prevention training (p=0.004). Most frequently adopted coping strategy were religious coping (M=5.98, SD=1.73), acceptance (M=5.59, SD=1.55) and coping planning (M=4.91, SD=1.85). CONCLUSION: A considerable proportion of HCWs are having generalized anxiety and depression during the ongoing COVID-19 pandemic. Our findings call for interventions to mitigate mental health risks in HCWs.

17.
Explor Res Clin Soc Pharm ; 5: 100101, 2022 Mar.
Article in English | MEDLINE | ID: covidwho-1586748

ABSTRACT

PURPOSE: In Pakistan, a wide range of repurposed drugs are recommended to manage hospitalized patients with COVID-19. Therefore, the current study was conducted to evaluate the pattern of utilization of repurposed drugs and other potential therapeutic options among hospitalized patients with COVID-19 in Pakistan. METHODS: This retrospective, multicenter, descriptive study enrolled consecutive hospitalized patients with COVID-19 who were admitted between March 1, 2021, and April 30, 2021, from three District Headquarter Hospitals in the Punjab province of Pakistan. We described patient and clinical characteristics and medications, stratified by COVID-19 severity during hospitalization: mild, moderate, and severe. In addition, an analytical study of drug utilization was conducted. FINDINGS: A total of 444 hospitalized patients with COVID-19 were included. Remdesvir, corticosteroids, antibiotics, and antithrombotics were administered to 45.0%, 93.9%, 84.9%, and 60.1% of patients, respectively. Specifically, dexamethasone was the most commonly used corticosteroid among the included patients (n = 405; 91.2%), irrespective of their clinical severity. Only 60.1% of patients hospitalized with COVID-19 in our cohort received antithrombotic therapy, and the prevalence of use was especially low (27.8%) in patients with mild illness. Of 444 patientsscreened, 399 (89.9%) patients had been discharged, and 45 patients (10.1%) died. IMPLICATIONS: We provided an important glimpse into the utilization patterns of several medications of interest for the treatment of COVID-19 in Pakistan, which had not been entirely evidence-based, especially concerning systemic corticosteroids and antibiotics.

18.
2021.
Preprint in English | Other preprints | ID: ppcovidwho-294172

ABSTRACT

Introduction Serological surveys are valuable tools to evaluate the extent of disease transmission, measuring preventive effectiveness and proportion of asymptomatic individuals. This age-stratified, serological survey was aimed to measure the COVID-19 distribution and determinants in district Islamabad of Pakistan. Methodology Three-stage cluster sampling, using population proportionate to size technique, starting with a random number was used. A structured, pretested questionnaire was used after taking informed written consent, to gather demographic, risk factor information. Results Seroprevalence was found 16.5% (AR: 16.5%/100,000). The mean age was 35 (±16 Years). The majority were male (64%), self-employed (29%), and had primary level education (33%). The highest seroprevalence was found in the 21-30 years age group (24.8%) while the 41-50 years age group showed the highest attack rate (112.9/100,000 population). The proportion of the population tested that were asymptomatic was 69% (n=711) while the most frequently reported sign/symptom was cough (99%) followed by fever (20%). No known co-morbidity was reported in 86% (n=884) of respondents while hypertension remained the most reported condition (8%). High seroprevalence was observed in urban areas (12.3%) compared to rural union councils (6.4%). Visiting a house where COVID-19 case was isolated (OR 2, CI 1.38-2.84, P < 0.001), history of contact with a known case of COVID-19 (OR 1.42, CI 1.11-1.82, P =0.005), and attending a mass gathering (OR 1.21, CI: 1.02-1.42, p=0.02) were significant risk factors associated with contracting an infection. A Chi-Square test of independence showed significant protection while using regular hand hygiene practices (6.5;p<0.05) and regular usage of face masks (8.6;p<0.05). Conclusion Seroprevalence gives a direct estimation of population groups exposed to the virus. A remarkable difference in prevalence is found in urban and rural areas, extreme age groups, and socioeconomic statuses, suggesting targeted public health interventions. Sero-studies are affordable counterparts of molecular testing where quick estimation, prevention effectiveness, and data-driven public health policies are priorities.

19.
Cureus ; 13(11): e19487, 2021 Nov.
Article in English | MEDLINE | ID: covidwho-1538807

ABSTRACT

INTRODUCTION: This study was conducted to determine whether remdesivir administration for treatment of coronavirus disease 2019 (COVID-19) is associated with reducing deaths among COVID-19 hospitalized patients. METHODOLOGY: It was a retrospective study, and the data was acquired at Ziauddin Hospital in Karachi, Pakistan. All patients admitted between February and May 2021 with severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2) infection confirmed by polymerase chain reaction testing from nasopharyngeal samples were included in the study, including those who received at least five-day treatment of remdesivir and who did not receive even a single dose of remdesivir. RESULTS: Data of overall 174 patients were used, out of which 71 (40.80%) received remdesivir. After propensity score matching, 71 patients in the remdesivir group were successfully matched with the non-remdesivir patients on the basis of age, gender, and disease severity. Results of multivariable logistic regression showed that there is no significant difference in deaths between patients who received remdesivir and patients who did not receive remdesivir (p-value=0.122). However, the length of hospital stay was significantly lower in the remdesivir group than in the control group (p-value=0.001). CONCLUSION: Results of this study can provide evidence that remdesivir can be efficient in reducing the duration of COVID-19 illness, and a five-day course of treatment is sufficient for patients to get clinical benefits.

20.
Pathog Glob Health ; : 1-7, 2021 Nov 16.
Article in English | MEDLINE | ID: covidwho-1517757

ABSTRACT

There are reports of high rates of antibiotic prescribing among hospitalized patients with COVID-19 around the world. To date, however, there are few reports of prescribing in relation to COVID-19 in Pakistan. Herein, we describe a point prevalence survey of antibiotic prescribing amongst patients hospitalized with suspected or proven COVID-19 in Pakistan. A Point Prevalence Survey (PPS) was undertaken in seven tertiary care health facilities in Punjab Provence, Pakistan. Baseline information about antimicrobial use according to the World Health Organization (WHO) standardized methodology was collected on a single day between 5th and 30 April 2021. A total of 617 patients' records were reviewed and 578 (97.3%) were documented to be receiving an antibiotic on the day of the survey. The majority (84.9%) were COVID-19 PCR positive, 61.1% were male and 34.9% were age 36 to 44 years. One quarter presented with severe disease, and cardiovascular disease was the major comorbidity in 13%. Secondary bacterial infection or co-infection (bacterial infection concurrent with COVID-19) was identified in only 1.4%. On the day of the survey, a mean of 1.7 antibiotics was prescribed per patient and 85.4% antibiotics were recorded as being prescribed for 'prophylaxis'. The most frequently prescribed antibiotics were azithromycin (35.6%), ceftriaxone (32.9%) and meropenem (7.6%). The majority (96.3%) of the antibiotics were empirical and all were from WHO Watch or Reserve categories. Overall, a very high consumption of antibiotics in patients hospitalized with suspected or proven COVID-19 was observed in Pakistan and this is concerning in view of already high rates of antimicrobial resistance in the region. Antimicrobial stewardship programs need to urgently address unnecessary prescribing in the context of COVID-19 infection.

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