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.

Assembling a global database of child pneumonia studies to inform WHO pneumonia management algorithm: Methodology and applications

Background

The existing World Health Organization (WHO) pneumonia case management guidelines rely on clinical symptoms and signs for identifying, classifying, and treating pneumonia in children up to 5 years old. We aimed to collate an individual patient-level data set from large, high-quality pre-existing studies on pneumonia in children to identify a set of signs and symptoms with greater validity in the diagnosis, prognosis, and possible treatment of childhood pneumonia for the improvement of current pneumonia case management guidelines.

Methods

Using data from a published systematic review and expert knowledge, we identified studies meeting our eligibility criteria and invited investigators to share individual-level patient data. We collected data on demographic information, general medical history, and current illness episode, including history, clinical presentation, chest radiograph findings when available, treatment, and outcome. Data were gathered separately from hospital-based and community-based cases. We performed a narrative synthesis to describe the final data set.

Results

Forty-one separate data sets were included in the Pneumonia Research Partnership to Assess WHO Recommendations (PREPARE) database, 26 of which were hospital-based and 15 were community-based. The PREPARE database includes 285 839 children with pneumonia (244 323 in the hospital and 41 516 in the community), with detailed descriptions of clinical presentation, clinical progression, and outcome. Of 9185 pneumonia-related deaths, 6836 (74%) occurred in children <1 year of age and 1317 (14%) in children aged 1-2 years. Of the 285 839 episodes, 280 998 occurred in children 0-59 months old, of which 129 584 (46%) were 2-11 months of age and 152 730 (54%) were males.

Conclusions

This data set could identify an improved specific, sensitive set of criteria for diagnosing clinical pneumonia and help identify sick children in need of referral to a higher level of care or a change of therapy. Field studies could be designed based on insights from PREPARE analyses to validate a potential revised pneumonia algorithm. The PREPARE methodology can also act as a model for disease database assembly.

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.

Early Life Experiences and Trajectories of Cognitive Development

BACKGROUND

Multiple factors constrain the trajectories of child cognitive development, but the drivers that differentiate the trajectories are unknown. We examine how multiple early life experiences differentiate patterns of cognitive development over the first 5 years of life in low-and middle-income settings.

METHODS

Cognitive development of 835 children from the Etiology, Risk Factors, and Interactions of Enteric Infections and Malnutrition and the Consequences for Child Health and Development (MAL-ED) multisite observational cohort study was assessed at 6, 15, 24 (Bayley Scales of Infant and Toddler Development), and 60 months (Wechsler Preschool and Primary Scale of Intelligence). Markers of socioeconomic status, infection, illness, dietary intake and status, anthropometry, and maternal factors were also assessed. Trajectories of development were determined by latent class-mixed models, and factors associated with class membership were examined by discriminant analysis.

RESULTS

Five trajectory groups of cognitive development are described. The variables that best discriminated between trajectories included presence of stimulating and learning resources in the home, emotional or verbal responsivity of caregiver and the safety of the home environment (especially at 24 and 60 months), proportion of days (0-24 months) for which the child had diarrhea, acute lower respiratory infection, fever or vomiting, maternal reasoning ability, mean nutrient densities of zinc and phytate, and total energy from complementary foods (9-24 months).

CONCLUSIONS

A supporting and nurturing environment was the variable most strongly differentiating the most and least preferable trajectories of cognitive development. In addition, a higher quality diet promoted cognitive development while prolonged illness was indicative of less favorable patterns of development.

Early Life Child Micronutrient Status, Maternal Reasoning, and a Nurturing Household Environment have Persistent Influences on Child Cognitive Development at Age 5 years: Results from MAL-ED

BACKGROUND

Child cognitive development is influenced by early-life insults and protective factors. To what extent these factors have a long-term legacy on child development and hence fulfillment of cognitive potential is unknown.

OBJECTIVE

The aim of this study was to examine the relation between early-life factors (birth to 2 y) and cognitive development at 5 y.

METHODS

Observational follow-up visits were made of children at 5 y, previously enrolled in the community-based MAL-ED longitudinal cohort. The burden of enteropathogens, prevalence of illness, complementary diet intake, micronutrient status, and household and maternal factors from birth to 2 y were extensively measured and their relation with the Wechsler Preschool Primary Scales of Intelligence at 5 y was examined through use of linear regression.

