COVID-19 situation in Pakistan: A broad overview

A qualitative study on behavioral and social drivers of COVID-19 vaccine amongst refugees and migrants in Pakistan

Migrants and refugees are among the most disadvantaged populations, with limited evidence on the access and uptake of COVID-19 vaccination among them. Therefore this qualitative study explores the behavioral and social drivers of the COVID-19 vaccine among the refugee and migrant population in Pakistan through in-depth interviews and focus group discussions with regular and irregular migrants and refugees residing in Pakistan. Key informant interviews were conducted with stakeholders responsible for overlooking the COVID-19 vaccination process. A total of 18 participants were interviewed to gather insights on COVID-19 vaccine access, uptake, and behaviours among migrants and refugees. Data was collection from June to July 2022, in Karachi, Hyderabad, and Quetta. All the interviews were audio recorded, transcribed, translated, and thematically analysed on Nvivo software. The study found that refugee and migrant communities in Pakistan faced significant challenges to COVID-19 vaccination uptake, with barriers including misconceptions about vaccine safety and efficacy, fears of side effects, and mistrust spread by religious leaders. Participants were refused vaccinations at many centers despite government directives allowing vaccines for those without Computerized National Identity Cards (CNIC). Limited outreach and awareness efforts from the government, fears of identification and deportation, long wait times at vaccination centers, and the absence of female vaccinators in communities with strict gender norms further hindered access. Many participants also reported being charged for vaccination leading to lower vaccine coverage. Despite these challenges, some individuals were motivated to vaccinate due to workplace requirements, peer influence, or personal health concerns. Facilitators included door-to-door vaccination campaigns and school vaccination mandates. Vaccination camps set up by NGOs and government agencies at border areas and migrant-rich districts facilitated access. The study suggests targeted strategies to improve vaccination coverage, including provision of identification documents to migrants, inclusion in policy, and enforcement of multilingual communication to improve healthcare access.

The introduction of the SARS-CoV-2 BA.4 lineage into Pakistan

Pakistan has experienced a total of six COVID-19 waves throughout the pandemic, each driven by distinct SARS-CoV-2 lineages. This study explores the introduction of Omicron lineage BA.4 into Pakistan, which contributed to the sixth wave between June and September 2022. A discrete phylogeographic reconstruction was conducted on a global dataset of 443 samples across 49 countries, of which 92 samples were collected in Pakistan. Samples collected in Pakistan were from 10 locations across the country: Balochistan, Gilgit Baltistan, Islamabad, Jhelum, Karachi, Khyber Pakhtunkhwa, Lahore, Mirpur, Punjab, and Swat. This analysis identified eight distinct introductions into Pakistan between May 2022 and January 2023. The majority of BA.4 cases in Pakistan descended from one introduction, indicating that most transmission occurred within the country rather than through multiple importations. Two exportation events were also identified. During this time, there were reduced public health interventions in place, following the lifting of international travel restrictions in March 2022. This work stems from a collaboration between the UKHSA New Variant Assessment Platform and the National Institute of Health of Pakistan to strengthen genomic surveillance in front-line public health laboratories for global pandemic preparedness and response. The benefit of such partnerships has been evidenced throughout the COVID-19 pandemic, where scientific collaboration through data sharing and knowledge exchange has facilitated risk assessment and action. As a result of this collaboration, we have conducted the first Bayesian phylodynamic analysis of SARS-CoV-2 in Pakistan. This work can lend evidence to support understanding of SARS-CoV-2 variant transmission patterns and inform public health containment measures for virus spread.

Estimation of unconfirmed COVID-19 cases from a cross-sectional survey of >10 000 households and a symptom-based machine learning model in Gilgit-Baltistan, Pakistan

Introduction

Robust estimates of COVID-19 prevalence in settings with limited capacity for SARS-CoV-2 molecular and serologic testing are scarce. We aimed to describe the epidemiology of confirmed and probable COVID-19 in Gilgit-Baltistan, and to develop a symptom-based predictive model to identify infected but undiagnosed individuals with COVID-19.

Methods

We conducted a cross-sectional survey in 10 257 randomly selected households in Gilgit-Baltistan from June to August 2021. Data regarding SARS-CoV-2 testing, healthcare worker (HCW) diagnoses, symptoms and outcomes since March 2020 were self-reported by households. 'Confirmed/probable' infection was defined as a positive test, HCW COVID-19 diagnosis or HCW pneumonia diagnosis with COVID-19-positive contact. Robust Poisson regression was conducted to assess differences in symptoms, outcomes and SARS-CoV-2 testing rates. We developed a symptom-based machine learning model to differentiate confirmed/probable infections from those with negative tests. We applied this model to untested respondents to estimate the total prevalence of SARS-CoV-2 infection.

