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1.
Infect Drug Resist ; 16: 1997-2006, 2023.
Article in English | MEDLINE | ID: covidwho-2304494

ABSTRACT

Background: During outbreaks of infectious diseases like COVID-19, the healthcare-associated infections (HCAIs) pose a burden on public health system. There are very limited data about infection prevention and control (IPC) implementation in the healthcare facilities of Pakistan. The aim of the study was to conduct assessment with the IPC Assessment Framework (IPCAF) tool in healthcare facilities of the least developed areas. Methods: A cross-sectional survey was conducted in 12 tertiary level healthcare facilities (HCF) located in the least developed provinces of Pakistan. The facilities were selected through multistage cluster random methods. A well-structured questionnaire, the "IPCAF tool", was used for data collection. The IPCAF comprises eight sections with a 100 score of each section, thus with a maximum score of 800. The scores from 0 to 800 of the HCFs were divided into four gradual ratings through IPCAF, ie from inadequate to advanced. Results: The median score of all facilities was 405, with a range from inadequate to advanced. One facility (8.3%) fell into the "inadequate" category with a score of 172.5; 5 (41.6%) facilities achieved "basic" category, another 5 (41.6%) being "intermediate", and only one (8.3%) hospital achieved "advanced" status. Region-wise median score of facilities of GB was 307.5, facilities in AJK scored 342.5, and a score of 520 was found for health facilities in KPK. The components of Education and Training, HCAIs Surveillance, and Multimodal Strategies achieved the lowest scores. Conclusion: Most of the facilities have developed an IPC program with key focal persons and IPC committees, but did not have relevant education and training. IPC core capacities are being implemented. Equitable attention is required on all eight components of IPC in all facilities.

2.
Vaccines (Basel) ; 11(4)2023 Mar 27.
Article in English | MEDLINE | ID: covidwho-2296235

ABSTRACT

Coronaviruses belong to the group of RNA family of viruses that trigger diseases in birds, humans, and mammals, which can cause respiratory tract infections. The COVID-19 pandemic has badly affected every part of the world. Our study aimed to explore the genome of SARS-CoV-2, followed by in silico analysis of its proteins. Different nucleotide and protein variants of SARS-CoV-2 were retrieved from NCBI. Contigs and consensus sequences were developed to identify these variants using SnapGene. Data of the variants that significantly differed from each other was run through Predict Protein software to understand the changes produced in the protein structure. The SOPMA web server was used to predict the secondary structure of the proteins. Tertiary structure details of the selected proteins were analyzed using the web server SWISS-MODEL. Sequencing results showed numerous single nucleotide polymorphisms in the surface glycoprotein, nucleocapsid, ORF1a, and ORF1ab polyprotein while the envelope, membrane, ORF3a, ORF6, ORF7a, ORF8, and ORF10 genes had no or few SNPs. Contigs were used to identify variations in the Alpha and Delta variants of SARS-CoV-2 with the reference strain (Wuhan). Some of the secondary structures of the SARS-CoV-2 proteins were predicted by using Sopma software and were further compared with reference strains of SARS-CoV-2 (Wuhan) proteins. The tertiary structure details of only spike proteins were analyzed through the SWISS-MODEL and Ramachandran plots. Through the Swiss-model, a comparison of the tertiary structure model of the SARS-CoV-2 spike protein of the Alpha and Delta variants was made with the reference strain (Wuhan). Alpha and Delta variants of the SARS-CoV-2 isolates submitted in GISAID from Pakistan with changes in structural and nonstructural proteins were compared with the reference strain, and 3D structure mapping of the spike glycoprotein and mutations in the amino acids were seen. The surprisingly increased rate of SARS-CoV-2 transmission has forced numerous countries to impose a total lockdown due to an unusual occurrence. In this research, we employed in silico computational tools to analyze the SARS-CoV-2 genomes worldwide to detect vital variations in structural proteins and dynamic changes in all SARS-CoV-2 proteins, mainly spike proteins, produced due to many mutations. Our analysis revealed substantial differences in the functionality, immunological, physicochemical, and structural variations in the SARS-CoV-2 isolates. However, the real impact of these SNPs can only be determined further by experiments. Our results can aid in vivo and in vitro experiments in the future.