RESULTS

Cognitive T-scores from 813 of 1198 (68%) children were examined and 5 variables had significant associations in multivariable models: mean child plasma transferrin receptor concentration (β: -1.81, 95% CI: -2.75, -0.86), number of years of maternal education (β: 0.27, 95% CI: 0.08, 0.45), maternal cognitive reasoning score (β: 0.09, 95% CI: 0.03, 0.15), household assets score (β: 0.64, 95% CI: 0.24, 1.04), and HOME child cleanliness factor (β: 0.60, 95% CI: 0.05, 1.15). In multivariable models, the mean rate of enteropathogen detections, burden of illness, and complementary food intakes between birth and 2 y were not significantly related to 5-y cognition.

CONCLUSIONS

A nurturing home context in terms of a healthy/clean environment and household wealth, provision of adequate micronutrients, maternal education, and cognitive reasoning have a strong and persistent influence on child cognitive development. Efforts addressing aspects of poverty around micronutrient status, nurturing caregiving, and enabling home environments are likely to have lasting positive impacts on child cognitive development.

Relationships among Common Illness Symptoms and the Protective Effect of Breastfeeding in Early Childhood in MAL-ED: An Eight-Country Cohort Study

Children in low-income countries experience multiple illness symptoms in early childhood. Breastfeeding is protective against diarrhea and respiratory infections, and these illnesses are thought to be risk factors of one another, but these relationships have not been explored simultaneously. In the eight-site MAL-ED study, 1,731 infants were enrolled near birth and followed for 2 years. We collected symptoms and diet information through twice-weekly household visits. Poisson regression was used to determine if recent illness history was associated with incidence of diarrhea or acute lower respiratory infections (ALRI), accounting for exclusive breastfeeding. Recent diarrhea was associated with higher risk of incident diarrhea after the first 6 months of life (relative risk [RR] 1.10, 95% confidence interval [CI] 1.04, 1.16) and with higher risk of incident ALRI in the 3- to 5-month period (RR 1.23, 95% CI 1.03, 1.47). Fever was a consistent risk factor for both diarrhea and ALRI. Exclusive breastfeeding 0-6 months was protective against diarrhea (0-2 months: RR 0.39, 95% CI 0.32, 0.49; 3-5 months: RR 0.83, 95% CI 0.75, 0.93) and ALRI (3-5 months: RR 0.81, 95% CI 0.68, 0.98). Children with recent illness who were exclusively breastfed were half as likely as those not exclusively breastfed to experience diarrhea in the first 3 months of life. Recent illness was associated with greater risk of new illness, causing illnesses to cluster within children, indicating that specific illness-prevention programs may have benefits for preventing other childhood illnesses. The results also underscore the importance of exclusive breastfeeding in the first 6 months of life for disease prevention.

Measuring home environments across cultures: Invariance of the HOME scale across eight international sites from the MAL-ED study

The home environment provides the context for much of a child's early development. Examples of important aspects of the home environment include safety, cleanliness, and opportunities for cognitive stimulation. This study sought to examine the psychometric properties of an adapted form of the Home Observation for the Measurement of the Environment (HOME; Caldwell & Bradley, 1984, 2003) across the eight international sites of the MAL-ED project (Dhaka, Bangladesh; Vellore, India; Bhakatapur, Nepal; Naushahro Feroze, Pakistan; Fortaleza, Brazil; Loreto, Peru; Venda, South Africa; Haydom, Tanzania), to identify a factor structure that fit the data at all sites, and to derive a subset of items that could be used to examine home environmental characteristics across sites. A three-factor structure (i.e., Emotional and Verbal Responsivity; Clean and Safe Environment; Child Cleanliness) was identified, and partial measurement equivalence/invariance across sites was supported. Overall, these findings lend support for the use of portions of this abbreviated and adapted version of the HOME for use among heterogeneous, cross-cultural groups in low- and middle-income nations.

