Rambaut A, Holmes EC, O’Toole Á, Hill V, McCrone JT, Ruis C, du Plessis L, Pybus OG. A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nat Microbiol. 2020;5(11):1403–7.

Article
CAS
Google Scholar

Classification of Omicron (B.1.1.529): SARS-CoV-2 Variant of Concern. https://www.who.int/news-room/statements/26-11-2021-classification-of-omicron-(b.1.1.529)-sars-cov-2-variant-of-concern.

Thakur V, Ratho RK. OMICRON (B. 1.1. 529): a new SARS-CoV-2 variant of concern mounting worldwide fear. J Med Virol. 2022;94(5):1821–4.

Article
CAS
Google Scholar

Kandeel M, Mohamed ME, Abd El-Lateef HM, Venugopala KN, El-Beltagi HS. Omicron variant genome evolution and phylogenetics. J Med Virol. 2022;94(4):1627–32.

Article
CAS
Google Scholar

COVID-19 variant of concern Omicron (B.1.1.529): risk assessment, January 12, 2022. Toronto, ON: Queen's Printer for Ontario; 2022. https://www.publichealthontario.ca/-/media/documents/ncov/voc/2022/01/covid-19-omicron-b11529-risk-assessment-jan-12.pdf?sc_lang=en.

Arora S, Grover V, Saluja P, Algarni YA, Saquib SA, Asif SM, Batra K, Alshahrani MY, Das G, Jain R. Literature review of omicron: a grim reality amidst COVID-19. Microorganisms. 2022;10(2):451.

Article
CAS
Google Scholar

Fan G, Song H, Yip S, Zhang T, He D. Impact of low vaccine coverage on the resurgence of COVID-19 in Central and Eastern Europe. One Health. 2022. https://doi.org/10.1016/j.onehlt.2022.100402.

Article
Google Scholar

Chu D-T, Vu Ngoc S-M, Vu Thi H, Nguyen Thi Y-V, Ho T-T, Hoang V-T, Singh V, Al-Tawfiq JA. COVID-19 in Southeast Asia: current status and perspectives. Bioengineered. 2022;13(2):3797–809.

Article
CAS
Google Scholar

Bi K, Herrera-Diestra JL, Bai Y, Du Z, Wang L, Gibson G, Johnson-Leon M, Fox S, Meyers LA. The risk of SARS-CoV-2 Omicron variant emergence in low and middle-income countries (LMICs). medRxiv. 2022.

Song H, Fan G, Liu Y, Wang X, He D. The second wave of COVID-19 in South and Southeast Asia and the effects of vaccination. Front Med. 2021;8. https://doi.org/10.3389/fmed.2021.773110.

Megasari NLA, Utsumi T, Yamani LN, Gunawan E, Furukawa K, Nishimura M, Lusida MI, Mori Y. Seroepidemiological study of SARS-CoV-2 infection in East Java, Indonesia. PLoS ONE. 2021;16(5): e0251234.

Article
CAS
Google Scholar

Population-based age-stratified seroepidemiological investigation protocol for COVID-19 virus infection, 17 March 2020. World Health Organization. License: CC BY-NC-SA 3.0 IGO. https://apps.who.int/iris/handle/10665/331656.

Bryant JE, Azman AS, Ferrari MJ, Arnold BF, Boni MF, Boum Y, Hayford K, Luquero FJ, Mina MJ, Rodriguez-Barraquer I. Serology for SARS-CoV-2: apprehensions, opportunities, and the path forward. Sci Immunol. 2020;5(47):eabc6347.

Article
CAS
Google Scholar

Murhekar MV, Bhatnagar T, Selvaraju S, Rade K, Saravanakumar V, Thangaraj JWV, Kumar MS, Shah N, Sabarinathan R, Turuk A. Prevalence of SARS-CoV-2 infection in India: findings from the national serosurvey, May–June 2020. Indian J Med Res. 2020;152(1–2):48.

Article
CAS
Google Scholar

Murhekar MV, Bhatnagar T, Thangaraj JWV, Saravanakumar V, Kumar MS, Selvaraju S, Rade K, Kumar CG, Sabarinathan R, Turuk A. SARS-CoV-2 seroprevalence among the general population and healthcare workers in India, December 2020–January 2021. Int J Infect Dis. 2021;108:145–55.

Article
CAS
Google Scholar

Shervani Z, Bhardwaj D, Nikhat R, Ibbrahim A, Khan I, Qazi UY, Agarwal A, Khan AA, Hasan S, Sherwani A. 4th National Sero Survey of India: vaccine generated antibodies enhancement. Eur J Med Health Sci. 2022;4(1):27–32.