Results

Data were collected for 77 924 people. Overall, 314 (0.5%) had confirmed/probable infections, 3263 (4.4%) had negative tests and 74 347 (95.1%) were untested. Children were tested less often than adults (adjusted prevalence ratio (aPR) 0.08, 95% CI 0.06 to 0.12 for ages 1-4 years vs 30-39 years), while males were tested more often than females (aPR 1.51, 95% CI 1.40 to 1.63). In the predictive model, area under the receiver operating characteristic curve was 0.92 (95% CI 0.90 to 0.93). We estimate there were 8-17 total SARS-CoV-2 infections for each positive test (8-17:1). The ratio of estimated to confirmed cases was higher for ages 1-4 years (211-480:1), 5-9 years (80-185:1) and for females (13-25:1).

Conclusions

From March 2020 to August 2021, the majority of SARS-CoV-2 infections in Gilgit-Baltistan went unconfirmed, particularly among women and children. Predictive models which incorporate self-reported symptoms may improve understanding of the burden of disease in settings lacking diagnostic capacity.

Cross-cultural adaptation and validation of an Urdu version of the Vaccine Attitudes Examination (VAX-U) scale

BACKGROUND

Martin and Petrie developed the Vaccine Attitudes Examination (VAX) scale with an aim to document general vaccination attitudes. Vaccine acceptance plays an important role in curbing COVID-19 infections. Thus, it was important to assess vaccination attitudes of Pakistani people towards novel COVID-19 vaccines. The VAX scale was not available in Urdu language for Pakistani population.

AIM

The study aimed to carry out cross-cultural adaptation and validation of an Urdu version of the Vaccine Attitude Examination (VAX) scale in a selected population sample from Pakistan.

METHODS

A cross sectional study was conducted in September 2021 in an outpatient department of a healthcare facility in Karachi, Pakistan. Adult visitors, eligible for COVID-19 vaccine and spoke Urdu as first language were invited. Convenient sampling was used, and sample size was based on an item response ratio of 1:20. An Urdu version of the VAX scale was developed. The reliability was assessed using Cronbach's alpha (α) and intraclass correlation coefficient (ICC). The model fitness was evaluated using confirmatory factor analysis (CFA) and fit indices namely goodness of fit index (GFI), adjusted goodness of fit index (AGFI), Tucker Lewis index (TLI), comparative fit index (CFI), and root mean square error of approximation (RMSEA). A structural equation model (SEM) was also developed. IBM SPSS and AMOS were used to analyse the data. The study had ethical clearance.

RESULTS

A total of 211 responses were analysed. The reliability (Cronbach's α) was 0.821. The ICC was 0.831 (95% CI: 0.795-0.863). CFA using a 4-factor model revealed the following values for fit indices; GFI = 0.944, AGFI = 0.909, TLI = 0.953, CFI = 0.966, and RMSEA = 0.051. All values reported were in the acceptable range.

CONCLUSION

The VAX Urdu version is a reliable and valid instrument for use in an Urdu speaking population and will enable clinicians to assess the public's attitude towards general vaccination including COVID-19 vaccination. Clinicians can use the VAX-U to document a person's vaccine hesitancy and tailor their counselling to address the issues in vaccine uptake.

Secondary attack rates and determinants of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) household transmission in Pakistan: A case-ascertained prospective, longitudinal study

BACKGROUND

Households are considered ideal settings for studying the transmission dynamics of an infectious disease.

METHODS

A prospective study was conducted, based on the World Health Organization FFX protocol from October 2020 to January,2021. Household contacts of laboratory-confirmed index cases were followed up for their symptomatic history, nasal swabs for RT-PCR,and blood samples for anti-SARS CoV-2 antibodies were collected at enrollment and days 7, 14 and 28. We estimated secondary attack rate (SAR), effective household case cluster size and determinants of secondary infection among susceptible household contacts using multivariable logistic regression.