5 NUCLEOLAR DEVELOPMENT REQUIRES TRANSCRIPTIONAL ACTIVITY DURING PORCINE EMBRYONIC GENOME ACTIVATION

The development of a functional nucleolus accompanying the major embryonic genome activation (EGA) is considered a marker for embryo quality and viability. However, the use of this marker is limited by the lack of accurate knowledge of the biology of embryonic nucleologenesis. The objective of this study was to elucidate the role of RNA polymerase I (RPI) and total transcriptional activity, reflecting EGA, for nucleologenesis in in vivo-developed porcine embryos. Late 4-cell-stage embryos were cultured in the absence (control) or presence of actinomycin D (AD; 0.2 �g mL-1, 3 h for RPI inhibition; 2.0 �g mL-1, 3 h for total transcriptional inhibition). Late 2-cell-stage embryos were cultured to the late 4-cell stage with 0.2 �g mL-1 AD (long-term inhibition) to prevent EGA. Embryos were fixed at the late 4-cell stage and processed for RT-PCR (de novo synthesized rRNA), autoradiography (ARG, following culture with 3H-uridine for the last 20 min before fixation), TEM, FISH (probe-labeling rRNA and rDNA), silver staining of nucleolar proteins, and immunofluorescence for RPI. Control embryos displayed typical extranucleolar and nucleolar ARG labeling, fibrillo-granular nucleoli, and focal RPI localization signaling de novo rRNA synthesis in functional nucleoli, confirmed by RT-PCR. All nuclei showed large FISH clusters (rRNA and rDNA) that in 88% of the cases were co-localized with large foci of silver-stained nucleolar proteins. After RPI inhibition, only extranucleolar ARG labeling was detected and, instead of fibrillo-granular nucleoli, a segregated dense-fibrillar component and a granular component, but no fibrillar centers, were observed. RPI was dispersed in all nuclei, the number of nuclei presenting large FISH clusters decreased to 40%, and only 42% of nuclei showed nucleolar proteins localized to large foci. After total transcriptional inhibition and long-term inhibition, the nuclei did not display any ARG labeling and presented inactive nucleolus precursor bodies indicating lack of rRNA (RT-PCR) and total RNA synthesis. However, 40% of the nuclei in both groups presented large FISH clusters of rRNA. This rRNA is considered as partially processed residues of maternally inherited molecules, and their clustering is most likely independent of EGA. Inhibition of transcriptional activity at the time of EGA caused the dispersion of RPI (de novo synthesized) but did not influence the localization of silver-stained nucleolar proteins to large foci (41%). On the other hand, EGA inhibition caused the lack of RPI labeling and hampered the localization of nucleolar proteins to foci. Differences between these 2 groups could be due to the activation of RNA polymerase II before the 3-h AD treatment. In conclusion, RPI transcription and de novo protein synthesis are required for formation of functional nucleoli. However, the clustering of maternally inherited nucleolar transcripts is independent on transcriptional activity at the time of EGA. Failure in constituent RNA polymerase activation during EGA leads to pattern-specific changes in nucleologenesis, which may serve as a marker for early embryo quality.

212 HETEROGENEITY OF RIBOSOMAL RNA GENE ACTIVATION AMONG CELLS OF IN VITRO-PRODUCED PORCINE EMBRYOS

In vitro production (IVP) of porcine embryos by in vitro maturation of oocytes followed by fertilization and culture in vitro is hampered by great deficiencies. Initiation of at least the major embryonic genome transcription, which includes activation of ribosomal RNA (rRNA) genes and the associated formation of a fibrillo-granular nuclealus, is normally seen during the 4-cell stage in pigs. We have investigated the activation of rRNA synthesis and the presence of silver staining nucleolar proteins in porcine IVP embryos as a marker of transcriptional activity and, thus, developmental competence. A total of 205 porcine IVP embryos from the 2-cell to the blastocyst stage were examined using sequential fluorescent in situ hybridization (FISH) to the rRNA genes and their transcripts and silver staining of nucleolar proteins as previously described (Viuff et al. 2002 Biol. Reprod. 66, 629–634). Briefly, cumulus-oocyte complexes with at least three cumulus cell layers and evenly granulated ooplasm were isolated from 2–5 mm ovarian follicles with stereomicroscopic evaluation. Subsequently, oocytes were matured in NCSU-37 and mechanically denuded followed by fertilization using frozen-thawed epididymal semen. Presumptive zygotes were then cultured in NCSU-23 at 39°C, 5% CO2. Around the time of expected cleavage, the embryos were examined every second hour to determine the time of cleavage. Embryos at the 2-cell stage were harvested at 5 h post-cleavage (hpc), 4-cell embryos late during the third cell cycle at 30 hpc, and tentative 8- and 16-cell embryos at 10 hpc. Blastocysts were harvested at Day 5 post-insemination. In general, nuclei of 2-cell embryos displayed 4 small foci of FITC labelling (presumably the rDNA), but no specific silver staining, and were consequently categorized as transcriptionally inactive. At the late 4-cell stage, 58% of the embryos resembled the 2-cell stage. However, in the remaining embryos (42%), some or all nuclei displayed large areas of FISH labelling (presumptive rDNA and rRNA) co-localized with silver staining, and were catagorized as transcriptionally active. Among the 8-cell embryos, 64% displayed a majority of transcriptionally active nuclei, whereas this was the case in 83% and 92% of the embryos in the 16-cell embryos and the blastocysts, respectively. In general, the majority of the embryos contained a mixture of transcriptionally active and inactive cells. These findings show that the porcine IVP embryos are often delayed and asynchronous with respect to activation of the rRNA genes. Table 1. Categorization of nuclei according to transcriptional activity This work was supported by grants from “Disease models, disease prevention and animal welfare improvement: The pig embryo as a model.” Danish Research Agency (Grant: 9901178), NATO (Grant: 978658), and Deutsche Forschungsgemeinschaft (DFG).

