Syed Hani Hassan Abidi

Dr Abidi’s laboratory works in the areas of virology, immunology, and viral oncology. The laboratory uses a wide range of bioinformatics (including mathematical modeling, machine learning, and Artificial Intelligence) and genetic, transcriptomic, and proteomic tool and approaches in their studies.  

His laboratory focuses on HIV molecular epidemiology, phylogenetics, and phylodynamics in different HIV key population groups and geographical regions such as Pakistan, Kenya, Afghanistan, and Kazakhstan. In addition to HIV, Dr Abidi also focuses on other viruses, such as HCV, HBV, RSV, Herpesviruses, and SARS-CoV-2, where he uses sequence data to drive inferences about viral evolution, and the emergence of drug and vaccine resistance mutations.

Dr Abidi’s laboratory also focuses on viral immunology studies, where the key research areas involve characterization of host response against viruses, identification of immune biomarkers for disease severity, and understating the relationship between microbiome, host immunity, and development of viral disease or viral infection-associated pathologies. Dr Abidi’s laboratory also uses sequence (along with mutational profiles) to develop approaches for designing effective drugs and vaccines against different viruses.

Dr Abidi’s laboratory also extensively studies the role of viral infections in the onset/progression of cancer. He especially focuses on the role of EBV in the progression of prostate cancer, where his laboratory has characterized EBV latency profiles in prostate cancer tissues, followed by the differential analysis of genetic, transcriptomic, and proteomic changes associated with EBV in prostate carcinoma.  

Dr Abidi’s teaching portfolio ranges from undergraduate and graduate teaching. In both forms, his focus is to enable students to build concepts and develop an understanding of the subject, rather than simply memorizing a topic. To achieve this goal, he actively relies on the use of technology, especially the use of animations, to explain difficult concepts, which makes it easy for the students to understand the concept as they are able to see the process being simulated in real-time. In addition, he has experimented with new teaching/learning tools in adult education that can help in effectively delivering important concepts to medical students. For example, he used films to teach empathy and ethics to medical students. The film-based course not only received very positive feedback from the students but also helped us in highlighting the use of cinematic films as a teaching/learning tool for adult education. This strategy was published in a revered international education journal (Abidi, et al. Canadian Journal for the Study of Adult Education, 2016). Furthermore, he has also successfully integrated new pedagogies and various mediums, such as Flip classroom, in his routine teaching with favorable outcomes. For example, he transformed a conventional Biochemistry LCF on memory and learning into an integrated (Biochemistry, Anatomy, Physiology and Pharmacology) session on memory and learning, where he taught students about “the Mozart effect”, the idea that listening to classical music (particularly Mozart) improves the brain functions, enhances memory and help with effects of Dementia. The session was well-received by the students. Additionally, in 2014, Dr Syed and Dr Abidi, in an effort to make education more accessible to the larger population, co-offered the first massive open online course (MOOC) on ‘Computer-Based Drug discovery’ from Pakistan. They went further to publish our experience on the first MOOC (Abidi et al. Current Issues in Emerging eLearning 2016), as well as provided a road map for offering MOOCs from a resource-limited country (Abidi, et al. Learning, Media and Technology, 2016). In 2022, he was awarded a SoTL grant to develop a new strategy to deliver theory and laboratory protocols in cell and molecular biology through the MOOC platform. This MOOC also received outstanding comments from the participants. His ‘outstanding contributions and academic pursuits in classroom teaching’ earned him the Outstanding Teachers Award in 2019 (Aga Khan University, Pakistan) and the Fellowship of Higher Education (UK) in 2022.

1. Ansari, Amna S., Muhammad R. Khanani, Syed H. Abidi, Farida Shah, Aniqa Shahid, and Syed H. Ali. "Patterns of HIV infection among native and refugee Afghans." AIDS 25, no. 11 (2011): 1427-1430.
2. Abidi Syed H. and Syed H. Ali. The battle against HIV in Afghanistan [Rapid Response]. BMJ (2011). http://www.bmj.com/rapid-response/2011/11/03/battle-against-hiv-afghanistan.