Google Scholar

Muniyappan A, Sundarappan B, Manoharan P, Hamdi M, Raahemifar K, Bourouis S, Varadarajan V. Stability and numerical solutions of second wave mathematical modeling on COVID-19 and omicron outbreak strategy of pandemic: analytical and error analysis of approximate series solutions by using hpm. Mathematics. 2022;10(3):343.

Article
Google Scholar

"BA.2 'stealth' variant makes up 80% of Kolkata's Omicron infections. https://timesofindia.indiatimes.com/city/kolkata/ba-2-stealth-variant-makes-up-80-of-kolkatas-o-infections/articleshow/88821640.cms.

Djalante R, Lassa J, Setiamarga D, Sudjatma A, Indrawan M, Haryanto B, Mahfud C, Sinapoy MS, Djalante S, Rafliana I. Review and analysis of current responses to COVID-19 in Indonesia: period of January to March 2020. Progress Disaster Sci. 2020;6: 100091.

Article
Google Scholar

Kadir A, Deby S, Muhammad A. A systematic review of omicron outbreak in Indonesia: a case record and Howthe country is weathering the new variant of COVID-19. Eur J Mol Clin Med. 2022;9:364–73.

Google Scholar

Pandey KR, Bhattarai A, Pant S, Barakoti R, Pandey J, Subedee A, Adhikari P, Aryal D, Pokharel PJ, Shrestha GS. Seroprevalence of COVID-19 among health workers in the Kathmandu valley, Nepal: a longitudinal cohort study. Nepal Med Coll J. 2022;24(3):197–205. https://doi.org/10.3126/nmcj.v24i3.48592.

Article
Google Scholar

Panthee B, Dhungana S, Panthee N, Paudel A, Gyawali S, Panthee S. COVID-19: the current situation in Nepal. New Microbes New Infect. 2020;37: 100737.

Article
CAS
Google Scholar

COVID: Nepal faces new omicron-fueled surge. https://frontline.thehindu.com/dispatches/covid-nepal-faces-new-omicron-fueled-surge/article65220520.ece.

Omicron: How prepared is Nepal? https://www.nepalnews.com/s/health/omicron-how-prepared-is-nepal.

Nepal faces new omicron-fueled coronavirus surge. https://www.dw.com/en/nepal-faces-new-omicron-fueled-coronavirus-surge/a-60481393.

Nepal reports new Omicron case. https://kathmandupost.com/health/2021/12/22/nepal-reports-new-omicron-case-third-to-date.

Ling HS, Pang X, Fong AYY, Ong TK, Khiew NZ, Cham YL, Said A, Oon YY, Koh KT, Tan CT. COVID-19 antibody surveillance among healthcare workers in a non-COVID designated cardiology centre. Authorea Preprints. 2020. https://doi.org/10.22541/au.158955330.06881415.

Sam I-C, Chong YM, Tan CW, Chan YF. Low postpandemic wave SARS-CoV-2 seroprevalence in Kuala Lumpur and Selangor, Malaysia. J Med Virol. 2021;93(2):647–8.

Article
CAS
Google Scholar

Woon YL, Lee YL, Chong YM, Ayub NA, Krishnabahawan SL, Lau JFW, Subramaniam-Kalianan R, Sam I-C, Chan YF, Sevalingam RK. Serology surveillance of SARS-CoV-2 antibodies among healthcare workers in COVID-19 designated facilities in Malaysia. Lancet Regional Health-Western Pac. 2021;9: 100123.

Article
Google Scholar

Noordin NM, Omar A, Isharudin IH, Idris R, Sahat ISM, Sengol S, Aziz ZA, Zhi Lim Z, Lim TO. Sero-prevalence of COVID-19 among workers in Malaysia. medRxiv. 2022. https://doi.org/10.1101/2022.01.16.22269388.

Law LN-S, Loo K-Y, Goh JXH, Pusparajah P. Omicron: The rising fear for another wave in Malaysia. Progress Microbes Mol Biol. 2021;4(1). https://doi.org/10.36877/pmmb.a0000261.

Ara J, Islam MS, Kader MTU, Das A, Hasib FY, Islam MS, Rahman T, Das S, Chowdhury MH, Das GB. Sero-prevalence of anti-SARS-CoV-2 antibodies in Chattogram Metropolitan Area, Bangladesh. medRxiv. 2022. https://doi.org/10.1101/2022.02.09.22270717.