3.
J Med Virol ; 2022 Nov 29.
Article in English | MEDLINE | ID: covidwho-2275682

ABSTRACT

BACKGROUND: The recently emerged novel coronavirus, "severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2)", caused a highly contagious disease called coronavirus disease 2019 (COVID-19). It has severely damaged the world's most developed countries and has turned into a major threat for low- and middle-income countries. Since its emergence in late 2019, medical interventions have been substantial, and most countries relied on public health measures collectively known as nonpharmaceutical interventions. AIMS: To centralize the accumulative knowledge on non-pharmaceutical interventions (NPIs) against COVID-19 for each country under one worldwide consortium. METHODS: International COVID-19 Research Network collaborators developed a cross-sectional online-survey to assess the implications of NPIs and sanitary supply on incidence and mortality of COVID-19. Survey was conducted between January 1 and February 1, 2021, and participants from 92 countries/territories completed it. The association between NPIs, sanitation supplies and incidence and mortality were examined by multivariate regression, with log-transformed value of population as an offset value. RESULTS: Majority of countries/territories applied several preventive strategies including social distancing (100.0%), quarantine (100.0%), isolation (98.9%), and school closure (97.8%). Individual-level preventive measures such as personal hygiene (100.0%) and wearing facial mask (94.6% at hospital; 93.5% at mass transportation; 91.3% in mass gathering facilities) were also frequently applied. Quarantine at a designated place was negatively associated with incidence and mortality compared to home quarantine. Isolation at a designated place was also associated with reduced mortality compared to home isolation. Recommendations to use sanitizer for personal hygiene reduced incidence compared to recommendation to use soap did. Deprivation of mask was associated with increased incidence. Higher incidence and mortality were found in countries/territories with higher economic level. Mask deprivation was pervasive regardless of economic level. CONCLUSION: NPIs against COVID-19 such as using sanitizer, quarantine, and isolation can decrease incidence and mortality of COVID-19. This article is protected by copyright. All rights reserved.

5.
JMIR Public Health Surveill ; 7(6): e26267, 2021 06 18.
Article in English | MEDLINE | ID: covidwho-2197896

ABSTRACT

In March 2020, the World Health Organization declared COVID-19 as a global pandemic. The COVID-19 pandemic has affected various public health functions and essential services in different ways and magnitudes. Although all countries have witnessed the effect of COVID-19, the impact differed based on many factors including the integrity and resiliency of the countries' health systems. This paper presents opinions and expectations of the authors about the anticipated changes in the future of public health at the global, regional, and national levels. The viewpoint is based on the current efforts and challenges that various stakeholders have carried out to control COVID-19 and the contribution from the literature on the future of public health. Numerous agencies and actors are involved in the fight against COVID-19 with variations in their effectiveness. The public health services showed weaknesses in most of the countries, in addition to the lack of adequate curative medicine settings. The pandemic highlighted the need for better governance and stronger and more resilient health systems and capacities. The COVID-19 experience has also emphasized the importance of coordination and collaboration among the countries and stakeholders. The COVID-19 pandemic might lead to a wide discussion to improve international and national approaches to prepare for and respond to similar events in terms of preparedness and response mechanisms and tools. Public health will not be the same as before COVID-19. New health priorities, approaches, and new agendas will be on the table of the global platforms and initiatives. More investment in research and technology to meet the demand for new vaccines and medicines, innovative methods like distance learning and working, more respect and remuneration to health professionals, and normalization of the public health and social measures that were induced during the COVID-19 pandemic are expected to be seen in future.


