Changing SARS-CoV-2 variants in Karachi, Pakistan from alpha to delta through COVID-19 waves three and four

Zahra Hasan; Uzma Bashir Aamir; Asghar Nasir; Azra Samreen; Sayed Ali Raza Bukhari; M Asif Syed; Mansoor Wassan; Syed Faisal Mahmood; Rumina Hasan

doi:10.21203/rs.3.rs-828919/v1

Changing SARS-CoV-2 variants in Karachi, Pakistan from alpha to delta through COVID-19 waves three and four

Zahra Hasan, Uzma Bashir Aamir, Asghar Nasir, Azra Samreen, Sayed Ali Raza Bukhari, M Asif Syed, Mansoor Wassan, Syed Faisal Mahmood, Rumina Hasan

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Abstract

We investigated the presence of SARS-CoV-2 variants of concern (VoC) in Karachi, Pakistan between April and July 2021 in specimens received at the Aga Khan University Clinical Laboratories. VoC were identified using a PCR based approach targeting lineage specific mutation. Of the 710 clinical isolates tested, 63% were VoC comprising; 36% alpha, 37% beta, 7% gamma and 21% delta variants. Alpha variants remained the majority whilst, delta strains increased to 43% of cases in July. Thirty-six per cent of all cases were admitted COVID-19 in-patient samples. Of the in-patient cases, 41% were alpha, 28% were beta, 8% were gamma and 24% were delta variants. Overall, we report an increase of delta variants in Karachi over the past two months which is concordant with the currently observed exacerbation in COVID-19 morbidity and mortality.

Original language	Undefined/Unknown
Journal	Department of Pathology and Laboratory Medicine
DOIs	https://doi.org/10.21203/rs.3.rs-828919/v1
Publication status	Published - 20 Aug 2021

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10.21203/rs.3.rs-828919/v1Licence: Unspecified

http://ecommons.aku.edu/pakistan_fhs_mc_pathol_microbiol/1546

Cite this

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title = "Changing SARS-CoV-2 variants in Karachi, Pakistan from alpha to delta through COVID-19 waves three and four",

abstract = "We investigated the presence of SARS-CoV-2 variants of concern (VoC) in Karachi, Pakistan between April and July 2021 in specimens received at the Aga Khan University Clinical Laboratories. VoC were identified using a PCR based approach targeting lineage specific mutation. Of the 710 clinical isolates tested, 63% were VoC comprising; 36% alpha, 37% beta, 7% gamma and 21% delta variants. Alpha variants remained the majority whilst, delta strains increased to 43% of cases in July. Thirty-six per cent of all cases were admitted COVID-19 in-patient samples. Of the in-patient cases, 41% were alpha, 28% were beta, 8% were gamma and 24% were delta variants. Overall, we report an increase of delta variants in Karachi over the past two months which is concordant with the currently observed exacerbation in COVID-19 morbidity and mortality.",

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T1 - Changing SARS-CoV-2 variants in Karachi, Pakistan from alpha to delta through COVID-19 waves three and four

AU - Hasan, Zahra

AU - Aamir, Uzma Bashir

AU - Nasir, Asghar

AU - Samreen, Azra

AU - Bukhari, Sayed Ali Raza

AU - Syed, M Asif

AU - Wassan, Mansoor

AU - Mahmood, Syed Faisal

AU - Hasan, Rumina

PY - 2021/8/20

Y1 - 2021/8/20

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AB - We investigated the presence of SARS-CoV-2 variants of concern (VoC) in Karachi, Pakistan between April and July 2021 in specimens received at the Aga Khan University Clinical Laboratories. VoC were identified using a PCR based approach targeting lineage specific mutation. Of the 710 clinical isolates tested, 63% were VoC comprising; 36% alpha, 37% beta, 7% gamma and 21% delta variants. Alpha variants remained the majority whilst, delta strains increased to 43% of cases in July. Thirty-six per cent of all cases were admitted COVID-19 in-patient samples. Of the in-patient cases, 41% were alpha, 28% were beta, 8% were gamma and 24% were delta variants. Overall, we report an increase of delta variants in Karachi over the past two months which is concordant with the currently observed exacerbation in COVID-19 morbidity and mortality.

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