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BACKGROUND: Pakistan reported 1.57 million COVID-19 cases between 2020 and 2022, based on approximately 30.6 million SARS-CoV-2 RT-PCR (reverse-transcription polymerase chain reaction) tests conducted. This study utilized data from one of the largest in-country testing facilities, Aga Khan University Hospital (AKUH) in Karachi, Pakistan, to explore gender and age-related in RT-PCR testing patterns. METHODS: We conducted a retrospective review of SARS-CoV-2 RT-PCR test data extracted from AKUH clinical laboratory records between February 2020 and February 2022. Gender and age distributions were examined in the context of testing patterns across the period. Multivariate regression models assessed independent associations between COVID-19 positivity and key variables. RESULTS: We reviewed 470,249 RT-PCR tests, finding that most tests were in those aged 21-40 years (48.1%). Overall, COVID-19 test positivity was 20.6%. In all, 57.7% were performed for males, predominant amongst those tested across all age groups and waves. Females had significantly lower odds of testing positive for COVID-19 (OR: 0.9; 95% CI: 0.9-1.0). However, when adjusted for gender, age and pandemic phases, the positivity rates between males and females were the same. The odds of a positive result increased significantly with age; individuals aged > 80 years had 2.5 times higher odds of testing positive than those aged 0-10 years (aOR 2.5, 95% CI 2.3-2.7). CONCLUSIONS: The analysis indicates a consistent male dominance in COVID-19 testing, with higher positivity rates in older age groups. Our study highlight the importance of examining demographic characteristics in disease associated data especially, representation of females amongst cohorts.
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COVID-19 , SARS-CoV-2 , Humanos , Paquistão/epidemiologia , Feminino , Masculino , Estudos Retrospectivos , COVID-19/epidemiologia , COVID-19/diagnóstico , Adulto , Pessoa de Meia-Idade , Adulto Jovem , Adolescente , Criança , Lactente , Pré-Escolar , Idoso , SARS-CoV-2/genética , Fatores Sexuais , Fatores Etários , Recém-Nascido , Disparidades em Assistência à Saúde , Teste para COVID-19/estatística & dados numéricos , Teste de Ácido Nucleico para COVID-19/estatística & dados numéricos , Idoso de 80 Anos ou mais , Distribuição por IdadeRESUMO
BACKGROUND: Linezolid-resistant Enterococcus faecium (LRE) is a global priority pathogen. Thirteen LRE were reported from clinical specimens between November 2021 and April 2023 at two laboratories in Karachi, Pakistan. We aimed to investigate the strain types and genes associated with linezolid resistance among these isolates. Whole genome sequencing (WGS) was performed and analyzed by multilocus sequence typing (MLST). The presence of linezolid resistance genes was identified using ResFinder v4.1.11 and the LRE-finder tool. RESULTS: Twelve isolates belonged to clonal complex 17 (CC17); ST80 (n = 10), ST612 (n = 1) and ST1380 (n = 1). Six isolates showed the presence of optrA gene and G2576T mutations in the 23S rRNA gene, while six showed poxtA and cfr(D) genes. One isolate showed the combination of optrA, cfr(D) and poxtA genes. CONCLUSION: Our findings show the circulation of CC17 sequence types with a known outbreak potential and we identified molecular mechanisms of resistance that were not previously reported from Pakistan.