3. Abidi, Syed H., Farwa Ali, Farida Shah, Farhat Abbas, and Syed Ali. "Burden of Communicable Disease among the Native and Repatriating Afghans." PLoS pathogens 8, no. 10 (2012): e1002926.
4. Raees, Muhammad A., Syed H. Abidi, Wajid Ali, Muhammad R. Khanani, and Syed Ali. "HIV among women and children in Pakistan." Trends in microbiology 21, no. 5 (2013): 213-214.
5. Abidi, Syed H., Aniqa Shahid, Laila S. Lakhani, Muhammad R. Khanani, Peter Ojwang, Nancy Okinda, Reena Shah, Farhat Abbas, Sarah Rowland-Jones, and Syed Ali. "Population-specific evolution of HIV Gag epitopes in genetically diverged patients." Infection, Genetics and Evolution 16 (2013): 78-86.
6. Sherwani, Sikandar Khan, Syed Hani Hassan Abidi, Faisal Rasheed, Jehan Alam, Muhammad Shoaib, and Shahana U. Kazmi. "Relationship between Lichen Planus and Helicobacter pylori positive patients in Karachi-Pakistan." European Academic Research 1, no. 6 (2013): 1309-1317.
7. Sherwani, Sikandar Khan, Syed H. Abidi, Faisal Rasheed, Shakeel Akhtar, and Shahana Urooj Kazmi. "Leifson Flagellar Staining: Rapid and Useful Diagnostic Procedure for H. Pylori Detection." Pakistan Journal of Health Research 1, no. 2 (2013): 1-3
8. Sherwani, Sikandar Khan, Faisal Rasheed, Syed H. Abidi, Asma Bashir, Shakeel Akhtar and Shahana U. Kazmi. “Evaluation of Suitable media for culturing and sub culturing of H. pylori clinical isolates.” International Journal of Chemical and Pharmaceutical Sciences 4, no. 2 (2013): 1-4
9. Abidi, Syed H., Sikandar K. Sherwani, Tarrunum R. Siddiqui, Asma Bashir, and Shahana U. Kazmi. "Drug resistance profile and biofilm forming potential of Pseudomonas aeruginosa isolated from contact lenses in Karachi-Pakistan." BMC ophthalmology 13, no. 1 (2013): 57.
10. Rai, Mohammad A., Yong-Hong Zhang, Hui-Ping Yan, Yan Zhao, Syed Hani Abidi, Wen-Yan Qu, Andrew McMichael, Tao Dong, Sarah Rowland-Jones, and Ke-Yi Xu. "ST111 Immune selection and vpu variability in a unique narrow source HIV-Positive village cohort." JAIDS Journal of Acquired Immune Deficiency Syndromes 62 (2013): 69.
11. Abidi, Syed H., Aniqa Shahid, Laila S. Lakhani, Reena Shah, Nancy Okinda, Peter Ojwang, Farhat Abbas, Sarah Rowland-Jones, and Syed Ali. "HIV-1 progression links with viral genetic variability and subtype, and patient’s HLA type: analysis of a Nairobi-Kenyan cohort." Medical microbiology and immunology 203, no. 1 (2014): 57-63.
12. Abidi, Syed H., Farhat Abbas, Sarah Rowland-Jones and Syed Ali. “Divergence and epitope evolution of HIV-1 subtype A. 2014.” PLoS One 9, no. 6 (2014): 
13. Abidi, Syed H., Khalid Ahmed, Sikander Khan Sherwani, and Shahana Urooj Kazmi. “Reduction and Removal of Pseudomonas aeruginosa Biofilm by Natural Agents.” International Journal of Chemical and Pharmaceutical Sciences. 5, no. 1 (2014): 28-34.
14. Abidi, Syed Hani, Khalid Ahmed, Sikander Khan Sherwani, and Shahana Urooj Kazmi. "Synergy between antibiotics and natural agents results in increased antimicrobial activity against Staphylococcus epidermidis." The Journal of Infection in Developing Countries 9, no. 09 (2015): 925-929.
