Breastfeeding has important benefits for long-term infant health, particularly in establishing an... more Breastfeeding has important benefits for long-term infant health, particularly in establishing and shaping the infant gut microbiome. However, the impact of combination antiretroviral therapy exposure and antibiotics on the breast milk microbiome in women living with HIV is not known.
Many industries are developing robust models, capable of analyzing huge and complex data by using... more Many industries are developing robust models, capable of analyzing huge and complex data by using machine learning (ML) while delivering faster and more accurate results on vast scales. ML is a subfield of artificial intelligence, which is broadly defined as the capability of a machine to imitate intelligent human behavior. ML tools enable organizations to swiftly identify profitable opportunities and potential risks. Besides these uses, ML also has a wide range of applications in our daily lives. So, the development in ML is most important in this age of digital system to solve more complex problems. In order to further develop ML and diminish the uncertainties to improve accuracy, an innovative concept of complex bipolar intuitionistic fuzzy sets (CBIFSs) is introduced in this article. Further, the Cartesian product of two CBIFSs is defined. Moreover, the complex bipolar intuitionistic fuzzy relations (CBIFRs) and their types with suitable examples are defined. In addition, some i...
A multitude of enzyme‐linked immunosorbent assays (ELISAs) has been developed to detect severe ac... more A multitude of enzyme‐linked immunosorbent assays (ELISAs) has been developed to detect severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) antibodies since the coronavirus disease 2019 pandemic started in late 2019. Assessing the reliability of these assays in diverse global populations is critical. This study compares the use of the commercially available Platelia Total Ab Assay (Bio‐Rad) nucleocapsid ELISA to the widely used Mount Sinai spike IgG ELISA in a Kenyan population seroprevalence study. Using longitudinal plasma specimens collected from a mother–infant cohort living in Nairobi, Kenya between May 2019 and December 2020, this study demonstrates that the two assays have a high qualitative agreement (92.7%) and strong correlation of antibody levels (R2 = 0.973) in repeated measures. Within this cohort, seroprevalence detected by either ELISA closely resembled previously published seroprevalence estimates for Kenya during the sampling period and no significant diffe...
SARS-CoV-2 is locked in a high-stakes arms race between the dynamics of rising population immunit... more SARS-CoV-2 is locked in a high-stakes arms race between the dynamics of rising population immunity and escape mutations. The E484K mutation in the spike protein reduces neutralization by post-vaccination sera and monoclonal antibody therapeutics. We detected the emergence of an E484K harboring variant B.1.243.1 from a common circulating variant (B.1.243) in the United States. In contrast to other instances when the E484K mutation was acquired independently in the parental lineage, genomic surveillance indicates that the B.1.243.1 variant of interest is in the process of being established in Arizona and beginning to cross state borders to New Mexico and Texas. Genomic, epidemiologic and phylogenetic evidence indicates that the B.1.243.1 variant of interest is poised to emerge. These findings demonstrate the critical need to continue tracking SARS-CoV-2 in real-time to inform public health strategies, diagnostics, medical countermeasures and vaccines.
ABSTRACTBackgroundHIV may increase SARS-CoV-2 infection risk and COVID-19 severity generally, but... more ABSTRACTBackgroundHIV may increase SARS-CoV-2 infection risk and COVID-19 severity generally, but data are limited about its impact on postpartum women and their infants. As such, we characterized SARS-CoV-2 infection among mother-infant pairs in Nairobi, Kenya.MethodsWe conducted a nested study of 53 HIV-uninfected and 51 healthy women living with HIV, as well as their HIV-exposed uninfected (N=41) and HIV-unexposed (N=48) infants, participating in a prospective cohort. SARS-CoV-2 serology was performed on plasma collected between 1 May-31 December 2020 to determine the incidence, risk factors, and symptoms of infection. SARS-CoV-2 RNA PCR and sequencing was also performed on stool samples from seropositive participants.ResultsSARS-CoV-2 seropositivity was found in 38% of the 104 mothers and in 17% of the 89 infants. There was no significant association between SARS-CoV-2 infection and maternal HIV (Hazard Ratio [HR]=1.51, 95% CI: 0.780-2.94) or infant HIV exposure (HR=1.48, 95% CI...
Additional file 2: Figure S2. Relative abundance of the 10 most frequently shared (mother-infant)... more Additional file 2: Figure S2. Relative abundance of the 10 most frequently shared (mother-infant) ASVs. Taxonomy shown at the genus level.