Akter A, Ahmed T, Tauheed I, Akhtar M, Rahman SIA, Khaton F, Ahmmed F, Ferdous J, Afrad MH, Kawser Z. Disease characteristics and serological responses in patients with differing severity of COVID-19 infection: a longitudinal cohort study in Dhaka, Bangladesh. PLoS Negl Trop Dis. 2022;16(1): e0010102.

Article
CAS
Google Scholar

Bangladesh to lift nearly all lockdown restrictions from Wednesday. https://archive.dhakatribune.com/bangladesh/2021/08/08/bangladesh-to-lift-nearly-all-lockdown-restrictions-from-wednesday-2.

In Bangladesh: First Omicron cases detected. https://www.thedailystar.net/health/disease/coronavirus/news/bangladesh-first-omicron-cases-detected-2915131.

COVID-19 pandemic in Myanmar. https://en.wikipedia.org/wiki/COVID-19_pandemic_in_Myanmar#cite_note-6.

Wang J, Chan Y-C, Niu R, Wong EW, van Wyk MA. Modeling the impact of vaccination on COVID-19 and its Delta and Omicron variants. Viruses. 2022;14(7):1482.

Article
Google Scholar

Oh J, Apio C, Park T. Mathematical modeling of the impact of Omicron variant on the COVID-19 situation in South Korea. Genomics Inform. 2022;20(2):e22. https://doi.org/10.5808/gi.22025.

Article
Google Scholar

Liang Y, Gong Z, Guo J, Cheng Q, Yao Z. Spatiotemporal analysis of the morbidity of global Omicron from November 2021 to February 2022. J Med Virol. 2022;94(11):5354–62. https://doi.org/10.1002/jmv.28013.

Article
CAS
Google Scholar

Agossou O, Atchadé MN, Djibril AM. Modeling the effects of preventive measures and vaccination on the COVID-19 spread in Benin Republic with optimal control. Results Phys. 2021;31: 104969.

Article
Google Scholar

Sokadjo YM, Atchadé MN. The influence of passenger air traffic on the spread of COVID-19 in the world. Transp Res Interdiscip Perspect. 2020;8: 100213.

Google Scholar

Atchadé MN, Sokadjo YM. Overview and cross-validation of COVID-19 forecasting univariate models. Alex Eng J. 2022;61(4):3021–36.

Article
Google Scholar

Bartels RH, Beatty JC, Barsky BA. An introduction to splines for use in computer graphics and geometric modelling. Burlington: Morgan Kaufmann; 1995.

Google Scholar

Vetterling WT, Press WH, Teukolsky SA, Flannery BP. Numerical recipes example book (c++): the art of scientific computing. Cambridge: Cambridge University Press; 2002.

Google Scholar

He D, Zhao S, Lin Q, Musa SS, Stone L. New estimates of the Zika virus epidemic attack rate in Northeastern Brazil from 2015 to 2016: a modelling analysis based on Guillain-Barré Syndrome (GBS) surveillance data. PLoS Negl Trop Dis. 2020;14(4): e0007502.

Article
Google Scholar

Stone L, He D, Lehnstaedt S, Artzy-Randrup Y. Extraordinary curtailment of massive typhus epidemic in the Warsaw Ghetto. Sci Adv. 2020;6(30):0927.

Article
Google Scholar

Zhao S, Stone L, Gao D, He D. Modelling the large-scale yellow fever outbreak in Luanda, Angola, and the impact of vaccination. PLoS Negl Trop Dis. 2018;12(1): e0006158.

Article
Google Scholar

Musa SS, Tariq A, Yuan L, Haozhen W, He D. Infection fatality rate and infection attack rate of COVID-19 in South American countries. Infect Dis Poverty. 2022;11(1):1–11.

Article
Google Scholar

Song H, Fan G, Zhao S, Li H, Huang Q, He D. Forecast of the COVID-19 trend in India: a simple modelling approach. Math Biosci Eng. 2021;18(6):9775–86. https://doi.org/10.3934/mbe.2021479.

Article
Google Scholar

Gavish N, Yaari R, Huppert A, Katriel G. Population-level implications of the Israeli booster campaign to curtail COVID-19 resurgence. Sci Transl Med. 2022;eabn9836.

Griffin J, Casey M, Collins Á, Hunt K, McEvoy D, Byrne A, McAloon C, Barber A, Lane EA, More S. Rapid review of available evidence on the serial interval and generation time of COVID-19. BMJ Open. 2020;10(11): e040263.

Article
Google Scholar

Bhuiyan MU, Stiboy E, Hassan MZ, Chan M, Islam MS, Haider N, Jaffe A, Homaira N. Epidemiology of COVID-19 infection in young children under five years: a systematic review and meta-analysis. Vaccine. 2021;39(4):667–77.

