We are in our fifth wave of the COVID pandemic with experts reporting the Omicron variant in the north and south of Pakistan. Now a paper has been published which shows which strains came for each wave.

On December 13, 2021, the new lineage BA.1 (Omicron) was identified in Pakistan. The government warned of a fifth wave on January 3, 2022.

Experts who have studied the mutations in the virus feel that it is likely that other strains are circulating in Pakistan.

New strains are introduced by international travelers and in local festivals. For example, in India a religious festival in Punjab in April 2021 showed a double mutant strain. This was followed by the appearance of the delta variant in the Pakistani population.

Expatriate Pakistanis from the UK, USA and Saudi Arabia and pilgrimage travels from Iran have contributed to the SARS-CoV-2 genomic diversity in the Pakistani population.

A paper was just published by experts from the National Institute of Health and Maroof International Hospital titled, Footprints of SARS-CoV-2 genome diversity in Pakistan, 2020–2021. It shows the strains for each wave of the pandemic in Pakistan.

It maps which strains have been circulating in Pakistan, and that B.1 and B.1.36.31 were dominant in the first and second waves. But in the third and fourth waves the B.1.1.7, B.1.351 and B.1.617.2 were dominant.

The SARS-CoV-2 virus are not genetically diverse but the coronaviruses are capable of recombining at a high rate which can lead to the emergence of novel viral derivatives.

The first confirmed case was reported in Pakistan on February 26, 2020. Cases went up slowly, and peaked in mid-June 2020 (over 6,000 a day). It dropped then and the curve flattened August and September 2020.

The government then said the second wave was hitting on October 28, 2020 and it lasted three months to end January 2021. The third outbreak struck after the B.1.1.7 SARS-CoV-2 variant was identified in December 2020.

Cases rose from March 2021 and peaked in late April 2021 (more than 5,500 cases per day).

It declined during the third wave in June 2021 but went up in the start of July 2021, marking the start of the fourth wave. The fourth wave lasted three months and dropped off in October 2021.

Pakistan’s first Omicron case was reported on December 13, 2021. Since then COVID-19 cases (Omicron) are going up. Till December 27, 2021, there were 75.

A database called PANGOLIN helps experts keep track of the variants. In 2020, Pakistan had a small number (296) to start with but this went up to 1,745 whole genomes from Pakistan.

Since the first SARS-CoV-2 genome sequence on January 10, 2020, there has been an explosion to 6,510,899 by the end of last year. The first and second wave probably did not have mutant strains. However, the third wave did.