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Antibacterianos , Farmacorresistência Bacteriana , Enterococcus faecium , Infecções por Bactérias Gram-Positivas , Linezolida , Testes de Sensibilidade Microbiana , Tipagem de Sequências Multilocus , Sequenciamento Completo do Genoma , Enterococcus faecium/genética , Enterococcus faecium/efeitos dos fármacos , Enterococcus faecium/isolamento & purificação , Enterococcus faecium/classificação , Paquistão , Linezolida/farmacologia , Humanos , Antibacterianos/farmacologia , Farmacorresistência Bacteriana/genética , Infecções por Bactérias Gram-Positivas/microbiologia , Infecções por Bactérias Gram-Positivas/epidemiologia , RNA Ribossômico 23S/genética , Feminino , Masculino , Genoma Bacteriano/genética , Genômica , Adulto , Proteínas de Bactérias/genética , Pessoa de Meia-Idade , MutaçãoRESUMO
This retrospective cohort study aims to describe the clinical characteristics and outcomes and assess risk factors for mortality across the epidemic waves in hospitalized COVID-19 patients in a major tertiary-care center in Pakistan. A total of 5368 patients with COVID-19, hospitalized between March 2020 and April 2022 were included. The median age was 58 years (IQR: 44-69), 41% were females, and the overall mortality was 12%. Comparative analysis of COVID-19 waves showed that the proportion of patients aged ≥ 60 years was highest during the post-wave 4 period (61.4%) and Wave 4 (Delta) (50%) (p < 0.001). Male predominance decreased from 65.2% in Wave 2 to 44.2% in Wave 5 (Omicron) (p < 0.001). Mortality rate was lowest at 9.4% in wave 5 and highest at 21.6% in the post-wave 4 period (p = 0.041). In multivariable analysis for risk factors of mortality, acute respiratory distress syndrome (ARDS) was most strongly associated with mortality (aOR 22.98, 95% CI 15.28-34.55, p < 0.001), followed by need for mechanical ventilation (aOR 6.81, 95% CI 5.13-9.05, p < 0.001). Other significant risk factors included acute kidney injury (aOR 3.05, 95% CI 2.38-3.91, p < 0.001), stroke (aOR 2.40, 95% CI 1.26-4.60, p = 0.008), pulmonary embolism (OR 2.07, 95% CI 1.28-3.35, p = 0.003), and age ≥ 60 years (aOR 2.45, 95% CI 1.95-3.09, p < 0.001). Enoxaparin use was associated with lower mortality odds (aOR 0.45, 95% CI 0.35-0.60, p < 0.001. Patients hospitalized during Wave 4 (aOR 2.22, 95% CI 1.39-3.56, p < 0.001) and the post-wave 4 period (aOR 2.82, 95% CI 1.37-5.80, p = 0.005) had higher mortality odds compared to other waves. The study identifies higher mortality risk in patients admitted in Delta wave and post-wave, aged ≥ 60 years, and with respiratory and renal complications, and lower risk with anticoagulation during COVID-19 waves.
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COVID-19 , Mortalidade Hospitalar , Hospitalização , Humanos , COVID-19/mortalidade , COVID-19/epidemiologia , Masculino , Feminino , Pessoa de Meia-Idade , Paquistão/epidemiologia , Fatores de Risco , Idoso , Estudos Retrospectivos , Adulto , Respiração Artificial , SARS-CoV-2/isolamento & purificação , Síndrome do Desconforto Respiratório/mortalidade , Centros de Atenção Terciária/estatística & dados numéricosRESUMO
The human immunodeficiency virus type-1 epidemic in Pakistan has significantly increased over the last two decades. In Karachi, Pakistan, there is a lack of updated information on the complexity of HIV-1 genetic diversity and the burden of drug resistance mutations (DRMs) that can contribute to ART failure and poor treatment outcomes. This study aimed to determine HIV-1 genetic diversity and identify drug-resistance mutations among people living with HIV in Karachi. A total of 364 HIV-positive individuals, with a median age of 36 years, were enrolled in the study. The HIV-1 partial pol gene was successfully sequenced from 268 individuals. The sequences were used to generate phylogenetic trees to determine clade diversity and also to assess the burden of DRMs. Based on the partial pol sequences, 13 distinct HIV-1 subtypes and recombinant forms were identified. Subtype A1 was the most common clade (40%), followed by CRF02_AG (33.2%). Acquired DRMs were found in 30.6% of the ART-experienced patients, of whom 70.7%, 20.7%, and 8.5% were associated with resistance to NNRTIs, NRTIs, and PIs, respectively. Transmitted DRMs were found in 5.6% of the ART-naïve patients, of whom 93% were associated with resistance against NNRTIs and 7% to PIs. The high prevalence of DRMs in ART-experienced patients poses significant challenges to the long-term benefits and sustainability of the ART program. This study emphasizes the importance of continuous HIV molecular epidemiology and drug resistance surveillance to support evidence-based HIV prevention, precise ART, and targeted AIDS care.