Article
CAS
Google Scholar

Svensson Å. A note on generation times in epidemic models. Math Biosci. 2007;208(1):300–11.

Article
Google Scholar

He D, Ali ST, Fan G, Gao D, Song H, Lou Y, Zhao S, Cowling BJ, Stone L. Evaluation of effectiveness of global COVID-19 vaccination campaign. Emerg Infect Dis. 2022;28(9):1873–6.

Article
Google Scholar

Tang X, Musa SS, Zhao S, Mei S, He D. Using proper mean generation intervals in modeling of COVID-19. Front Public Health. 2021;9: 691262.

Article
Google Scholar

Brozak SJ, Pant B, Safdar S, Gumel AB. Dynamics of COVID-19 pandemic in India and Pakistan: a metapopulation modelling approach. Infect Dis Model. 2021;6:1173–201.

Google Scholar

Data on COVID-19 (coronavirus) by our world in data. https://covid.ourworldindata.org.

Dong E, Du H, Gardner L. An interactive web-based dashboard to track COVID-19 in real time. Lancet Infect Dis. 2020;20(5):533–4.

Article
CAS
Google Scholar

Ritchie H, Mathieu E, Rodés-Guirao L, Appel C, Giattino C, Ortiz-Ospina E, Hasell J, Macdonald B, Beltekian D, Roser M. Coronavirus pandemic (COVID-19). Our World Data. 2020.

Mathieu E, Ritchie H, Ortiz-Ospina E. et al. A global database of COVID-19 vaccinations. Nat Hum Behav. 2021;5:947–53. https://doi.org/10.1038/s41562-021-01122-8.

Article
Google Scholar

King AA, Nguyen D, Ionides EL. Statistical inference for partially observed Markov processes via the R package pomp. arXiv preprint arXiv:150900503. 2015.

King A, Ionides E, Asfaw K. Simulation-based inference for epidemiological dynamics (kingaa.github.io).

Working With Ordinary Differential Equations in Pomp. 2017. https://kingaa.github.io/clim-dis/parest/odes.html.

He D, Ionides EL, King AA. Plug-and-play inference for disease dynamics: measles in large and small populations as a case study. J R Soc Interface. 2010;7(43):271–83.

Article
Google Scholar

Pulliam JR, van Schalkwyk C, Govender N, von Gottberg A, Cohen C, Groome MJ, Dushoff J, Mlisana K, Moultrie H. Increased risk of SARS-CoV-2 reinfection associated with emergence of Omicron in South Africa. Science. 2022;376(6593):eabn4947.

Article
CAS
Google Scholar

Yang W, Shaman J. COVID-19 pandemic dynamics in India, the SARS-CoV-2 Delta variant and implications for vaccination. J R Soc Interface. 2022;19(191):20210900.

Article
Google Scholar

Cohen C, Kleynhans J, von Gottberg A, McMorrow ML, Wolter N, Bhiman JN, Moyes J, du Plessis M, Carrim M, Buys A, Martinson NA, Kahn K, Tollman S, Lebina L, Wafawanaka F, du Toit JD, Gómez-Olivé FX, Dawood FS , Mkhencele T, Sun K, Viboud C, Tempia S. SARS-CoV-2 incidence, transmission and reinfection in a rural and an urban setting: results of the PHIRST-C cohort study, South Africa, 2020–2021. Lancet Infect Dis. 2021;22(6):821–34. https://doi.org/10.1016/S1473-3099(22)00069-X.

Allen H, Vusirikala A, Flannagan J, Twohig KA, Zaidi A, Chudasama D, Lamagni T, Groves N, Turner C, Rawlinson C. Household transmission of COVID-19 cases associated with SARS-CoV-2 delta variant (B. 1.617. 2): national case-control study. Lancet Regional Health-Europe. 2022;12: 100252.

Article
Google Scholar

Jha P, Deshmukh Y, Tumbe C, Suraweera W, Bhowmick A, Sharma S, Novosad P, Fu SH, Newcombe L, Gelband H. COVID mortality in India: National survey data and health facility deaths. Science. 2022;375(6581):667–71.

Article
CAS
Google Scholar

Wang H, Paulson KR, Pease SA, Watson S, Comfort H, Zheng P, Aravkin AY, Bisignano C, Barber RM, Alam T. Estimating excess mortality due to the COVID-19 pandemic: a systematic analysis of COVID-19-related mortality, 2020–21. Lancet. 2022;399(10334):1513–36.

Article
CAS
Google Scholar

Coronavirus Pandemic (COVID-19). https://ourworldindata.org/coronavirus.