Subject(s)
COVID-19 , Forecasting , Global Health/trends , Public Health/trends , Health Priorities/trends , Humans , SARS-CoV-2
7.
BMC Infect Dis ; 22(1): 887, 2022 Nov 26.
Article in English | MEDLINE | ID: covidwho-2139176

ABSTRACT

BACKGROUND: Persons in Pakistan have suffered from various infectious diseases over the years, each impacted by various factors including climate change, seasonality, geopolitics, and resource availability. The COVID-19 pandemic is another complicating factor, with changes in the reported incidence of endemic infectious diseases and related syndromes under surveillance. METHODS: We assessed the monthly incidence of eight important infectious diseases/syndromes: acute upper respiratory infection (AURI), viral hepatitis, malaria, pneumonia, diarrhea, typhoid fever, measles, and neonatal tetanus (NNT), before and after the onset of the COVID-19 pandemic. Administrative health data of monthly reported cases of these diseases/syndromes from all five provinces/regions of Pakistan for a 3-year interval (March 2018-February 2021) were analyzed using an interrupted time series approach. Reported monthly incidence for each infectious disease agent or syndrome and COVID-19 were subjected to time series visualization. Spearman's rank correlation coefficient between each infectious disease/syndrome and COVID-19 was calculated and median case numbers of each disease before and after the onset of the COVID-19 pandemic were compared using a Wilcoxon signed-rank test. Subsequently, a generalized linear negative binomial regression model was developed to determine the association between reported cases of each disease and COVID-19. RESULTS: In late February 2020, concurrent with the start of COVID-19, in all provinces, there were decreases in the reported incidence of the following diseases: AURI, pneumonia, hepatitis, diarrhea, typhoid, and measles. In contrast, the incidence of COVID was negatively associated with the reported incidence of NNT only in Punjab and Sindh, but not in Khyber Pakhtunkhwa (KPK), Balochistan, or Azad Jammu & Kashmir (AJK) & Gilgit Baltistan (GB). Similarly, COVID-19 was associated with a lowered incidence of malaria in Punjab, Sindh, and AJK & GB, but not in KPK and Balochistan. CONCLUSIONS: COVID-19 was associated with a decreased reported incidence of most infectious diseases/syndromes studied in most provinces of Pakistan. However, exceptions included NNT in KPK, Balochistan and AJK & GB, and malaria in KPK and Balochistan. This general trend was attributed to a combination of resource diversion, misdiagnosis, misclassification, misinformation, and seasonal patterns of each disease.


Subject(s)
COVID-19 , Communicable Diseases , Malaria , Measles , Pneumonia , Respiratory Tract Infections , Infant, Newborn , Humans , Incidence , COVID-19/epidemiology , Pakistan/epidemiology , Pandemics , Communicable Diseases/epidemiology , Syndrome , Malaria/epidemiology , Respiratory Tract Infections/epidemiology , Pneumonia/epidemiology , Measles/epidemiology , Diarrhea/epidemiology
8.
Front Public Health ; 10: 987452, 2022.
Article in English | MEDLINE | ID: covidwho-2080295

ABSTRACT

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.


Subject(s)
COVID-19 , SARS-CoV-2 , COVID-19/epidemiology , Female , Humans , Male , Pakistan/epidemiology , Pandemics , SARS-CoV-2/genetics
10.
Int J Infect Dis ; 112: 76-80, 2021 Nov.
Article in English | MEDLINE | ID: covidwho-1400316

ABSTRACT

OBJECTIVES: To evaluate infection prevention and control (IPC) training workshops using Kirkpatrick model level 1 and 2 regarding satisfaction of trainees and improvement of their knowledge and skills. METHODS: A cross-sectional study was conducted on 353 healthcare workers from January 2020 to March 2020, at four hospitals in Islamabad, Pakistan. Training feedback questionnaires and pre and post tests were employed for data collection. The authors analyzed data using SPSS version 25. RESULTS: The majority (52%) of participants rated the trainings as "Excellent", 44% rated "Good" while 2% graded "Average". Pre and post-tests mean scores demonstrated statistically significant improvement in knowledge and skills (p< 0.001). CONCLUSION: The training workshops significantly improved healthcare workers' knowledge and skills regarding Infection Prevention and Control and earned high satisfaction scores from the trainees.