RESULTS

We enrolled 77 index cases and their 543 contacts. Out of these, 252 contacts were susceptible at the time of enrollment. There were 77 household clusters, out of which, transmission took place in 20 (25.9%) giving rise to 34 cases. The acquired secondary attack rate (SAR) was 14.0% (95% CI 9.0-18.0). The effective household case cluster size was 0.46 (95%CI 0.33,0.56). Reported symptoms of nausea and vomiting (aOR, 7.9; 95% CI, 1.4-45.5) and fatigue (aOR, 9.3; 95% CI, 3.8-22.7) were associated with SARS-CoV-2 transmission.

CONCLUSIONS

We observed a low SARS-CoV-2 secondary attack rate in the backdrop of high seroprevalence and asymptomatic transmission among households in Karachi, Pakistan.

COVID-19 vaccine coverage, determinants and inequity amongst refugees and migrants in Pakistan: a cross-sectional study

OBJECTIVE

Migrants and refugees are at a disadvantage in accessing basic necessities. The objective of this study is to assess the inequity in access, needs and determinants of COVID-19 vaccination among refugees and migrant populations in Pakistan.

DESIGN

We conducted a mixed-method study comprising a cross-sectional survey and a qualitative study. In this paper, we will only report the findings from the cross-sectional survey.

SETTING

This survey was conducted in different cities of Pakistan including Quetta, Karachi and Hyderabad.

PARTICIPANTS

A total of 570 participants were surveyed including refugees and migrants, both in regular and irregular situations.

PRIMARY AND SECONDARY OUTCOME MEASURES

The primary outcome of the study was to estimate the proportion of refugees and migrants, both in regular and irregular situations vaccinated against COVID-19 and assess the inequity. The χ2 test and Fisher's exact test were used to determine the significant differences in proportions between refugees and migrants and between regions.

RESULTS

The survey showed that only 26.9% of the refugee and migrant population were tested for COVID-19, 4.56% contracted coronavirus, and 3.85% were hospitalised due to COVID-19. About 66% of the refugees and migrants were fully vaccinated including those who received the single-dose vaccine or received all two doses, and 17.6% were partially vaccinated. Despite vaccination campaigns by the government, 14.4% of the refugee and migrant population remained unvaccinated mostly because of vaccines not being offered, distant vaccination sites, limited access, unavailability of COVID-19 vaccine or due to a difficult registration process. Vaccination rates varied across provinces, genders and migrant populations due to misconceptions, and several social, cultural and geographical barriers.

CONCLUSION

This study highlights the COVID-19 vaccine coverage, access and inequity faced by refugees and migrants during the pandemic. It suggests early prioritisation of policies inclusive of all refugees and migrants and the provision of identification documents to ease access to basic necessities.

Bacterial co-infections, secondary infections and antimicrobial use among hospitalized COVID-19 patients in the sixth wave in Pakistan: findings and implications

INTRODUCTION

Previous studies in Pakistan have shown considerable over prescribing of antibiotics in patients hospitalized with COVID-19 despite very low prevalence of bacterial infections. Irrational use of antibiotics will worsen antimicrobial resistance (AMR).

METHODS

Retrospective analysis of medical records of patients in the COVID-19 wards of three tertiary care hospitals to assess antibiotic use during the sixth COVID-19 wave.

RESULTS

A total of 284 patients were included, most were male (66.9%), aged 30-50 years (50.7%) with diabetes mellitus the most common comorbidity. The most common symptoms at presentation were cough (47.9%) and arthralgia-myalgia (41.5%). Around 3% were asymptomatic, 34.9% had mild, 30.3% moderate, and 23.6% had severe disease, with 8.1% critical. Chest X-ray abnormalities were seen in 43.3% of patients and 37% had elevated white cell counts, with 35.2% having elevated C-reactive protein levels. Around 91% COVID-19 patients were prescribed antibiotics during their hospital stay, with only a few with proven bacterial co-infections or secondary bacterial infections. Most antibiotics were from the 'Watch' category (90.8%) followed by the 'Reserve' category (4.8%), similar to previous COVID-19 waves.

CONCLUSION

There continued to be excessive antibiotics use among hospitalized COVID-19 patients in Pakistan. Urgent measures are needed to address inappropriate prescribing including greater prescribing of Access antibiotics where pertinent.