15. Abidi, Syed H., Muhammad Aanish Raees, and Syed Ali. "How Pakistan’s media spreads the message about reproductive and sexual health." BMJ 350 (2015): h1309.
16. Shah, Adil A., Syed H. Abidi, Marcia L. Kalish, Sten H. Vermund, and Syed Ali. "Viral co-infections in high-risk communities of Pakistan." The Lancet HIV 2, no. 4 (2015): e124-e125.
17. Onsongo, Simon, Syed Hani Abidi, Samoel Khamadi, Reena Shah, Sheila Kageha, Peter Ojwang, Syed Ali, and Nancy Okinda. "Prevalence of Transmitted Drug Resistance Mutations in HIV-1-Infected Drug-Naive Patients from Urban and Suburban Regions of Kenya." AIDS Research and Human Retroviruses 32, no. 3 (2016): 220-225.
18. Abidi, Syed Hani, Aamna Pasha, Greg Moran, and Syed Ali. "A roadmap for offering MOOC from an LMIC institution." Learning, Media and Technology (2016): 1-6. IF:
19. Abidi, Syed Hani, Aamna Pasha, and Syed Ali. "Participant Experience of the First Massive Open Online Course (MOOC) from Pakistan." Current Issues in Emerging eLearning 3, no. 1 (2016): 11.
20. Abidi, Syed H., Khalid Ahmed, Fatin Zehra, Nouman Mughal, and Shahana U. Kazmi. "Rabbit Serum Raised against P. aeruginosa Biofilm Exhibit Significant Biofilm Reduction and Removal Activity." Int. J. Curr. Microbiol. App. Sci 5, no. 7 (2016): 275-279.
21. Ahmed, Khalid, Syeda Atia Qudsia, Syed Hani Abidi, Rabia Malik, Muhammad Awais, and Abdul Rehman. "Proteinase 3-antineutrophil cytoplasmic antibody positive necrotizing vasculitis induced by ciprofloxacin." International Journal of Basic & Clinical Pharmacology 5, no. 3 (2016): 1145-1147. IF:
22. Pasha, Aamna, Syed Hani Abidi, and Syed Ali. "Challenges of Offering a MOOC from an LMIC." The International Review of Research in Open and Distributed Learning 17, no. 6 (2016).
23. Abidi, Syed Hani, Sarosh Madhani, Aamna Pasha, and Syed Ali. "Use of Cinematic Films as a Teaching/Learning Tool for Adult Education." The Canadian Journal for the Study of Adult Education (Online) 29, no. 1 (2017): 37.
24. Fatima, Sadia S., Zehra Jamil, Syed Hani Abidi, Daniyal Nadeem, Zara Bashir, Ahmed Ansari. “Interleukin-18 polymorphism as an inflammatory index in metabolic syndrome: A preliminary study”. World J Diabetes 8, no. 6 (2017): 304-310.
25. Farooq, Syeda Ayesha, Mohammad Hafiz Rasooly, Syed Hani Abidi, Kayvon Modjarrad, and Syed Ali. "Opium trade and the spread of HIV in the Golden Crescent." Harm Reduction Journal 14, no. 1 (2017): 47.
26. Tariq U, Parveen A, Akhtar F, Mahmood F, Ali S, Abidi SH. Emergence of circulating recombinant form 56_cpx in Pakistan. AIDS research and human retroviruses. 2018 Nov 1;34(11):1002-4.
27. Anwar, Muhammad Faraz, Shamshad Zarina, Syed Ali, and Syed Hani Abidi. "Two for one: Viral helicases as an ideal target for HIV and HCV co-infection." Medical hypotheses 116 (2018): 139-140. IF:
28. Naqvi, Haider Ali, Shafqat Huma, Hira Waseem, Kashaf Aqeel Zaidi, Hina Zuberi, and Syed Hani Abidi. "Association between a single nucleotide polymorphism in neuregulin-1 and schizophrenia in Pakistani patients." JPMA. The Journal of the Pakistan Medical Association 68, no. 5 (2018): 747-752.