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Fármacos Anti-HIV , Farmacorresistência Viral , Variação Genética , Infecções por HIV , HIV-1 , Mutação , Filogenia , Humanos , HIV-1/genética , HIV-1/efeitos dos fármacos , HIV-1/classificação , Paquistão/epidemiologia , Infecções por HIV/virologia , Infecções por HIV/epidemiologia , Farmacorresistência Viral/genética , Adulto , Masculino , Feminino , Fármacos Anti-HIV/farmacologia , Fármacos Anti-HIV/uso terapêutico , Pessoa de Meia-Idade , Adulto Jovem , Genótipo , AdolescenteRESUMO
BACKGROUND: COVID-19 epidemiology changed with the emergence of SARS-CoV-2 variants of concern (VOC). Pakistan administered mostly inactivated vaccines. We investigated the association between VOC and breakthrough infections in a mixed-vaccination-status population of Karachi. METHODS: We investigated SARS-CoV-2 VOC tested in 392 respiratory specimens collected between May and December 2021. Data for age, sex, hospital admission, vaccinations, together with CT values of the diagnostic PCR test were analyzed. RESULTS: The median age of COVID-19 cases tested was 40 (27-57) years and 43.4% were female. Delta variants were most common (56.4%) followed by Alpha (15.9%), Omicron (12.2%), Beta/Gamma (11.3%), and others (4.3%). Eighteen percent of cases were hospitalized whereby, predominant VOC were Beta/Gamma (40.8%), Alpha (35.2%) and Delta (22.5%). Overall, 55.4% of individuals were fully vaccinated, 7.4% were partially vaccinated and 37.2% were unvaccinated. Most (74.6%) inpatients were unvaccinated. Vaccines comprised inactivated (85.34%), single-shot vector (8.62%), two-shot vector (3.02%) and mRNA (3.02%) types. Omicron variants showed lower viral loads as compared to Alpha, Beta/Gamma, and Delta (p = 0.017). The risk of infection with Delta and Omicron variants was higher, 8 weeks after vaccination. The majority of those with breakthrough infections after receiving inactivated vaccines acquired COVID-19 within 4 months of vaccination. CONCLUSION: Our data highlights the shifting of VOC from Delta to Omicron during 2021 and that COVID-19 vaccinations reduced both hospitalizations and viral transmission. It informs on the increased risk of breakthrough infection within 8 weeks of vaccination, indicating the need for booster vaccinations.
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Vacinas contra COVID-19 , COVID-19 , Hospitalização , SARS-CoV-2 , Humanos , COVID-19/epidemiologia , COVID-19/prevenção & controle , COVID-19/virologia , Feminino , Masculino , SARS-CoV-2/genética , SARS-CoV-2/imunologia , Adulto , Pessoa de Meia-Idade , Vacinas contra COVID-19/administração & dosagem , Vacinas contra COVID-19/imunologia , Hospitalização/estatística & dados numéricos , Paquistão/epidemiologia , Índice de Gravidade de Doença , Vacinação/estatística & dados numéricos , Infecções IrruptivasRESUMO
The objective of this study was to assess the psychological impact of isolation on individuals with Covid-19 and determine the experiences of people in isolation. All adults with Covid-19 who reported to the infectious disease tele-clinic were included in the study; participants were sent the survey form via email. The email was sent to 146 people and 47 responses were received. IES-R questionnaire was submitted to all individuals on Day 7 of quarantine, along with a qualitative questionnaire. The mean score on IES-R for all the respondents was 18.77. Out of 47 participants, for 6 (12.8%) PTSD was a clinical concern, 3 (6.4%) participants had a probable diagnosis of PTSD, and 6 (12.8%) participants scored high enough to suppress immune function. The majority of participants reported stress due to confinement in an isolated space and interruption in daily routine, specifically work-related routine. Praying, meditation, and having social support helped the participants cope with the isolation.