Unraveling the genetic variations underlying virulence disparities among SARS-CoV-2 strains across global regions: insights from Pakistan

Over the course of the COVID-19 pandemic, several SARS-CoV-2 variants have emerged that may exhibit different etiological effects such as enhanced transmissibility and infectivity. However, genetic variations that reduce virulence and deteriorate viral fitness have not yet been thoroughly investigated. The present study sought to evaluate the effects of viral genetic makeup on COVID-19 epidemiology in Pakistan, where the infectivity and mortality rate was comparatively lower than other countries during the first pandemic wave. For this purpose, we focused on the comparative analyses of 7096 amino-acid long polyprotein pp1ab. Comparative sequence analysis of 203 SARS-CoV-2 genomes, sampled from Pakistan during the first wave of the pandemic revealed 179 amino acid substitutions in pp1ab. Within this set, 38 substitutions were identified within the Nsp3 region of the pp1ab polyprotein. Structural and biophysical analysis of proteins revealed that amino acid variations within Nsp3's macrodomains induced conformational changes and modified protein-ligand interactions, consequently diminishing the virulence and fitness of SARS-CoV-2. Additionally, the epistatic effects resulting from evolutionary substitutions in SARS-CoV-2 proteins may have unnoticed implications for reducing disease burden. In light of these findings, further characterization of such deleterious SARS-CoV-2 mutations will not only aid in identifying potential therapeutic targets but will also provide a roadmap for maintaining vigilance against the genetic variability of diverse SARS-CoV-2 strains circulating globally. Furthermore, these insights empower us to more effectively manage and respond to potential viral-based pandemic outbreaks of a similar nature in the future.

COVID-19 Testing Trend: A Retrospective Analysis of the Three Major Pandemic Waves in Punjab, Pakistan

BACKGROUND/OBJECTIVES

There is some evidence in the literature of under-testing of COVID-19 cases in Pakistan. This study aims to explore COVID-19 testing trends and the factors affecting them in a lower middle-income country for future infectious disease policy-making and intervention strategies.

METHODOLOGY

The study was conducted as a serial cross-sectional study during the three major peaks from March 2020 to June 2021 on 1616 participants in Punjab, Pakistan. This is the first study to explore COVID-19 testing trends in association with flu-like symptoms (FLS) and the factors affecting all three major waves in Pakistan.

RESULTS

The results show that in all three waves, only 18.8% reported COVID-19 tested despite that 86.7% thought they had already had COVID-19, with 51.3% reporting having FLS and 35.6% with exposure to FLS from their families and 19.8% of positive testing rate among their family members. Out of the survey participants, 66% received vaccination, and over 80% had their eligible family members immunized. Fear of contracting COVID-19 was 69.7% in all three waves. Factors positively associated with the uptake of testing were the age group of 31-40 years with an adjusted odds ratio of 3.27 (95% confidence interval (CI): 2.09-5.12) for the second wave and an adjusted odds ratio of 13.75 (95% CI: 9.43-20.01) for the third wave and traveling abroad with odds of 3.08 times when the reference was inland traveling. The adjusted odds ratio to test for FLS was 1.62 (95% CI: 1.21-2.16).

CONCLUSION

In this study, there is convincing evidence of COVID-19 under-testing and thus under-reporting. This study also suggests that fear-based interventions may be counterproductive; however, economic factors such as education, employment, and traveling are significant in guiding the behavior for infectious disease prevention and management.

Sequential viral introductions and spread of BA.1 across Pakistan provinces during the Omicron wave

BACKGROUND

COVID-19 waves caused by specific SARS-CoV-2 variants have occurred globally at different times. We focused on Omicron variants to understand the genomic diversity and phylogenetic relatedness of SARS-CoV-2 strains in various regions of Pakistan.

METHODS

We studied 276,525 COVID-19 cases and 1,031 genomes sequenced from December 2021 to August 2022. Sequences were analyzed and visualized using phylogenetic trees.

RESULTS

The highest case numbers and deaths were recorded in Sindh and Punjab, the most populous provinces in Pakistan. Omicron variants comprised 93% of all genomes, with BA.2 (32.6%) and BA.5 (38.4%) predominating. The first Omicron wave was associated with the sequential identification of BA.1 in Sindh, then Islamabad Capital Territory, Punjab, Khyber Pakhtunkhwa (KP), Azad Jammu Kashmir (AJK), Gilgit-Baltistan (GB) and Balochistan. Phylogenetic analysis revealed Sindh to be the source of BA.1 and BA.2 introductions into Punjab and Balochistan during early 2022. BA.4 was first introduced in AJK and BA.5 in Punjab. Most recent common ancestor (MRCA) analysis revealed relatedness between the earliest BA.1 genome from Sindh with Balochistan, AJK, Punjab and ICT, and that of first BA.1 from Punjab with strains from KPK and GB.