29. Baig, Samina, Syed H. Abidi, Zahid Azam, Shahid Majid, Saeed Khan, Muhammad R. Khanani, and Syed Ali. "Evolution of HBV S‐gene in the backdrop of HDV co‐infection." Journal of medical virology 90, no. 8 (2018): 1328-1336.
30. Siddiqui, Sammer, Muhammad F. Anwar, Sadaf Naeem, Syed Hani Abidi, Shamshad Zarina, and Syed Ali. "Simian Virus 40 Large T Antigen as a Model to Test the Efficacy of Flouroquinolones against Viral Helicases." Bioinformation 14, no. 2 (2018): 75.
31. Ahmed, Khalid, Syeda Atia Qudsia, Abdul Rehman, and Syed Hani Abidi. "Fatal elizabethkingia meningoseptica cholangitis following biliary stent placement." J Coll Physicians Surg Pak, 28(3): S35-S36. (2018).
32. Anwar, Muhammad Faraz, Ramsha Khalid, Alina Hasanain, Sadaf Naeem, Shamshad Zarina, Syed Hani Abidi, and Syed Ali. "Integrated Chemoinformatics-Molecular Docking Approach to Drug Discovery Against Viruses." Infectious disorders drug targets (2018).
33. Tariq U, Mahmood F, Naeem S, Ali S, Abidi SH. Emergence of HIV-1 Unique DG Recombinant Form in Pakistan. AIDS research and human retroviruses. 2019 Nov 4.
34. Abidi, Syed Hani, Fareena Bilwani, Kulsoom Ghias, and Farhat Abbas. "Viral etiology of prostate cancer: genetic alterations and immune response. A literature review." International Journal of Surgery 52 (2018): 136-140.
35. Davlidova S, Abidi SH*, Ali S*. Healthcare malpractice and continuing HIV outbreaks in Pakistan. BMJ Global Health. 2019 Nov 1;4(6).
36. Abidi SH, Ahmed K, Kazmi SU. The antibiofilm activity of Acetylsalicylic acid, Mefenamic acid, Acetaminophen against biofilms formed by P. aeruginosa and S. epidermidis. JPMA. The Journal of the Pakistan Medical Association. 2019 Oct;69(10):1493.
37. Ahmed K, Ahmed H, Ahmed FA, Ali AA, Akbar J, Rana J, Tariq U, Abidi SH. Analysis of anti-microbial and anti-biofilm activity of hand washes and sanitizers against S. aureus and P. aeruginosa. JPMA. 2020 Sep 4;2019.
38. Mir F, Mahmood F, Siddiqui AR, Baqi S, Abidi SH, Kazi AM, Nathwani AA, Ladhani A, Qamar FN, Soofi SB, Memon SA. HIV infection predominantly affecting children in Sindh, Pakistan, 2019: a cross-sectional study of an outbreak. The Lancet Infectious Diseases. 2019 Dec 19.
39. Anwar MF, Khalid R, Hasanain A, Naeem S, Zarina S, Abidi SH*, Ali S*. Application of an integrated cheminformatics-molecular docking approach for discovery for physicochemically similar analogs of fluoroquinolones as putative HCV inhibitors. Computational Biology and Chemistry. 2020 Feb 1;84:107167.
40. Tariq U, Iftikhar A, Zahid D, Sultan F, Mahmood F, Naeem S, Ali S, Abidi SH. The Emergence of an Unassigned Complex Recombinant Form in Pakistani HIV-Infected Individual. Archives of Virology (accepted).
41. Siddiqui AR, Nathwani AA, Abidi SH, Mahmood SF, Azam I, Sawani S, Kazi AM, Hotwani A, Memon SA, Soomro J, Shaikh SA. Investigation of an extensive outbreak of HIV infection among children in Sindh, Pakistan: protocol for a matched case–control study. BMJ open. 2020 Mar 1;10(3):e036723.
42. Efstathiou, C., Syed Hani Abidi, J. Harker, and N. J. Stevenson. "Revisiting respiratory syncytial virus’s interaction with host immunity, towards novel therapeutics." Cellular and Molecular Life Sciences (2020): 1-14.