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COVID-19 , Transtornos de Estresse Pós-Traumáticos , Adulto , Humanos , Transtornos de Estresse Pós-Traumáticos/diagnóstico , Transtornos de Estresse Pós-Traumáticos/epidemiologia , Transtornos de Estresse Pós-Traumáticos/psicologia , Centros de Atenção Terciária , Apoio Social , Inquéritos e QuestionáriosRESUMO
Background and Aims: COVID-19 morbidity and mortality varied globally through the pandemic. We studied the relationship of SARS-CoV-2 variants of concern (VOC) with COVID-19 severity and mortality among hospitalized patients in Pakistan. Methods: A retrospective review of clinical, laboratory, and vaccination data of 197 COVID-19 adult patients at the Aga Khan University Hospital, Karachi between April 2021, and February 2022 was performed. SARS-CoV-2 VOC identified in respiratory samples were analyzed. Univariate and multivariate analysis was conducted to identify factors associated with COVID-19 outcomes. Results: The median age of cases was 55 years and 51.8% were males. Twenty-four percent of females were pregnant. Of COVID-19 cases, 48.2% had nonsevere disease, while 52.8% had severe/critical disease. Hypertension (48%) and diabetes mellitus (41%) were common comorbids. SARS-CoV-2 VOC identified comprised; Omicron (55.3%), Beta (14.7%), Alpha (13.7%), Delta (12.7%), and Gamma (3.6%) variants. Most (59.7%) study subjects were unvaccinated. Of vaccines, 88% had received inactivated virus COVID-19 vaccines. Increased risk of severe disease was associated with age ≥50 years (odds ratio [OR]: 5.73; 95% confidence interval [CI]: [2.45-13.7]), as well as with diabetes mellitus (OR: 4.24; 95% CI: [1.82-9.85]). Full vaccination (OR: 0.25; 95% CI: [0.11-0.58]) or infection with Omicron (OR: 0.42; 95% CI: [0.23-0.74]) was associated with reduced disease severity. The risk of mortality increased with age ≥50 years (OR: 5.07; 95% CI: [1.92-13.42]) and a history of myocardial infarction (OR: 5.11; 95% CI: [1.45-17.93]) whilst, infection with Omicron was found to reduce the risk (OR: 0.22; 95% CI: [0.10-0.53]). Conclusion: Our study describes the relationship between the severity of COVID-19, in-hospital mortality in relation to SARS-CoV-2 variants, and the impact of COVID-19 vaccination in Pakistan. Outcomes were more favorable in younger individuals, after vaccinations and with Omicron variant infections. Most cases received inactivated virus vaccines therefore these data highlight the protection provided against severe COVID-19.
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BACKGROUND: Protection against SARS-CoV-2 is mediated by humoral and T cell responses. Pakistan faced relatively low morbidity and mortality from COVID-19 through the pandemic. To examine the role of prior immunity in the population, we studied IgG antibody response levels, virus neutralizing activity and T cell reactivity to Spike protein in a healthy control group (HG) as compared with COVID-19 cases and individuals from the pre-pandemic period (PP). METHODS: HG and COVID-19 participants were recruited between October 2020 and May 2021. Pre-pandemic sera was collected before 2018. IgG antibodies against Spike and its Receptor Binding Domain (RBD) were determined by ELISA. Virus neutralization activity was determined using a PCR-based micro-neutralization assay. T cell - IFN-γ activation was assessed by ELISpot. RESULTS: Overall, the magnitude of anti-Spike IgG antibody levels as well as seropositivity was greatest in COVID-19 cases (90%) as compared with HG (39.8%) and PP (12.2%). During the study period, Pakistan experienced three COVID-19 waves. We observed that IgG seropositivity to Spike in HG increased from 10.3 to 83.5% during the study, whilst seropositivity to RBD increased from 7.5 to 33.3%. IgG antibodies to Spike and RBD were correlated positively in all three study groups. Virus neutralizing activity was identified in sera of COVID-19, HG and PP. Spike reactive T cells were present in COVID-19, HG and PP groups. Individuals with reactive T cells included those with and without IgG antibodies to Spike. CONCLUSIONS: Antibody and T cell responses to Spike protein in individuals from the pre-pandemic period suggest prior immunity against SARS-CoV-2, most likely from cross-reactive responses. The rising seroprevalence observed in healthy individuals through the pandemic without known COVID-19 may be due to the activation of adaptive immunity from cross-reactive memory B and T cells. This may explain the more favourable COVID-19 outcomes observed in this population.