Additional file 4: Figure S4. VirSorter viral contig transmission analysis. Analyses of VirSorter... more Additional file 4: Figure S4. VirSorter viral contig transmission analysis. Analyses of VirSorter contigs were performed as in Fig. 4. (A) The number of infant VirSorter viral contigs shared with their mother (top), and their proportion out of the total infant virome (VirSorter identified) is shown (bottom). Percent of infant VirSorter contigs that are shared with their mother is shown in blue and infant only VirSorter contigs are shown in green. (B) Average VirSorter contig proportion of mothers' virome that is shared with infant or unique to the mother. (C) Average VirSorter contig proportion of infant virome that is shared with mother by delivery route. Statistical significance assessed by Mann-Whitney test. (D) Average VirSorter contig proportion of maternal virome that is shared with infant by delivery route. Statistical significance assessed by Mann-Whitney test. (E) Plot of the number of infant shared VirSorter viral contigs vs. the total number of maternal VirSorter cont...
Additional file 5: Figure S5. Transkingdom interaction between bacteria and bacteriophage. Correl... more Additional file 5: Figure S5. Transkingdom interaction between bacteria and bacteriophage. Correlation of shared bacterial ASVs and viral contigs. (A) Heatmap shows the Pearson correlation between bacterial ASVs and bacteriophage contigs in infants from C-section delivery (left) clustered by hierarchical clustering. Second heatmap shows correlations from infants delivered vaginally clustered in the same order as correlations from infants delivered by C-section. B) Heatmap shows the Pearson correlation between bacterial ASVs and VirSorter identified bacteriophage contigs in infants delivered vaginally (left) clustered by hierarchical clustering. Second heatmap shows correlations from infants delivered by C-section clustered in the same order as correlations from infants delivered vaginally. These VirSorter analyses corroborate the contig analyses shown in Fig. 5.
Additional file 3: Figure S3. Metadata analysis of viral species. (A) Number of sequencing reads ... more Additional file 3: Figure S3. Metadata analysis of viral species. (A) Number of sequencing reads in infant and maternal samples. Statistical significance assessed by Mann-Whitney. (B) Output of MaAslin and random forest analysis. (C) Important viral species and their statistical significance as assessed by MaAslin and random forest. (D) Heatmap of MaAslin identified viral species for mothers and infants. (E) ROC curves and AUC measures for delivery route and mother/infant classification using random forest and pROC packages in R. Pseudo-probabilities are plotted on graph using Out-Of-Bag (OOB) sample tree classification votes. Only infant data used in vaginal vs. C-section classification while both mother and infant data used for mother vs. infant classification. (F) Bray-Curtis Dissimilarity pairwise comparisons. Statistical significance assessed by Mann-Whitney. Kruskal-Wallis with Dunn's multiple correction was used to assess feeding type (breastmilk vs. formula; breastmilk v...
Studies of viruses that coevolved with lemurs provide an opportunity to understand the basal trai... more Studies of viruses that coevolved with lemurs provide an opportunity to understand the basal traits of primate viruses and provide an evolutionary context for host-virus interactions. Germline integration of endogenous retroviruses (ERVs) are fossil evidence of past infections. Hence, characterization of novel ERVs provides insight into the ancient precursors of extant viruses and the evolutionary history of their hosts. Here, we report the discovery of a novel endogenous retrovirus present in the genome of a lemur, Coquerel’s sifaka (Propithecus coquereli). Using next-generation sequencing, we identified and characterized the complete genome sequence of a retrovirus, named prosimian retrovirus 1 (PSRV1). Phylogenetic analyses indicate that PSRV1 is a gamma-type betaretrovirus basal to the other primate betaretroviruses and most closely related to simian retroviruses. Molecular clock analysis of PSRV1 long terminal repeat (LTR) sequences estimated the time of endogenization within 4...
Breastfeeding plays an important role in seeding the infant gut microbiome and mammary health. Al... more Breastfeeding plays an important role in seeding the infant gut microbiome and mammary health. Although most studies focus on the diverse breast milk bacterial communities, little is known about the viral communities harbored in breast milk.
In December of 2019, a novel coronavirus, SARS-CoV-2, emerged in the city of Wuhan, China causing... more In December of 2019, a novel coronavirus, SARS-CoV-2, emerged in the city of Wuhan, China causing severe morbidity and mortality. Since then, the virus has swept across the globe causing millions of confirmed infections and hundreds of thousands of deaths. To better understand the nature of the pandemic and the introduction and spread of the virus in Arizona, we sequenced viral genomes from clinical samples tested at the TGen North Clinical Laboratory, provided to us by the Arizona Department of Health Services, and at Arizona State University and the University of Arizona, collected as part of community surveillance projects. Phylogenetic analysis of 79 genomes we generated from across Arizona revealed a minimum of 9 distinct introductions throughout February and March. We show that >80% of our sequences descend from clades that were initially circulating widely in Europe but have since dominated the outbreak in the United States. In addition, we show that the first reported cas...