CONCLUSIONS

Phylogenetic analysis provides insights into the introduction and transmission dynamics of the Omicron variant in Pakistan, identifying Sindh as a hotspot for viral dissemination. Such data linked with public health efforts can help limit surges of new infections.

Temporal study of wastewater surveillance from September 2020 to March 2021: an estimation of COVID-19 patients in Lahore, Pakistan

The first aim of study was to quantify the viral load in the wastewater samples by RT-qPCR testing in Lahore population to estimate the number of patients affected and predict the next resurgence of COVID-19 wave in the city. The second aim of the study was to determine the hotspot areas of Lahore which remained positive more often for virus with high viral load. In this study, n = 420 sewage samples were collected on an average of two weeks intervals from 30 different sewage water disposal stations (14 sampling events) from Sept 2020 to March 2021. RNA was extracted and quantified by RT-qPCR without concentrating the virus in samples. Number of positive disposal sites (7-93%), viral load from sewage samples (100.296 to 103.034), and estimated patients (660-17,030) ranged from low to high according to the surge and restrain of 2nd and 3rd COVID-19 waves in the country. The viral load and estimated patients were reported high in January 2021 and March 2021 which were similar to the peak of 2nd and 3rd waves in Pakistan. Site 18 (Niaz Baig village DS) showed the highest viral load among all sites. Findings of the present study helped to estimate the number of patients and track the resurgence in COVID-19 waves in Lahore particularly, and in Punjab generally. Furthermore, it emphasizes the role of wastewater-based epidemiology to help policymakers strengthen the quarantine measures along with immunization to overcome enteric viral diseases. Local and national stake holders should work in collaboration to improve the environmental hygiene to control the disease.

COVID-19 Vaccines Status, Acceptance and Hesitancy among Maintenance Hemodialysis Patients: A Cross-Sectional Study and the Implications for Pakistan and Beyond

COVID-19 vaccine hesitancy continues to be a widespread problem in Pakistan due to various conspiracy beliefs, myths and misconceptions. Since the hemodialysis population is at a higher risk of contracting infections, we sought to investigate the current COVID-19 immunization status and reasons for any vaccine hesitancy among these patients in Pakistan. This cross-sectional study was conducted among maintenance hemodialysis patients at six hospitals in the Punjab Province of Pakistan. Data were collected anonymously using a questionnaire. A total of 399 hemodialysis patients took part in the survey, the majority of them were male (56%) and aged 45-64 years. A calculated 62.4% of the patients reported receiving at least one dose of the COVID-19 vaccine. Of those vaccinated (249), 73.5% had received two doses and 16.9% had received a booster dose. The most common reasons for vaccination were "being aware they were at high risk" (89.6%), "fear of getting infected" (89.2%) and "willingness to fight against COVID-19-pandemic" (83.9%). Of the 150 patients who had not yet been vaccinated, only 10 showed a willingness to take the COVID-19 vaccine. The major reasons for refusal included "COVID-19 is not a real problem" (75%), the "corona vaccine is a conspiracy (72.1%)" and "I don't need the vaccine" (60.7%). Our study revealed that only 62% patients receiving hemodialysis were partially or completely vaccinated against COVID-19. Consequently, there is a need to initiate aggressive approaches to educate this high-risk population in order to address their concerns with vaccine safety and efficacy as well as correct current myths and misconceptions to improve the COVID-19 immunization status in this population.

Prevalence and risk factors of Severe Acute Respiratory Syndrome Coronavirus 2 infection in women and children in peri-urban communities in Pakistan: A prospective cohort study

Background

Population-based seroepidemiological surveys provide accurate estimates of disease burden. We compare the COVID-19 prevalence estimates from two serial serological surveys and the associated risk factors among women and children in a peri-urban area of Karachi, Pakistan.

Methods

The AMANHI-COVID-19 study enrolled women and children between November 2020 and March 2021. Blood samples were collected from March to June 2021 (baseline) and September to December 2021 (follow-up) to test for anti-SARS-CoV-2 antibodies using ROCHE Elecsys®. Participants were visited or called weekly during the study for recording symptoms of COVID-19. We report the proportion of participants with anti-SARS-CoV-2 antibodies and symptoms in each survey and describe infection risk factors using step-wise binomial regression analysis.