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COVID-19 , SARS-CoV-2 , Humanos , COVID-19/epidemiologia , Paquistão/epidemiologia , Pandemias , Estudos Soroepidemiológicos , Glicoproteína da Espícula de Coronavírus , Linfócitos T , Imunoglobulina G , ELISPOT , Anticorpos Antivirais , Anticorpos Neutralizantes , Imunidade HumoralRESUMO
Background and Aims: COVID-19 vaccinations have reduced morbidity and mortality from the disease. Antibodies against severe acute respiratory syndrome coronavirus 2 (SARSCoV2) have been associated with immune protection. Seroprevalence studies revealed high immunoglobulin G (IgG) antibody levels to SARS-CoV-2 in the Pakistani population before vaccinations. We investigated the effect of BBIBP-CorV vaccination on circulating IgG antibodies and interferon (IFN)-γ from T cells measured in a cohort of healthy individuals, with respect to age, gender, and history of COVID-19. Methods: The study was conducted between April and October 2021. BBIBP-CorV vaccinated participants were followed up to 24 weeks. Antibodies to SARS-CoV-2 Spike protein and its receptor-binding domain (RBD) were measured. IFNγ secreted by whole blood stimulation of Spike protein and extended genome antigens was determined. Results: Study participants with a history of prior COVID-19 displayed a higher magnitude of IgG antibodies to Spike and RBD. IgG seropositivity was greater in those with prior COVID-19, aged 50 years or younger and in females. At 24 weeks after vaccination, 37.4% of participants showed IFN-γ responses to SARS-CoV-2 antigens. T cell IFN-γ release was higher in those with prior COVID-19 and those aged 50 years or less. Highest IFN-γ release was observed to extended genome antigens in individuals both with and without prior COVID-19. Conclusion: We found that IgG seropositivity to both Spike and RBD was affected by prior COVID-19, age and gender. Importantly, seropositive responses persisted up to 24 weeks after vaccination. Persistence of vaccine induced IgG antibodies may be linked to the high seroprevalence observed earlier in unvaccinated individuals. Increased T cell reactivity to Spike and extended genome antigens reflects cellular activation induced by BBIBP-CorV. COVID-19 vaccination may have longer lasting immune responses in populations with a higher seroprevalence. These data inform on vaccination booster policies for high-risk groups.
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BACKGROUND: Antiretroviral therapy (ART) effectiveness is compromised by the emergence of HIV drug resistance mutations (DRM) and can lead to the failure of ART. Apart from intrinsic viral factors, non-compliance with drugs and/or the use of sub-optimum therapy can lead to the emergence of DRMs. In Pakistan HIV currently exists as a concentrated epidemic, however, ART coverage is very low, and drug adherence is poor. ART is selected assuming without baseline genotyping. Pakistan has recently seen a rise in treatment failures, but the country's actual burden of DRM is still unknown. In this study, we perform the genetic and drug resistance analysis of the pol gene from Pakistani HIV-positive ART-naïve and ART-experienced individuals. METHODS: In this study, HIV-1 pol was sequenced from 146 HIV-1 positive individuals, divided into ART-naïve (n = 37) and ART-experienced (n = 109). The sequences were also used to determine HIV-1 subtypes, the prevalence of DRM, and pol genetic variability. RESULTS: DRM analysis identified numerous DRMs against reverse transcriptase inhibitors in both ART-naïve and ART-experienced groups, including a few that are classified as rare. Additionally, the ART-experienced group showed mutations associated with resistance to protease inhibitors. Genetic analysis showed negative selection pressure in both groups, but a higher rate of evolution in the ART-naïve group. CONCLUSION: High prevalence of DRMs, especially against previous first-line treatment in ART- naïve and the accumulation of DRMs in ART-experienced groups is concerning and warrants that a more extensive DRM survey be carried out to inform first-line and second-line ART regimen recommendations.
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Antirretrovirais , Farmacorresistência Viral Múltipla , Genes pol , Infecções por HIV , HIV-1 , Humanos , Antirretrovirais/farmacologia , Antirretrovirais/uso terapêutico , Farmacorresistência Viral Múltipla/genética , Genes pol/genética , Infecções por HIV/tratamento farmacológico , Infecções por HIV/genética , Soropositividade para HIV , HIV-1/efeitos dos fármacos , HIV-1/genética , Peptídeo Hidrolases/genética , DNA Polimerase Dirigida por RNA/genéticaRESUMO
BACKGROUND: There is no consensus on the use of postoperative antibiotic prophylaxis (PAP) after mastectomy with indwelling drains. We explored the utility of continued PAP in reducing surgical site infection (SSI) rates after mastectomy without immediate reconstruction and with indwelling drains. PATIENTS AND METHODS: A multicenter, two-armed, randomized control superiority trial was conducted in Pakistan. We enrolled all consenting adult patients undergoing mastectomy without immediate reconstruction. All patients received a single preoperative dose of cephalexin within 60 min of incision, and postoperatively were randomized to receive either continued PAP using cephalexin (intervention) or a placebo (control) for the duration of indwelling, closed-suction drains. The primary outcome was the development of SSI within 30 days and 90 days postoperatively. Secondary outcomes included study-drug-associated adverse events. Intention-to-treat analysis was performed using multivariable Cox regression. RESULTS: A total of 369 patients, 180 (48.8%) in the intervention group and 189 (51.2%) in the control group, were included in the final analysis. Overall cumulative SSI rates were 3.5% at 30 days and 4.6% at 90 days postoperatively. PAP was not associated with SSI reduction at 30 (hazard ratio, HR 1.666 [95% confidence interval CI 0.515-5.385]) or 90 (1.575 [0.558-4.448]) days postoperatively, or with study-drug-associated adverse effects (0.529 [0.196-1.428]). CONCLUSIONS: Continuing antibiotic prophylaxis for the duration of indwelling drains after mastectomy without immediate reconstruction offers no additional benefit in terms of SSI reduction. There is a need to update existing guidelines to provide clearer recommendations regarding use of postoperative antibiotic prophylaxis after mastectomy in the setting of indwelling drains.
