Tracking SARS-CoV-2 variants through pandemic waves using RT-PCR testing in low-resource settings.

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.

Impact of COVID-19 on mental health of primary healthcare workers in Pakistan: lessons from a qualitative inquiry.

OBJECTIVES: The existing literature regarding the mental health consequences of COVID-19 among healthcare workers revolves predominantly around specialised hospital settings, while neglecting primary healthcare workers (PHCW) who are the first point of contact for patients. In view of negligible evidence, this study explored the mental health impact of COVID-19 and health system response, and sought suggestions and recommendations from the PHCWs to address their mental health needs during the pandemic crisis. DESIGN: We employed a qualitative exploratory design. SETTING: A total of 42 primary healthcare facilities across 15 districts in Sindh and Punjab provinces of Pakistan. PARTICIPANTS: We telephonically conducted 47 in-depth interviews with health service providers and hospital managers. A combination of inductive and deductive approach was used for data analyses using NVivo V.11.0. RESULTS: There was immense fear, stress and anxiety among PHCWs being infected and infecting their families at the beginning of this outbreak and its peak which tapered off over time. It was triggered by lack of information about the virus and its management, false rumours, media hype, lack of personal protective measures (personal protective equipment, PPE) and non-cooperation from patients and community people. Trainings on awareness raising and the PPEs provided by the healthcare system, with emotional support from coworkers and supervisors, were instrumental in addressing their mental health needs. Additionally, they recommended appreciation and recognition, and provision of psychosocial support from mental health professionals. CONCLUSION: Primary healthcare system should be prepared to provide timely informational (eg, continuous updates in training and guidelines), instrumental (eg, provision of PPE, appreciation and recognition), organisational (eg, safe and conducive working environment) and emotional and psychosocial support (eg, frequent or needs-based session from mental health professionals) to PHCWs in order to mitigate the mental health impact of pandemic crisis.

Understanding the mental health impact and needs of public healthcare professionals during COVID-19 in Pakistan : a qualitative study.

OBJECTIVES: A dearth of qualitative studies constrains in-depth understanding of health service providers' perspectives and experiences regarding the impact of COVID-19 on their mental health. This study explored the mental health impact and needs of of public sector healthcare workers during COVID-19 who working in secondary-level and tertiary-level healthcare settings of Pakistan. DESIGN: An exploratory qualitative study. SETTING: Twenty-five secondary-level and eight tertiary-level public hospitals of Sindh and Punjab provinces of Pakistan. PARTICIPANTS: In-depth interviews were conducted with 16 health service providers and 40 administrative personnel. Study data were analysed on NVivo V.11 using the conventional content analysis technique. RESULTS: The study identified three overarching themes: (1) mental health impact of COVID-19 on health service providers that included the fear of acquiring the infection and transmitting it to their family members, fear of social isolation and stigma, anxiety related to the uncertainty of COVID-19, nervousness due to media exaggeration and stress associated with excessive workload; (2) mental health needs of health service providers involved in the COVID-19 crisis and available support from the healthcare system, including the expression of the need for counselling services and safe working conditions, the need for paid rest periods, and the need for appreciation and motivation to work in the pandemic; and (3) suggestions to address mental health needs of healthcare workers, including provision of specialised mental healthcare/services, formal training of health managers on managing mental health needs of health facility staff, and assessment and addressing of these needs of the health workforce. CONCLUSION: The study emphasises the need to strengthen health system preparedness for recognising and addressing the needs of healthcare professionals. At the system level, there is a need for a specialised unit to provide mental health services and better communication strategies. At the staff level, continuous motivation and appreciation should be given to healthcare professionals either through monetary incentives or formal acknowledgement of their performance.

Evolutionary history and introduction of SARS-CoV-2 Alpha VOC/B.1.1.7 in Pakistan through international travelers.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants continue to emerge, and their identification is important for the public health response to coronavirus disease 2019 (COVID-19). Genomic sequencing provides robust information but may not always be accessible, and therefore, mutation-based polymerase chain reaction (PCR) approaches can be used for rapid identification of 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). 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. The 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. 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.