BackgroundThe earliest microbial colonizers of the human gut can have life-long consequences for ... more BackgroundThe earliest microbial colonizers of the human gut can have life-long consequences for their hosts. Precisely how the neonatal gut bacterial microbiome and virome are initially populated is not well understood. To better understand how the maternal gut microbiome influences acquisition of the infant gut microbiome, we studied the early life bacterial microbiomes and viromes of 28 infant twin pairs and their mothers.ResultsInfant bacterial and viral communities more closely resemble those of their related co-twin than unrelated infants. We found that 63% of an infant’s bacterial microbiome can be traced to their mother’s gut microbiota. In contrast, only 15% of their viral communities are acquired from their mother. Delivery route did not determine how much of the bacterial microbiome or virome was shared from mother to infant. However, bacteria-bacteriophage interactions were altered by delivery route.ConclusionsThe maternal gut microbiome significantly influences infant g...
Gulf War illness (GWI) is characterized by the persistence of inflammatory bowel disease, chronic... more Gulf War illness (GWI) is characterized by the persistence of inflammatory bowel disease, chronic fatigue, neuroinflammation, headache, cognitive impairment, and other medically unexplained conditions. Results using a murine model show that enteric viral populations especially bacteriophages were altered in GWI. The increased viral richness and alpha diversity correlated positively with gut bacterial dysbiosis and proinflammatory cytokines. Altered virome signature in GWI mice also had a concomitant weakening of intestinal epithelial tight junctions with a significant increase in Claudin-2 protein expression and decrease in ZO1 and Occludin mRNA expression. The altered virome signature in GWI, decreased tight junction protein level was followed by the presence an activation of innate immune responses such as increased Toll-like receptor (TLR) signaling pathways. The altered virome diversity had a positive correlation with serum IL-6, IL-1β, and IFN-γ, intestinal inflammation (IFN-γ)...
Breastfeeding has important benefits for long-term infant health, particularly in establishing an... more Breastfeeding has important benefits for long-term infant health, particularly in establishing and shaping the infant gut microbiome. However, the impact of combination antiretroviral therapy exposure and antibiotics on the breast milk microbiome in women living with HIV is not known.
Many industries are developing robust models, capable of analyzing huge and complex data by using... more Many industries are developing robust models, capable of analyzing huge and complex data by using machine learning (ML) while delivering faster and more accurate results on vast scales. ML is a subfield of artificial intelligence, which is broadly defined as the capability of a machine to imitate intelligent human behavior. ML tools enable organizations to swiftly identify profitable opportunities and potential risks. Besides these uses, ML also has a wide range of applications in our daily lives. So, the development in ML is most important in this age of digital system to solve more complex problems. In order to further develop ML and diminish the uncertainties to improve accuracy, an innovative concept of complex bipolar intuitionistic fuzzy sets (CBIFSs) is introduced in this article. Further, the Cartesian product of two CBIFSs is defined. Moreover, the complex bipolar intuitionistic fuzzy relations (CBIFRs) and their types with suitable examples are defined. In addition, some i...
A multitude of enzyme‐linked immunosorbent assays (ELISAs) has been developed to detect severe ac... more A multitude of enzyme‐linked immunosorbent assays (ELISAs) has been developed to detect severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) antibodies since the coronavirus disease 2019 pandemic started in late 2019. Assessing the reliability of these assays in diverse global populations is critical. This study compares the use of the commercially available Platelia Total Ab Assay (Bio‐Rad) nucleocapsid ELISA to the widely used Mount Sinai spike IgG ELISA in a Kenyan population seroprevalence study. Using longitudinal plasma specimens collected from a mother–infant cohort living in Nairobi, Kenya between May 2019 and December 2020, this study demonstrates that the two assays have a high qualitative agreement (92.7%) and strong correlation of antibody levels (R2 = 0.973) in repeated measures. Within this cohort, seroprevalence detected by either ELISA closely resembled previously published seroprevalence estimates for Kenya during the sampling period and no significant diffe...