Case management of childhood pneumonia in developing countries: recent relevant research and current initiatives

Acute respiratory infections (ARI), mostly pneumonia, are one of the leading causes of death in young children in developing countries, accounting for 28% of childhood mortality. This paper provides a summary of the research and technical development efforts made in the last 15 years which contributed to improving the effectiveness of the case management strategy to reduce mortality from pneumonia in children in developing countries. Community intervention studies provided strong evidence that the strategy was feasible and effective in producing a substantial impact on pneumonia mortality. Clinical studies provided the rationale for improving the sensitivity and specificity of key signs of pneumonia, and for enhancing the therapeutic efficacy of standard home treatment. Research also provided data to deal with the problem of the clinical overlap of pneumonia and malaria in children. Technological initiatives succeeded in making appropriate diagnostic and therapeutic devices available. An important body of socio-cultural knowledge about family practices regarding pneumonia and ARI in children was built up and provided orientation on effective communication between health workers and families about home care of children with ARI. Health systems research focused on methods for surveillance of bacterial drug resistance and methodologies for evaluating the control programmes. Despite advances in the development of vaccines against respiratory bacteria and in the prevention of risk factors for pneumonia in children, case management will continue to be a central strategy for preventing mortality. Current international research initiatives are looking into measures that can improve the referral of severe pneumonia and effective management of severe pneumonia at first level hospitals.

Measles outbreak in a northern Pakistani village: epidemiology and vaccine effectiveness

In the spring of 1990, local community health workers reported a measles outbreak in several partially vaccinated villages in the Punial Valley in northern Pakistan. The authors conducted an investigation in one of these villages to assess vaccine coverage and vaccine efficacy and to describe the patterns of measles outbreaks that prevailed in this community. The results of a survey of the entire village revealed two major gaps in vaccine coverage: the small minority Sunni community and children over 3 years of age. Vaccine efficacy was estimated to range from 73 to 90% but was markedly reduced in children who were vaccinated under 12 months of age. The occurrence of an outbreak in a community in which a relatively new vaccination program is primarily directed at younger children has been predicted by theoretical models of measles dynamics and is consistent with the experience of other vaccination programs in the developing world. These observations suggest that, in some areas of the developing world, the age groups targeted to receive measles vaccinations may need to be broadened to ensure adequate coverage to prevent recurrent outbreaks.

Cause-specific child mortality in a mountainous community in Pakistan by verbal autopsy

In Pakistan's rural areas population-based cause of death data from systematic verbal autopsies are rare. Using verbal autopsy algorithms with multiple coding and decision rules, we assigned causes of death among 79% of children under age five years dying between July, 1988 and December, 1991 in Oshikhandass, a remote mountainous community in Pakistan's Northern Areas. Main causes of death were pneumonia (44%), diarrhoea (35%), and neonatal sepsis (6%). Combined (main plus associated) analysis revealed 48% died with diarrhoea, 46% with malnutrition, 44% with pneumonia, 15% with neonatal sepsis, and 15% with low birth weight. Median age of death with pneumonia was 2 months, with diarrhoea 8 months. Half died by month 4. The inquiry was well received by villagers. Population-based verbal autopsy surveillance is a cost-effective strategy to guide health managers. Plans are underway to institute it for the surrounding population of 400,000. Creative ways to access, treat and reduce risk among young infants are needed.