Subject(s)
Health Personnel , Infection Control , Cross-Sectional Studies , Humans , Pakistan
13.
J Med Virol ; 94(10): 4869-4877, 2022 10.
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.


Subject(s)
COVID-19 , SARS-CoV-2 , COVID-19/epidemiology , Genome, Viral , Genomics , Humans , Mutation , Pakistan/epidemiology , Pandemics , Phylogeny , SARS-CoV-2/genetics
14.
N Engl J Med ; 386(22): 2097-2111, 2022 06 02.
Article in English | MEDLINE | ID: covidwho-1830291

ABSTRACT

BACKGROUND: The ZF2001 vaccine, which contains a dimeric form of the receptor-binding domain of severe acute respiratory syndrome coronavirus 2 and aluminum hydroxide as an adjuvant, was shown to be safe, with an acceptable side-effect profile, and immunogenic in adults in phase 1 and 2 clinical trials. METHODS: We conducted a randomized, double-blind, placebo-controlled, phase 3 trial to investigate the efficacy and confirm the safety of ZF2001. The trial was performed at 31 clinical centers across Uzbekistan, Indonesia, Pakistan, and Ecuador; an additional center in China was included in the safety analysis only. Adult participants (≥18 years of age) were randomly assigned in a 1:1 ratio to receive a total of three 25-µg doses (30 days apart) of ZF2001 or placebo. The primary end point was the occurrence of symptomatic coronavirus disease 2019 (Covid-19), as confirmed on polymerase-chain-reaction assay, at least 7 days after receipt of the third dose. A key secondary efficacy end point was the occurrence of severe-to-critical Covid-19 (including Covid-19-related death) at least 7 days after receipt of the third dose. RESULTS: Between December 12, 2020, and December 15, 2021, a total of 28,873 participants received at least one dose of ZF2001 or placebo and were included in the safety analysis; 25,193 participants who had completed the three-dose regimen, for whom there were approximately 6 months of follow-up data, were included in the updated primary efficacy analysis that was conducted at the second data cutoff date of December 15, 2021. In the updated analysis, primary end-point cases were reported in 158 of 12,625 participants in the ZF2001 group and in 580 of 12,568 participants in the placebo group, for a vaccine efficacy of 75.7% (95% confidence interval [CI], 71.0 to 79.8). Severe-to-critical Covid-19 occurred in 6 participants in the ZF2001 group and in 43 in the placebo group, for a vaccine efficacy of 87.6% (95% CI, 70.6 to 95.7); Covid-19-related death occurred in 2 and 12 participants, respectively, for a vaccine efficacy of 86.5% (95% CI, 38.9 to 98.5). The incidence of adverse events and serious adverse events was balanced in the two groups, and there were no vaccine-related deaths. Most adverse reactions (98.5%) were of grade 1 or 2. CONCLUSIONS: In a large cohort of adults, the ZF2001 vaccine was shown to be safe and effective against symptomatic and severe-to-critical Covid-19 for at least 6 months after full vaccination. (Funded by the National Science and Technology Major Project and others; ClinicalTrials.gov number, NCT04646590.).


Subject(s)
COVID-19 Vaccines , COVID-19 , Vaccines, Subunit , Adolescent , Adult , COVID-19/prevention & control , COVID-19 Vaccines/adverse effects , COVID-19 Vaccines/therapeutic use , Double-Blind Method , Humans , SARS-CoV-2 , Vaccination , Vaccines , Vaccines, Subunit/adverse effects , Vaccines, Subunit/therapeutic use , Young Adult
15.
Lancet ; 399(10321): 237-248, 2022 01 15.
Article in English | MEDLINE | ID: covidwho-1815307