Results

The adjusted seroprevalence among women was 45.3% (95% confidence interval (CI) = 42.6-47.9) and 82.3% (95% CI = 79.9-84.4) at baseline and follow-up survey, respectively. Among children, it was 18.4% (95% CI = 16.1-20.7) and 57.4% (95% CI = 54.3-60.3) at baseline and follow-up, respectively. Of the women who were previously seronegative, 404 (74.4%) tested positive at the follow-up survey, as did 365 (50.4%) previously seronegative children. There was a high proportion of asymptomatic infection. At baseline, being poorest and lacking access to safe drinking water lowered the risk of infection for both women (risk ratio (RR) = 0.8, 95% CI = 0.7-0.9 and RR = 1.2, 95% CI = 1.1-1.4, respectively) and children (RR = 0.7, 95% CI = 0.5-1.0 and RR = 1.4, 95% CI = 1.0-1.8, respectively). At the follow-up survey, the risk of infection was lower for underweight women and children (RR = 0.4, 95% CI = 0.3-0.7 and RR = 0.7, 95% CI = 0.5-0.8, respectively) and for women in the 30-39 years age group and children who were 24-36 months of age (RR = 0.6, 95% CI = 0.4-0.9 and RR = 0.7, 95% CI = 0.5-0.9, respectively). In both surveys, paternal employment was an important predictor of seropositivity among children (RR = 0.7, 95% CI = 0.6-0.9 and RR = 0.8, 95% CI = 0.7-1.0, respectively).

Conclusion

There was a high rate of seroconversion among women and children. Infection was generally mild. Parental education plays an important role in protection of children from COVID-19.

Lessons learnt of the COVID-19 contact tracing strategy in Islamabad Capital Territory, Pakistan using systems thinking processes

The strategy of test, trace and isolate has been promoted and seen as a crucial tool in the fight against the COVID-19 pandemic. As simple as the slogan sounds, effectively implementing it turns into a complex endeavor with multiple moving parts and the need for multisector collaboration. In this study, we apply a systems thinking lens to analyse the design and implementation of the contact tracing strategy for COVID-19 in the district of Islamabad, Pakistan. The data collection included participatory observation, reflective exercises, key informant interviews and participatory workshops with district health managers and health providers. The information gathered was structured using process and stakeholder mapping to identify the lessons learned of the COVID-19 contact tracing strategy. The results showed that the elements crucial for implementation were, good coordination during a crisis, available resources mobilized effectively and establishment of early active surveillance for contact tracing. Furthermore, the main aspects to be improved were lack of preparedness and existing surveillance systems and task shifting leading to impact on regular health services. The results of this study highlight the importance of developing information systems that are coherent with existing processes and resources, even in times of crisis.

IgG antibodies to SARS-CoV-2 in asymptomatic blood donors at two time points in Karachi

INTRODUCTION

An estimated 1.5 million cases were reported in Pakistan until 23 March, 2022. However, SARS-CoV-2 PCR testing capacity has been limited and the incidence of COVID-19 infections is unknown. Volunteer healthy blood donors can be a control population for assessment of SARS-CoV-2 exposure in the population. We determined COVID-19 seroprevalence during the second pandemic wave in Karachi in donors without known infections or symptoms in 4 weeks prior to enrollment.

MATERIALS AND METHODS

We enrolled 558 healthy blood donors at the Aga Khan University Hospital between December 2020 and February 2021. ABO blood groups were determined. Serum IgG reactivity were measured to spike and receptor binding domain (RBD) proteins.

RESULTS

Study subjects were predominantly males (99.1%) with a mean age of 29.0±7.4 years. Blood groups were represented by; B (35.8%), O (33.3%), A (23.8%) and AB (7%). Positive IgG responses to spike were detected in 53.4% (95% CI, 49.3-37.5) of blood donors. Positive IgG antibodies to RBD were present in 16.7% (95% CI; 13.6-19.8) of individuals. No significant difference was found between the frequency of IgG antibodies to spike or RBD across age groups. Frequencies of IgG to Spike and RBD antibodies between December 2020 and February 2021 were found to be similar. Seropositivity to either antigen between individuals of different blood groups did not differ. Notably, 31.2% of individuals with IgG antibodies to spike also had IgG antibodies to RBD. Amongst donors who had previously confirmed COVID-19 and were seropositive to spike, 40% had IgG to RBD.