SARS-CoV-2 is locked in a high-stakes arms race between the dynamics of rising population immunit... more SARS-CoV-2 is locked in a high-stakes arms race between the dynamics of rising population immunity and escape mutations. The E484K mutation in the spike protein reduces neutralization by post-vaccination sera and monoclonal antibody therapeutics. We detected the emergence of an E484K harboring variant B.1.243.1 from a common circulating variant (B.1.243) in the United States. In contrast to other instances when the E484K mutation was acquired independently in the parental lineage, genomic surveillance indicates that the B.1.243.1 variant of interest is in the process of being established in Arizona and beginning to cross state borders to New Mexico and Texas. Genomic, epidemiologic and phylogenetic evidence indicates that the B.1.243.1 variant of interest is poised to emerge. These findings demonstrate the critical need to continue tracking SARS-CoV-2 in real-time to inform public health strategies, diagnostics, medical countermeasures and vaccines.
ABSTRACTBackgroundHIV may increase SARS-CoV-2 infection risk and COVID-19 severity generally, but... more ABSTRACTBackgroundHIV may increase SARS-CoV-2 infection risk and COVID-19 severity generally, but data are limited about its impact on postpartum women and their infants. As such, we characterized SARS-CoV-2 infection among mother-infant pairs in Nairobi, Kenya.MethodsWe conducted a nested study of 53 HIV-uninfected and 51 healthy women living with HIV, as well as their HIV-exposed uninfected (N=41) and HIV-unexposed (N=48) infants, participating in a prospective cohort. SARS-CoV-2 serology was performed on plasma collected between 1 May-31 December 2020 to determine the incidence, risk factors, and symptoms of infection. SARS-CoV-2 RNA PCR and sequencing was also performed on stool samples from seropositive participants.ResultsSARS-CoV-2 seropositivity was found in 38% of the 104 mothers and in 17% of the 89 infants. There was no significant association between SARS-CoV-2 infection and maternal HIV (Hazard Ratio [HR]=1.51, 95% CI: 0.780-2.94) or infant HIV exposure (HR=1.48, 95% CI...
Additional file 2: Figure S2. Relative abundance of the 10 most frequently shared (mother-infant)... more Additional file 2: Figure S2. Relative abundance of the 10 most frequently shared (mother-infant) ASVs. Taxonomy shown at the genus level.
Additional file 4: Figure S4. VirSorter viral contig transmission analysis. Analyses of VirSorter... more Additional file 4: Figure S4. VirSorter viral contig transmission analysis. Analyses of VirSorter contigs were performed as in Fig. 4. (A) The number of infant VirSorter viral contigs shared with their mother (top), and their proportion out of the total infant virome (VirSorter identified) is shown (bottom). Percent of infant VirSorter contigs that are shared with their mother is shown in blue and infant only VirSorter contigs are shown in green. (B) Average VirSorter contig proportion of mothers' virome that is shared with infant or unique to the mother. (C) Average VirSorter contig proportion of infant virome that is shared with mother by delivery route. Statistical significance assessed by Mann-Whitney test. (D) Average VirSorter contig proportion of maternal virome that is shared with infant by delivery route. Statistical significance assessed by Mann-Whitney test. (E) Plot of the number of infant shared VirSorter viral contigs vs. the total number of maternal VirSorter cont...
Additional file 5: Figure S5. Transkingdom interaction between bacteria and bacteriophage. Correl... more Additional file 5: Figure S5. Transkingdom interaction between bacteria and bacteriophage. Correlation of shared bacterial ASVs and viral contigs. (A) Heatmap shows the Pearson correlation between bacterial ASVs and bacteriophage contigs in infants from C-section delivery (left) clustered by hierarchical clustering. Second heatmap shows correlations from infants delivered vaginally clustered in the same order as correlations from infants delivered by C-section. B) Heatmap shows the Pearson correlation between bacterial ASVs and VirSorter identified bacteriophage contigs in infants delivered vaginally (left) clustered by hierarchical clustering. Second heatmap shows correlations from infants delivered by C-section clustered in the same order as correlations from infants delivered vaginally. These VirSorter analyses corroborate the contig analyses shown in Fig. 5.
Additional file 3: Figure S3. Metadata analysis of viral species. (A) Number of sequencing reads ... more Additional file 3: Figure S3. Metadata analysis of viral species. (A) Number of sequencing reads in infant and maternal samples. Statistical significance assessed by Mann-Whitney. (B) Output of MaAslin and random forest analysis. (C) Important viral species and their statistical significance as assessed by MaAslin and random forest. (D) Heatmap of MaAslin identified viral species for mothers and infants. (E) ROC curves and AUC measures for delivery route and mother/infant classification using random forest and pROC packages in R. Pseudo-probabilities are plotted on graph using Out-Of-Bag (OOB) sample tree classification votes. Only infant data used in vaginal vs. C-section classification while both mother and infant data used for mother vs. infant classification. (F) Bray-Curtis Dissimilarity pairwise comparisons. Statistical significance assessed by Mann-Whitney. Kruskal-Wallis with Dunn's multiple correction was used to assess feeding type (breastmilk vs. formula; breastmilk v...