ABSTRACT

BACKGROUND: The Ad5-nCoV vaccine is a single-dose adenovirus type 5 (Ad5) vectored vaccine expressing the SARS-CoV-2 spike protein that was well-tolerated and immunogenic in phase 1 and 2 studies. In this study, we report results on the final efficacy and interim safety analyses of the phase 3 trial. METHODS: This double-blind, randomised, international, placebo-controlled, endpoint-case driven, phase 3, clinical trial enrolled adults aged 18 years older at study centres in Argentina, Chile, Mexico, Pakistan, and Russia. Participants were eligible for the study if they had no unstable or severe underlying medical or psychiatric conditions; had no history of a laboratory-confirmed SARS-CoV-2 infection; were not pregnant or breastfeeding; and had no previous receipt of an adenovirus-vectored, coronavirus, or SARS-CoV-2 vaccine. After informed consent was obtained, 25 mL of whole blood was withdrawn from all eligible participants who were randomised in a 1:1 ratio to receive a single intramuscular dose of 0·5 mL placebo or a 0·5 mL dose of 5 × 1010 viral particle (vp)/mL Ad5-nCoV vaccine; study staff and participants were blinded to treatment allocation. All participants were contacted weekly by email, telephone, or text message to self-report any symptoms of COVID-19 illness, and laboratory testing for SARS-CoV-2 was done for all participants with any symptoms. The primary efficacy objective evaluated Ad5-nCoV in preventing symptomatic, PCR-confirmed COVID-19 infection occurring at least 28 days after vaccination in all participants who were at least 28 days postvaccination on Jan 15, 2021. The primary safety objective evaluated the incidence of any serious adverse events or medically attended adverse events postvaccination in all participants who received a study injection. This trial is closed for enrolment and is registered with ClinicalTrials.gov (NCT04526990). FINDINGS: Study enrolment began on Sept 22, 2020, in Pakistan, Nov 6, 2020, in Mexico, Dec 2, 2020, in Russia and Chile, and Dec 17, 2020, in Argentina; 150 endpoint cases were reached on Jan 15, 2021, triggering the final primary efficacy analysis. One dose of Ad5-nCoV showed a 57·5% (95% CI 39·7-70·0, p=0·0026) efficacy against symptomatic, PCR-confirmed, COVID-19 infection at 28 days or more postvaccination (21 250 participants; 45 days median duration of follow-up [IQR 36-58]). In the primary safety analysis undertaken at the time of the efficacy analysis (36 717 participants), there was no significant difference in the incidence of serious adverse events (14 [0·1%] of 18 363 Ad5-nCoV recipients and 10 [0·1%] of 18 354 placebo recipients, p=0·54) or medically attended adverse events (442 [2·4%] of 18 363 Ad5-nCoV recipients and 411 [2·2%] of 18 354 placebo recipients, p=0·30) between the Ad5-nCoV or placebo groups, or any serious adverse events considered related to the study product (none in both Ad5-nCoV and placebo recipients). In the extended safety cohort, 1004 (63·5%) of 1582 of Ad5-nCoV recipients and 729 (46·4%) of 1572 placebo recipients reported a solicited systemic adverse event (p<0·0001), of which headache was the most common (699 [44%] of Ad5-nCoV recipients and 481 [30·6%] of placebo recipients; p<0·0001). 971 (61·3%) of 1584 Ad5-nCoV recipients and 314 (20·0%) of 1573 placebo recipients reported an injection-site adverse event (p<0·0001), of which pain at the injection site was the most frequent; reported by 939 (59%) Ad5-nCoV recipients and 303 (19%) placebo recipients. INTERPRETATION: One dose of Ad5-nCoV is efficacious and safe in healthy adults aged 18 years and older. FUNDING: CanSino Biologics and the Beijing Institute of Biotechnology.