CONCLUSIONS

Our study provides insights into the seroprevalence of antibodies to COVID-19 in a healthy cohort in Karachi. The differential dynamics of IgG to spike and RBD likely represent both exposure to SARS-CoV-2 and associate with protective immunity in the population.

SARS-CoV-2 RT-PCR positivity in relation to clinical and demographic characteristics in residents of border quarantine centres, Khyber Pakhtunkhwa, Pakistan: a prospective cohort study

Background

As international travellers were the primary source of sever acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, border checkpoints became an important tool to isolate cases. We determined the period prevalence and SARS-CoV-2 reverse transcription polymerase chain reaction positivity in relation to clinical and demographic characteristics in healthy travellers quarantined at the Pakistan–Afghanistan border.

Methods

The study was conducted from 15 to 25 April 2020. Period prevalence was calculated and the association between positivity and individuals’ age, sex and occupation were assessed using χ² and Mantel–Haenszel tests. Logistic regression was used to calculate adjusted odds ratios (ORs) for each age group. Time-to-event (TTE) analysis was conducted to check the difference in positivity among various groups.

Results

In a total of 708 individuals, 71 tested positive (10%). Compared with those ≤20 y of age, the sex- and occupation-adjusted odds of testing positive were less among the older age group (41–60 y; OR 0.26, p=0.008). Taxi drivers had higher odds of testing positive (OR 4.08, p<0.001). Kaplan–Meier curves and hazard ratios (0.32, p<0.01) showed that the positivity period differed significantly across the pre-symptomatic vs asymptomatic group (26 vs 14 d).

Conclusions

The cases who were likely to acquire infection through occupational exposure largely remained asymptomatic. For effective control of transmission and the emergence of new variants, testing capacities should be revamped with effective isolation measures.

Co-Infections, Secondary Infections, and Antimicrobial Use in Patients Hospitalized with COVID-19 during the First Five Waves of the Pandemic in Pakistan; Findings and Implications

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.

The clinical course, biochemical markers, and clinical outcomes of COVID-19 positive patients from the third wave in Pakistan: A retrospective cohort study

Background

Third wave of COVID-19 has affected several countries. Case fatality rates from first and second waves are expected to be surpassed by the current wave due to various variant transmissions. This study was aimed to compare and contrast the significant clinical markers between survivors and non-survivors during the third wave of COVID-19 to assess severity and prognosis.

Methods

It includes all the patients who were diagnosed with COVID-19 polymerase chain reaction (PCR) during the third wave, and were monitored for their disease course and outcomes. A total of 209 patients were included in the analysis via non-probability consecutive sampling method.

Results

The median age was higher in non-surviving patients (p = 0.010). Majority of deaths occurred in intensive care patients (p < 0.001) and those with diabetes (p = 0.032) and hypertension (p = 0.003). Fever was the most predominant symptom in all patients (78.9%), dyspnea was common among expired individuals (p = 0.043) while recovered patients were more likely to be asymptomatic (p = 0.044). Gastrointestinal symptoms were not found marked during this wave. Being on ventilator has higher mortality (p < 0.001). Predominant radiological findings were interstitial patches or infiltrate (43.7%). Multivariable analysis showed hypertension (p = 0.042), BiPAP/CPAP (p < 0.001), being on ventilator (p = 0.004), and ARDS (p < 0.001) was associated with poor survival while patchy interstitial infiltrates on X-ray had good survival probability (p = 0.032). On Kaplan-Meier survival analysis, hypertension (p = 0.003), BiPAP/CPAP (p = 0.008), ventilator (p = 0.025), ICU stay (p = 0.001), high-grade fever (p = 0.001), and ARDS (p < 0.001) had reduced cumulative survival.

Conclusion

Certain biochemical markers were more predictive of disease severity in the third-wave than the preceding waves.

Evolutionary History and Introduction of SARS-CoV-2 Alpha VOC/B.1.1.7 in Pakistan Through International Travelers