43. Ahmed, Khalid, Hamza Ahmed, Fasih Ali Ahmed, Alisha Akbar Ali, Jehangir Akbar, Junaid Rana, Uroosa Tariq, and Syed Hani Abidi. "Analysis of anti-microbial and anti-biofilm activity of hand washes and sanitizers against S. aureus and P. aeruginosa." JPMA 2019 (2020).
44. Sajjad M, Ali S, Baig S, Sharafat S, Khan BA, Khan S, Mughal MN, Abidi SH. HBV S antigen evolution in the backdrop of HDV infection affects epitope processing and presentation. Journal of Medical Virology. 2020 Dec 7.
45. Khalid R, Anwar MF, Raees MA, Naeem S, Abidi SH, Ali S. An in silico approach to analyze HCV genotype-specific binding-site variation and its effect on drug–protein interaction. Scientific reports. 2020 Nov 30;10(1):1-7.
46. Rizwan-Ul-Hasa S, Abdullah A, Siddiqui SA, Ahmed S, Shah SA, Mir F, Abidi SH. Probabilistic measures of HIV-1 transmission in different HIV-1 key population groups of Larkana, Pakistan. JPMA. The Journal of the Pakistan Medical Association. 2021;71(8 (Suppl 4)):S26.
47. Rizwan-ul-Hasan S, Farrukh F, Ahmed S, Abidi SH. A mathematical modeling approach to measure the probability of HIV-1 transmission for different high-risk groups of Pakistan. The Journal of Infection in Developing Countries. 2021 Aug 31;15(08):1212-5.
48. Akbay B*, Abidi SH*, Ibrahim MA, Mukhatayev Z, Ali S. Multi-subunit sars-cov-2 vaccine design using evolutionarily conserved t-and b-cell epitopes. Vaccines. 2021 Jul;9(7):702. (*co-first author)
49. Abidi SH, Almansour NM, Amerzhanov D, Allemailem KS, Rafaqat W, Ibrahim MA, la Fleur P, Lukac M, Ali S. Repurposing potential of posaconazole and grazoprevir as inhibitors of SARS-CoV-2 helicase. Scientific reports. 2021 May 13;11(1):1-1.
50. Abidi SH, Nduva GM, Siddiqui D, Rafaqat W, Mahmood SF, Amna R, Ali A, Hotwani A, Shah SA, Memon S, Saqib A. Phylogenetic and drug-resistance analysis of HIV-1 sequences from an extensive paediatric HIV-1 outbreak in Larkana, Pakistan. Frontiers in microbiology. 2021 Aug 17:2305.
51. Mir F, Nathwani AA, Simms V, Abidi SH, Siddiqui AR, Hotwani A, Memon SA, Shaikh SA, Soomro J, Shah SA, Achakzai B. Factors associated with HIV infection among children in Larkana District, Pakistan: a matched case-control study. The Lancet HIV. 2021 Jun 1;8(6):e342-52.
52. Ibrahim MA, Abdelrahman AH, Atia MA, Mohamed TA, Moustafa MF, Hakami AR, Khalifa SA, Alhumaydhi FA, Alrumaihi F, Abidi SH, Allemailem KS. Blue biotechnology: Computational screening of Sarcophyton cembranoid diterpenes for SARS-CoV-2 main protease inhibition. Marine drugs. 2021 Jul;19(7):391.
53. Alam F, Rehman R, Farooqui N, Jehan F, Abidi SH. Oxidative stress and Metformin; an in-vitro study on serum and primary human granulosa cell cultures. InHUMAN REPRODUCTION 2021 Jul 1 (Vol. 36, pp. 239-239). GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND: OXFORD UNIV PRESS.
54. Ghanchi NK, Nasir A, Masood KI, Abidi SH, Mahmood SF, Kanji A, Razzak S, Khan W, Shahid S, Yameen M, Raza A. Higher entropy observed in SARS-CoV-2 genomes from the first COVID-19 wave in Pakistan. PloS one. 2021 Aug 31;16(8):e0256451.