Studies of viruses that coevolved with lemurs provide an opportunity to understand the basal trai... more Studies of viruses that coevolved with lemurs provide an opportunity to understand the basal traits of primate viruses and provide an evolutionary context for host-virus interactions. Germline integration of endogenous retroviruses (ERVs) are fossil evidence of past infections. Hence, characterization of novel ERVs provides insight into the ancient precursors of extant viruses and the evolutionary history of their hosts. Here, we report the discovery of a novel endogenous retrovirus present in the genome of a lemur, Coquerel’s sifaka (Propithecus coquereli). Using next-generation sequencing, we identified and characterized the complete genome sequence of a retrovirus, named prosimian retrovirus 1 (PSRV1). Phylogenetic analyses indicate that PSRV1 is a gamma-type betaretrovirus basal to the other primate betaretroviruses and most closely related to simian retroviruses. Molecular clock analysis of PSRV1 long terminal repeat (LTR) sequences estimated the time of endogenization within 4...
Breastfeeding plays an important role in seeding the infant gut microbiome and mammary health. Al... more Breastfeeding plays an important role in seeding the infant gut microbiome and mammary health. Although most studies focus on the diverse breast milk bacterial communities, little is known about the viral communities harbored in breast milk.
In December of 2019, a novel coronavirus, SARS-CoV-2, emerged in the city of Wuhan, China causing... more In December of 2019, a novel coronavirus, SARS-CoV-2, emerged in the city of Wuhan, China causing severe morbidity and mortality. Since then, the virus has swept across the globe causing millions of confirmed infections and hundreds of thousands of deaths. To better understand the nature of the pandemic and the introduction and spread of the virus in Arizona, we sequenced viral genomes from clinical samples tested at the TGen North Clinical Laboratory, provided to us by the Arizona Department of Health Services, and at Arizona State University and the University of Arizona, collected as part of community surveillance projects. Phylogenetic analysis of 79 genomes we generated from across Arizona revealed a minimum of 9 distinct introductions throughout February and March. We show that >80% of our sequences descend from clades that were initially circulating widely in Europe but have since dominated the outbreak in the United States. In addition, we show that the first reported cas...
BackgroundThe earliest microbial colonizers of the human gut can have life-long consequences for ... more BackgroundThe earliest microbial colonizers of the human gut can have life-long consequences for their hosts. Precisely how the neonatal gut bacterial microbiome and virome are initially populated is not well understood. To better understand how the maternal gut microbiome influences acquisition of the infant gut microbiome, we studied the early life bacterial microbiomes and viromes of 28 infant twin pairs and their mothers.ResultsInfant bacterial and viral communities more closely resemble those of their related co-twin than unrelated infants. We found that 63% of an infant’s bacterial microbiome can be traced to their mother’s gut microbiota. In contrast, only 15% of their viral communities are acquired from their mother. Delivery route did not determine how much of the bacterial microbiome or virome was shared from mother to infant. However, bacteria-bacteriophage interactions were altered by delivery route.ConclusionsThe maternal gut microbiome significantly influences infant g...
Gulf War illness (GWI) is characterized by the persistence of inflammatory bowel disease, chronic... more Gulf War illness (GWI) is characterized by the persistence of inflammatory bowel disease, chronic fatigue, neuroinflammation, headache, cognitive impairment, and other medically unexplained conditions. Results using a murine model show that enteric viral populations especially bacteriophages were altered in GWI. The increased viral richness and alpha diversity correlated positively with gut bacterial dysbiosis and proinflammatory cytokines. Altered virome signature in GWI mice also had a concomitant weakening of intestinal epithelial tight junctions with a significant increase in Claudin-2 protein expression and decrease in ZO1 and Occludin mRNA expression. The altered virome signature in GWI, decreased tight junction protein level was followed by the presence an activation of innate immune responses such as increased Toll-like receptor (TLR) signaling pathways. The altered virome diversity had a positive correlation with serum IL-6, IL-1β, and IFN-γ, intestinal inflammation (IFN-γ)...
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Papers by Rabia Maqsood