SARS-CoV-2 variants continue to emerge, and their identification is important for the public health response to COVID-19. Genomic sequencing provides robust information but may not always be accessible and therefore rapid mutation-based PCR approaches can be used to identify known variants. International travelers arriving in Karachi between December 2020 and February 2021 were tested for SARS-CoV-2 by PCR. A subset of positive samples was tested for S-Gene Target Failure (SGTF) on TaqPathTM COVID-19 (Thermo Fisher Scientific) and for mutations using the GSD NovaType SARS-CoV-2 (Eurofins Technologies) assays. Sequencing was conducted on the MinION platform (Oxford Nanopore Technologies (ONT). Bayesian phylogeographic inference was performed integrating the patients’ travel history information. Of the thirty-five COVID-19 cases screened, thirteen had isolates with SGTF. The travelers transmitted infection to sixty-eight contact cases. The B.1.1.7 lineage was confirmed through sequencing and PCR. Phylogenetic analysis of sequence data available for six cases included four B.1.1.7 strains and one B.1.36 and B.1.1.212 lineage isolate, respectively. Phylogeographic modeling estimated at least three independent B.1.1.7 introductions into Karachi, Pakistan, originating from the UK. B.1.1.212 and B.1.36 were inferred to be introduced either from the UK or the travelers’ layover location. We report the introduction of SARS-CoV-2 B.1.1.7 and other lineages in Pakistan by international travelers arriving via different flight routes. This highlights SARS-CoV-2 transmission through travel, importance of testing and quarantine post-travel to prevent transmission of new strains, as well as recording detailed patients’ metadata. Such results help inform policies on restricting travel from destinations where new highly transmissible variants have emerged.

Upregulated type I interferon responses in asymptomatic COVID-19 infection are associated with improved clinical outcome

Understanding key host protective mechanisms against SARS-CoV-2 infection can help improve treatment modalities for COVID-19. We used a blood transcriptome approach to study biomarkers associated with differing severity of COVID-19, comparing severe and mild Symptomatic disease with Asymptomatic COVID-19 and uninfected Controls. There was suppression of antigen presentation but upregulation of inflammatory and viral mRNA translation associated pathways in Symptomatic as compared with Asymptomatic cases. In severe COVID-19, CD177 a neutrophil marker, was upregulated while interferon stimulated genes (ISGs) were downregulated. Asymptomatic COVID-19 cases displayed upregulation of ISGs and humoral response genes with downregulation of ICAM3 and TLR8. Compared across the COVID-19 disease spectrum, we found type I interferon (IFN) responses to be significantly upregulated (IFNAR2, IRF2BP1, IRF4, MAVS, SAMHD1, TRIM1), or downregulated (SOCS3, IRF2BP2, IRF2BPL) in Asymptomatic as compared with mild and severe COVID-19, with the dysregulation of an increasing number of ISGs associated with progressive disease. These data suggest that initial early responses against SARS-CoV-2 may be effectively controlled by ISGs. Therefore, we hypothesize that treatment with type I interferons in the early stage of COVID-19 may limit disease progression by limiting SARS-CoV-2 in the host.

Higher entropy observed in SARS-CoV-2 genomes from the first COVID-19 wave in Pakistan

BACKGROUND

We investigated the genome diversity of SARS-CoV-2 associated with the early COVID-19 period to investigate evolution of the virus in Pakistan.

MATERIALS AND METHODS

We studied ninety SARS-CoV-2 strains isolated between March and October 2020. Whole genome sequences from our laboratory and available genomes were used to investigate phylogeny, genetic variantion and mutation rates of SARS-CoV-2 strains in Pakistan. Site specific entropy analysis compared mutation rates between strains isolated before and after June 2020.

RESULTS

In March, strains belonging to L, S, V and GH clades were observed but by October, only L and GH strains were present. The highest diversity of clades was present in Sindh and Islamabad Capital Territory and the least in Punjab province. Initial introductions of SARS-CoV-2 GH (B.1.255, B.1) and S (A) clades were associated with overseas travelers. Additionally, GH (B.1.255, B.1, B.1.160, B.1.36), L (B, B.6, B.4), V (B.4) and S (A) clades were transmitted locally. SARS-CoV-2 genomes clustered with global strains except for ten which matched Pakistani isolates. RNA substitution rates were estimated at 5.86 x10-4. The most frequent mutations were 5' UTR 241C > T, Spike glycoprotein D614G, RNA dependent RNA polymerase (RdRp) P4715L and Orf3a Q57H. Strains up until June 2020 exhibited an overall higher mean and site-specific entropy as compared with sequences after June. Relative entropy was higher across GH as compared with GR and L clades. More sites were under selection pressure in GH strains but this was not significant for any particular site.

CONCLUSIONS

The higher entropy and diversity observed in early pandemic as compared with later strains suggests increasing stability of the genomes in subsequent COVID-19 waves. This would likely lead to the selection of site-specific changes that are advantageous to the virus, as has been currently observed through the pandemic.