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Antibioticoprofilaxia , Mastectomia , Infecção da Ferida Cirúrgica , Humanos , Infecção da Ferida Cirúrgica/epidemiologia , Infecção da Ferida Cirúrgica/prevenção & controle , Método Duplo-Cego , Paquistão , Cuidados Pós-Operatórios , Resultado do Tratamento , Feminino , Adulto , Pessoa de Meia-Idade , IdosoRESUMO
OBJECTIVE: During the COVID-19 pandemic, several vaccines that were efficacious in randomised controlled trials were authorised for mass vaccination. In developing countries, inactivated vaccines were widely administered. While inactivated vaccines have been deemed effective in reducing disease severity, for healthcare personnel (HCP), effectiveness against SARS-CoV-2 infections is essential to reduce the risk to vulnerable patients and ensure a stable healthcare workforce. There are limited studies examining inactivated vaccines' effectiveness against SARS-CoV-2 variants of concern (VOCs) in real-world settings. We estimated the effectiveness of inactivated vaccines (BBIBP-CorV and CoronaVac) against reverse transcription PCR (RT-PCR)-confirmed SARS-CoV-2 infections among HCP in the setting of emerging SARS-CoV-2 VOCs in Pakistan. DESIGN: A retrospective matched, test-negative case-control analysis using existing data from an Employee Health database on HCP at a large, private healthcare system in Pakistan. PARTICIPANTS: 4599 HCP were tested between 1 April and 30 September 2021. Each case (PCR positive) was matched to two to six controls (PCR negative) by the date of the RT-PCR test (±7 days) to reduce bias. PRIMARY AND SECONDARY OUTCOME MEASURES: The primary outcome was vaccine effectiveness (VE) against SARS-CoV-2 infection. The secondary outcome was VE against symptomatic SARS-CoV-2 infection. Per cent VE was calculated using (1-OR)*100, with the OR of getting a PCR-confirmed SARS-COV-2 infection estimated using conditional logistic regression, after adjusting for age, gender, work area and history of SARS-CoV-2 infection. RESULTS: Inactivated vaccines were ineffective against SARS-CoV-2 infections after receiving the first dose (VE 17%, 95% CI -10, 39; p=0.261). They showed modest effectiveness ≥14 days after the second dose against SARS-CoV-2 infections (VE 30%, 95% CI 7, 48; p=0.015) and symptomatic SARS-CoV-2 infections (VE 33%, 95% CI 6, 52; p=0.002). CONCLUSIONS: Inactivated vaccines show modest effectiveness against SARS-CoV-2 infections in the setting of emerging VOCs. This builds a strong case for boosters and/or additional vaccination.