55. Ahmed MA, Mughal N, Abidi SH, Bari MF, Mustafa M, Vohra F, Alrahlah A. Factors Affecting the Outcome of Periapical Surgery; a Prospective Longitudinal Clinical Study. Applied Sciences. 2021 Jan;11(24):11768.
56. Ahmed MA, Anwar MF, Ahmed K, Aftab M, Nazim F, Bari MF, Mustafa M, Vohra F, Alrahlah A, Mughal N, Abidi SH. Baseline MMP expression in periapical granuloma and its relationship with periapical wound healing after surgical endodontic treatment. BMC Oral Health. 2021 Dec;21(1):1-9.
57. Abidi SH, Imtiaz K, Kanji A, Qaiser S, Khan E, Iqbal K, Veldhoen M, Ghias K, Simas JP, Hasan Z. A rapid real-time polymerase chain reaction-based live virus microneutralization assay for detection of neutralizing antibodies against SARS-CoV-2 in blood/serum. Plos one. 2021 Dec 10;16(12):e0259551.
58. Abidi SH, Aibekova L, Davlidova S, Amangeldiyeva A, Foley B, Ali S. Origin and evolution of HIV-1 subtype A6. PloS one. 2021 Dec 13;16(12):e0260604.
59. Rashid A, Li K, Feng Y, Ahmad T, Getaneh Y, Yu Y, Hu X, Abidi SH, Shao Y. HIV-1 genetic diversity a challenge for AIDS vaccine development: a retrospective bibliometric analysis. Human vaccines & immunotherapeutics. 2022 Jan 9:1-1.
60. Naeem A, Sheikh A, Naeem S, Abidi SH. Molecular docking analysis of fluoroquinolones and other natural and synthetic compounds with the HCV NS3 helicase. Bioinformation. 2022;18(3):147-54.
61. Rafaqat W, Tariq U, Farooqui N, Zaidi M, Raees A, Zuberi M, Batool A, Abidi SH. Analysis of temporal changes in HIV-1 CRF01_AE gag genetic variability and CD8 T-cell epitope evolution. Plos one. 2022 May 10;17(5):e0267130.
62. Abidi SH, Siddiqui D, Mahmood SF, Rehana S, Nathwani AA, Hotwani A, Shah SA, Khan P, Ferrand RA, Mir F. Unassigned complex unique recombinant forms related to CRF36_cpx in children identified in an HIV-1 outbreak in Pakistan. AIDS Research and Human Retroviruses. 2022 (accepted)

Books

1. Abidi, Syed H., and Syed Ali. “Immunoevolution of HIV Subtype A in Genetically Diverse Cohorts: Molecular Divergence and Immunoevolution of HIV-1 Subtype A.” LAP LAMBERT Academic Publishing, Germany. ISBN-13: 978-3659908187 (2016)
2. Abidi, Syed H., Khalid Ahmed, Shahana Urooj Kazmi. “A Beginner’s Guide to Microbial Biofilm Research: Overview, Protocols, Applications” LAP LAMBERT Academic Publishing, Germany. ISBN-13: 978-613-8-34128-4 (2018)

Book Chapters

1. Abidi, Syed H., Farhat Abbas and Syed Ali. “Immunoinformatics of the MHC class I antigen presentation pathway.”  Introduction to Sequence and Genome Analysis. iConcept Press. ISBN: 978-14775549-1-3 (2013)
2. Syed Hani Abidi, Syed S. Ali, Muhammad A. Raees, Marcia Kalish, Sten H. Vermund and Syed Ali. The State of HIV Epidemic in Pakistan. In Research on Virology and Cytopathology. iConcept Press. ISBN:978-1-922227-70-6 (2016).
3. Syed Hani Abidi, Muhammad A. Raees, Farhat Abbas, Sarah Rowland-Jones, Marcia Kalish, Sten H. Vermund and Syed Ali. Population-specific Immuno-evolution of HIV-Subtype A. In Research on Virology and Cytopathology. iConcept Press. ISBN:978-1-922227-70-6 (2016).