In this study, we investigated the genomic variability of alpha-VOC of SARS-CoV-2 in Pakistan, in context of the global population of this variant. A set of 461 whole-genome sequences of Pakistani samples of alpha-variant, retrieved from GISAID, were aligned in MAFFT and used as an input to the Coronapp web-application. Phylogenetic tree was constructed through maximum-likelihood method by downloading the 100 whole-genome sequences of alpha-variant for each of the 12 countries having the largest number of Pakistani diasporas. We detected 1725 mutations, which were further categorized into 899 missense mutations, 654 silent mutations, 52 mutations in non-coding regions, 25 in-frame deletions, 01 in-frame insertion, 51 frameshift deletions, 21 frameshift insertions, 21 stop-gained variants, and 1 stop-gained deletion. We found NSP3 and Spike as the most variable proteins with 355 and 233 mutations respectively. However, some characteristic mutations like Δ144(S), G204R(N), and T1001I, I2230T, del3675–3677(ORF1ab) were missing in the Pakistani population of alpha-variant. Likewise, R1518K(NSP3), P83L(NSP9), and A52V, H164Y(NSP13) were found for the first time in this study. Interestingly, Y145 deletion(S) had 99% prevalence in Pakistan but globally it was just 4.2% prevalent. Likewise, R68S substitution (ORF3a), F120 frameshift deletion, L120 insertion, L118V substitution (ORF8), and N280Y(NSP2) had 20.4%, 14.3%, 14.8%, 9.1%, 13.9% prevalence locally but globally they were just 0.1%, 0.2%, 0.04%, 1.5%, and 2.4% prevalent respectively. The phylogeny analysis revealed that majority of Pakistani samples were grouped together in the same clusters with Italian, and Spanish samples suggesting the transmission of alpha-variant to Pakistan from these western European countries.

Current methods of ruminant ration formulation in Pakistan use foreign-based nutrient availability values. These values may not be optimal for all geographic areas, as variation in environment, agronomic factors, animal species, and diet characteristics may not be considered. The aim of present study was to establish a database of the chemical composition and dry matter degradation parameters of tropical forage commonly fed to ruminants in Pakistan and South Asian countries using Nili-Ravi buffalo and Cholistani cattle at heifer and lactating stages. Six cereal grain and four legume species were grown in 3 locations under standard agronomic conditions and sampled at booting and at 50% flowering stage for cereal and legumes, respectively. Dried and milled feeds were analyzed for chemical composition and in situ dry matter degradation parameters using 1 g samples in bags placed in the rumen of 2 Nili-Ravi buffalo heifers, 2 lactating Nili-Ravi buffaloes, 2 Cholistani heifers, and 2 lactating Cholistani cows. The forage family (cereal vs. legumes), species, and geographic location of growth significantly influenced (P < 0.001) chemical composition and in situ degradation fractions. Animal species and developmental stage showed no effect on degradation fractions (P > 0.05). Legume-by-heifer interactions significantly increased (P < 0.05), and legume-by-lactating cow interaction tended (P = 0.065), to increase the rate of degradation (Kd). The selected forages were degraded to a similar extent independent of animal species or developmental stage, and legumes are degraded at higher rates and to a greater extent than are cereals. A moderately significant relationship between Kd and effective dry matter degradability (DMD) suggests that Kd could be the single most important predictor of forage degradability in the rumen.

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