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Vacinas contra COVID-19 , COVID-19 , Humanos , COVID-19/epidemiologia , COVID-19/prevenção & controle , Estudos de Casos e Controles , Estudos Retrospectivos , Paquistão/epidemiologia , Pandemias , SARS-CoV-2 , Vacinas de Produtos InativadosRESUMO
COVID-19 resulted in extensive morbidity and mortality worldwide. SARS-CoV-2 evolved rapidly, with increasing transmission due to Variants of Concern (VOC). Identifying VOC became important but genome submissions from low-middle income countries (LMIC) remained low leading to gaps in genomic epidemiology. We demonstrate the use of a specific mutation RT-PCR based approach to identify VOC in SARS-CoV-2 positive samples through the pandemic in Pakistan. We selected 2150 SARS-CoV-2 PCR positive respiratory specimens tested between April 2021 and February 2022, at the Aga Khan University Hospital Clinical Laboratories, Karachi, Pakistan. Commercially available RT-PCR assays were used as required for mutations in Spike protein (N501Y, A570D, E484K, K417N, L452R, P681R and deletion69_70) to identify Alpha, Beta, Gamma, Delta, and Omicron variants respectively. Three pandemic waves associated with Alpha, Delta and Omicron occurred during the study period. Of the samples screened, VOC were identified in 81.7% of cases comprising mainly; Delta (37.2%), Alpha (29.8%) and Omicron (17.1%) variants. During 2021, Alpha variants were predominant in April and May; Beta and Gamma variants emerged in May and peaked in June; the Delta variant peaked in July and remained predominant until November. Omicron (BA.1) emerged in December 2021 and remained predominant until February 2022. The CT values of Alpha, Beta, Gamma and Delta were all significantly higher than that of Omicron variants (p<0.0001). We observed VOC through the pandemic waves using spike mutation specific RT-PCR assays. We show the spike mutation specific RT-PCR assay is a rapid, low-cost and adaptable for the identification of VOC as an adjunct approach to NGS to effectively inform the public health response. Further, by associating the VOC with CT values of its diagnostic PCR we gain information regarding the viral load of samples and therefore the level of transmission and disease severity in the population.
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Anticipating staff shortage during the Omicron variant surge, we modified the US Centers for Disease Control and Prevention's contingency guidelines at a healthcare system in Pakistan. Infected staff had a SARS-CoV-2 rapid antigen test after 5-7 days of isolation, to decide a safe return-to-work. This led to signifcant cost savings without compromising patient/staff safety.
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BACKGROUND: Early identification of COVID-19-associated pulmonary aspergillosis (CAPA) is particularly challenging in low- middle-income countries where diagnostic capabilities are limited, and risk factors for CAPA have not been identified. It is also essential to recognise CAPA patients who are likely to have a poorer outcome to decide on aggressive management approaches. Therefore, this study aimed to identify risk factors and outcomes for CAPA among admitted moderate to critical COVID-19 patients at our centre in Pakistan. METHODS: An unmatched case-control study with ratio of 1:2 was conducted on hospitalised adult patients with COVID-19 from March 2020-July 2021. Cases were defined according to European Confederation of Medical Mycology and the International Society for Human and Animal Mycology consensus criteria. Controls were defined as patients hospitalised with moderate, severe or critical COVID-19 without CAPA. RESULTS: A total of 100 CAPA cases (27 probable CAPA; 73 possible CAPA) were compared with 237 controls. Critical disease at presentation (aOR 5.04; 95% CI 2.18-11.63), age ≥ 60 years (aOR 2.00; 95% CI 1.20-3.35) and underlying co-morbid of chronic kidney disease (CKD) (aOR 3.78; 95% CI 1.57-9.08) were identified as risk factors for CAPA. Patients with CAPA had a significantly greater proportion of complications and longer length of hospital stay (p-value < .001). Mortality was higher in patients with CAPA (48%) as compared to those without CAPA (13.5%) [OR = 6.36(95% CI 3.6-11)]. CONCLUSIONS: CAPA was significantly associated with advanced age, CKD and critical illness at presentation, along with a greater frequency of complications and higher mortality.
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COVID-19 , Aspergilose Pulmonar , Insuficiência Renal Crônica , Adulto , Animais , Humanos , Pessoa de Meia-Idade , Estudos de Casos e Controles , COVID-19/complicações , COVID-19/epidemiologia , Paquistão/epidemiologia , Fatores de RiscoRESUMO
INTRODUCTION: HIV-1 and hepatitis B virus (HBV) share common routes of transmission and therefore co-infection is common. In 2019, an HIV-1 outbreak that resulted in >1000 children being infected, predominantly through nosocomial transmission, occurred in Sindh, Pakistan. We conducted a phylogenetic and drug resistance analysis of the HBV Reverse Transcriptase (RT) gene in children with HIV-1 and HBV co-infection. METHODOLOGY: Blood samples were collected from 321 children with HIV who were recruited as part of a study to investigate the HIV-1 outbreak. All samples were tested for HBV surface antigen (HBsAg) using an ELISA assay, and positive samples were used to amplify and sequence the HBV RT gene. The phylogenetic relationship between sequences was analyzed, and drug- and vaccine- resistance mutations in the RT gene were explored. RESULTS: Of 321 samples, 23% (n = 75) were positive for HBsAg on ELISA. Phylogenetic analysis of the sequences revealed that 63.5% of HBV sequences were sub-genotype D1, while the rest were sub-genotype D2. Cluster analysis revealed grouping of sub-genotype D1 sequences exclusively with Pakistani sequences, while clustering of sub-genotypes D2 predominantly with global sequences. The 236Y mutation associated with resistance to tenofovir was observed in 2.8% of HBV sequences. Additionally, seven vaccine escape mutations were observed, the most common being 128 V. CONCLUSION: Our study suggests ongoing transmission of HBV D1 and D2 sub-genotypes in the HIV-1 co-infected population, likely nosocomially, given common routes of HVB and HIV-1 transmission. The prevalence of major HBV drug- and vaccine-resistant mutations remains low. Surveillance for further transmissions and the possible emergence of major drug- or vaccine-resistant variants is required.
