Search

This study aimed at updating previous data on HIV-1 integrase variability, by using effective bioinformatics methods combining different statistical instruments from simple entropy and mutation rate to more specific approaches such as Hellinger distance. A total of 2133 HIV-1 integrase sequences were analyzed in: i) 1460 samples from drug-naïve [DN] individuals; ii) 386 samples from drug-experienced but INI-naïve [IN] individuals; iii) 287 samples from INI-experienced [IE] individuals. Within the three groups, 76 amino acid positions were highly conserved (≤0.2% variation, Hellinger distance:0.25%), with 35 fully invariant positions; while, 80 positions were conserved (0.2% to1% variation, Hellinger distance:1%). The H12-H16-C40-C43 and D64-D116-E152 motifs were all well conserved. Some residues were affected by dramatic changes in their mutation distributions, especially between DN and IE samples (Hellinger distance ≥1%). In particular, 15 positions (D6, S24, V31, S39, L74, A91, S119, T122, T124, T125, V126, K160, N222, S230, C280) showed a significant decrease of mutation rate in IN and/or IE samples compared to DN samples. Conversely, 8 positions showed significantly higher mutation rate in samples from treated individuals (IN and/or IE) compared to DN. Some of these positions, such as E92, T97, G140, Y143, Q148 and N155, were already known to be associated with resistance to integrase inhibitors; other positions including S24, M154, V165 and D270 are not yet documented to be associated with resistance. Our study confirms the high conservation of HIV-1 integrase and identified highly invariant positions using robust and innovative methods. The role of novel mutations located in the critical region of HIV-1 integrase deserves further investigation.

BackgroundScientometrics enables scholars to assess and visualize emerging research trends and hot-spots in the scientific literature from a quantitative standpoint. In the last decades, Africa has nearly doubled its absolute count of scholarly output, even though its share in global knowledge production has dramatically decreased. This limited contribution of African scholars to the global research output is in part impacted by the availability of adequate infrastructures and research collaborative networks. The still ongoing COVID-19 pandemic has profoundly impacted the way scholarly research is conducted, published and disseminated. However, the COVID-19 related research focus, the scientific productivity and the research collaborative network of African researchers during the ongoing COVID-19 pandemic remain to be elucidated yet.MethodsThis study aimed to clarify the COVID-19 research patterns among African researchers and estimate the strength of collaborations and partnerships between African researchers and scholars from the rest of the world during the COVID-19 pandemic, collecting data from electronic scholarly databases such as Web of Sciences (WoS), PubMed/MEDLINE and African Journals OnLine (AJOL), the largest and prominent platform of African-published scholarly journals.ResultsIn the present bibliometric study, we found that COVID-19 related collaboration patterns varied among African regions, being shaped and driven by historical, social, cultural, linguistic, and even religious determinants. For instance, most of the scholarly partnerships occurred with formerly colonial countries (like European or North-American countries). In other cases, scholarly ties of North African countries were above all with the Kingdom of Saudi Arabia. In terms of amount of publications, South Africa and Egypt were among the most productive countries.DiscussionBibliometrics and, in particular, scientometrics can help scholars identify research areas of particular interest, as well as emerging topics, such as the COVID-19 pandemic. With a specific focus on the still ongoing viral outbreak, they can assist decision- and policy-makers in allocating funding and economic-financial, logistic, organizational, and human resources, based on the specific gaps and needs of a given country or research area.ConclusionsIn conclusion, the ongoing COVID-19 pandemic has exerting a subtle, complex impact on research and publishing patterns in African countries. On the one hand, it has distorted and even amplified existing inequalities and disparities in terms of amount of scholarly output, share of global knowledge, and patterns of collaborations. On the other hand, COVID-19 provided new opportunities for research collaborations.