Subject(s)
COVID-19 Vaccines/administration & dosage , COVID-19/prevention & control , Adolescent , Adult , Antibodies, Neutralizing/blood , Antibodies, Viral/blood , COVID-19/diagnosis , COVID-19/immunology , COVID-19/virology , COVID-19 Nucleic Acid Testing/statistics & numerical data , COVID-19 Vaccines/adverse effects , COVID-19 Vaccines/immunology , Double-Blind Method , Female , Follow-Up Studies , Humans , Immunogenicity, Vaccine , Male , Middle Aged , SARS-CoV-2/genetics , SARS-CoV-2/immunology , Vaccination/methods , Young Adult
16.
J Med Virol ; 94(6): 2402-2413, 2022 06.
Article in English | MEDLINE | ID: covidwho-1718416

ABSTRACT

The aim of this study is to provide a more accurate representation of COVID-19's case fatality rate (CFR) by performing meta-analyses by continents and income, and by comparing the result with pooled estimates. We used multiple worldwide data sources on COVID-19 for every country reporting COVID-19 cases. On the basis of data, we performed random and fixed meta-analyses for CFR of COVID-19 by continents and income according to each individual calendar date. CFR was estimated based on the different geographical regions and levels of income using three models: pooled estimates, fixed- and random-model. In Asia, all three types of CFR initially remained approximately between 2.0% and 3.0%. In the case of pooled estimates and the fixed model results, CFR increased to 4.0%, by then gradually decreasing, while in the case of random-model, CFR remained under 2.0%. Similarly, in Europe, initially, the two types of CFR peaked at 9.0% and 10.0%, respectively. The random-model results showed an increase near 5.0%. In high-income countries, pooled estimates and fixed-model showed gradually increasing trends with a final pooled estimates and random-model reached about 8.0% and 4.0%, respectively. In middle-income, the pooled estimates and fixed-model have gradually increased reaching up to 4.5%. in low-income countries, CFRs remained similar between 1.5% and 3.0%. Our study emphasizes that COVID-19 CFR is not a fixed or static value. Rather, it is a dynamic estimate that changes with time, population, socioeconomic factors, and the mitigatory efforts of individual countries.


Subject(s)
COVID-19 , Asia , COVID-19/epidemiology , Europe/epidemiology , Humans , SARS-CoV-2 , Socioeconomic Factors
17.
J Med Virol ; 94(3): 1115-1129, 2022 03.
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.


Subject(s)
COVID-19 , SARS-CoV-2 , COVID-19/diagnosis , COVID-19/epidemiology , Genomics , Humans , Pakistan/epidemiology , SARS-CoV-2/genetics
20.
J Public Health (Oxf) ; 43(Suppl 3): iii1-iii11, 2021 12 08.
Article in English | MEDLINE | ID: covidwho-1607646

ABSTRACT

BACKGROUND: This study aimed to compare knowledge, attitude and practice (KAP) regarding COVID-19 between public health workers (PHWs) attended field epidemiology training program (FETP-trained) and those who did not attend FETP (non-FETP trained). METHODS: Multi-country cross-sectional survey was conducted among PHWs who participated in COVID-19 pandemic in 10 countries at EMR. Online questionnaire that included demographic information, KAP regarding COVID-19 pandemic was distributed among HCWs. Scoring system was used to quantify the answers, bivariate and Multivariate analysis performed to compare FETP-trained with non-FETP trained PHWs. RESULTS: Overall, 1337 PHWs participated, with 835 (62.4%) < 40 years of age, and 851 (63.6%) males. Of them, 423 (31.6%) had FETP, including that 189 (44.7%) had advanced level, 155 (36.6%) intermediate and 79 (18.7%) basic level training. Compared with non-FETP trained, FETP trained were older, having higher KAP scores. FETP participation was low in infection control, and PH laboratories. KAP mean scores for intermediate level attendees are comparable to advanced level. CONCLUSIONS: FETP-trained are having better KAP than non-FETP PHWs. Expanding the intermediate level, maintain the Rapid Response training and introduce the laboratory component are recommended to maximize the benefit from FETP. Infection control, antimicrobial resistance and coordination are areas where training should include.


Subject(s)
COVID-19 , Cross-Sectional Studies , Health Knowledge, Attitudes, Practice , Humans , Male , Pandemics , Public Health , SARS-CoV-2 , Surveys and Questionnaires
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