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Coinfecção , Infecções por HIV , Soropositividade para HIV , HIV-1 , Hepatite B , Humanos , Criança , Vírus da Hepatite B , Filogenia , Antígenos de Superfície da Hepatite B/genética , Paquistão/epidemiologia , Hepatite B/complicações , Hepatite B/epidemiologia , Infecções por HIV/complicações , Infecções por HIV/epidemiologia , Mutação , Genótipo , Vacinas contra Hepatite B , HIV-1/genética , DNA Viral/genéticaRESUMO
In 2019, an outbreak of HIV infection predominantly affecting children occurred in Larkana district, Pakistan. This is the largest outbreak ever reported in this age group in Pakistan. In this study, we report two HIV-1 unique recombinant forms identified during the outbreak. Blood samples were collected from HIV-positive children as part of a case-control study to investigate the outbreak. The pol gene was sequenced and used to detect HIV subtype/recombinant forms using subtype, recombination, and phylogenetic analyses. Drug resistance mutation (DRM) analysis was performed to characterize the DRMs in each sequence. We observed the emergence of two unassigned unique recombinant forms related to CRF36_cpx in 15 individuals of the 344 samples collected. Genotype analysis revealed the presence of multiple DRMs associated with resistance to reverse transcriptase inhibitors. The discovery of these unassigned unique recombinant forms in our population highlights the need for comprehensive molecular epidemiological studies to fully understand the distribution and drug resistance patterns to aid control efforts.
Assuntos
Infecções por HIV , Soropositividade para HIV , HIV-1 , Criança , Humanos , Infecções por HIV/epidemiologia , Infecções por HIV/tratamento farmacológico , Inibidores da Transcriptase Reversa/uso terapêutico , Farmacorresistência Viral/genética , Filogenia , Paquistão/epidemiologia , Estudos de Casos e Controles , Soropositividade para HIV/epidemiologia , Surtos de Doenças , GenótipoRESUMO
Waning of neutralizing titres along with decline of protection efficacy after the second dose of COVID-19 vaccines was observed, including China-made inactivated vaccines. Efficacy of a heterologous boosting using one dose of a recombinant SARS-CoV-2 fusion protein vaccine (V-01) in inactivated vaccine-primed population was studied, aimed to restore the immunity. A randomized, double-blind and placebo-controlled phase III trial was conducted in healthy people aged 18 years or older in Pakistan and Malaysia. Each eligible participant received one dose of the V-01 vaccine developed by Livzon Mabpharm Inc. or placebo within the 3-6 months after the two-dose primary regimen, and was monitored for safety and efficacy. The primary endpoint was protection against confirmed symptomatic SARS-CoV-2 infection. A total of 10,218 participants were randomly assigned to receive a vaccine or placebo. Virus-neutralizing antibodies were assessed in 419 participants. A dramatic increase (11.3-fold; 128.3-1452.8) of neutralizing titres was measured in the V-01 group at 14 days after the booster. Over two months of surveillance, vaccine efficacy was 47.8% (95%CI: 22.6-64.7) according to the intention-to-treat principle. The most common adverse events were transient, mild-to-moderate pain at the injection site, fever, headache, and fatigue. Serious adverse events occurred almost equally in V-01 (0.12%) and placebo (0.16%) groups. The heterologous boosting with the V-01 vaccine was safe and efficacious, which could elicit robust humoral immunity under the epidemic of the Omicron variant.Trial registration: ClinicalTrials.gov identifier: NCT05096832.